diff --git a/docs/pvacseq/output_files.rst b/docs/pvacseq/output_files.rst index fd6b7632..2d6f67be 100644 --- a/docs/pvacseq/output_files.rst +++ b/docs/pvacseq/output_files.rst @@ -279,7 +279,13 @@ transcripts covered by those epitopes, as well as the HLA alleles that those epitopes are well-binding to. Lastly, the report will bin variants into tiers that offer suggestions as to the suitability of variants for use in vaccines. -Only epitopes meeting the ``--aggregate-inclusion-binding-threshold`` are included in this report (default: 5000). +Additionally, a metrics.json file gets created, containing metadata about the +Best Peptide as well as alternate neoantigen canddiates for each variant. This +file can be loaded into pVACview in conjunction with the aggregated report in +order to visualize the candidates. In order to limit the size of the +metrics.json file, only a limited number of neoantigen candidates are included +in this file. Only neoantigen candidates meeting the ``--aggregate-inclusion-binding-threshold`` +are included in this file (default: 5000). If the number of unique epitopes for a mutation meeting this threshold exceeds the ``--aggregate-inclusion-count-limit``, only the top n epitopes up to this limit are included (default: 15). The method for selecting the top n epitopes is analogous to @@ -293,8 +299,12 @@ anchor criteria was passed, the MT IC50 score, the transcript length, and the MT percentile. From this sorted list the top n entries are selected up to the ``--aggregate-inclusion-count-limit``. +If the Best Peptide does not meet the aggregate inclusion criteria, it will be still be +included in the metrics.json file and counted in the ``Num Included +Peptides``. + Whether the median or the lowest binding affinity metrics are used for determining the -included eptiopes, selecting the best-scoring epitope, and which values are output in the ``IC50 MT``, +included epitopes, selecting the best-scoring epitope, and which values are output in the ``IC50 MT``, ``IC50 WT``, ``%ile MT``, and ``%ile WT`` columns is controlled by the ``--top-score-metric`` parameter. @@ -371,9 +381,7 @@ included eptiopes, selecting the best-scoring epitope, and which values are outp Best Peptide Criteria _____________________ -To determine the Best Peptide, all peptides meeting the -``--aggregate-inclusion-threshold`` and ``--aggregate-inclusion-count-limit`` -(see above) are evaluated as follows: +To determine the Best Peptide, all peptides for a variant are evaluated as follows: - Pick all entries with a variant transcript that have a ``protein_coding`` Biotype - Of the remaining entries, pick the ones with a variant transcript having diff --git a/docs/pvacsplice/output_files.rst b/docs/pvacsplice/output_files.rst index ffea541a..5ae0d5f4 100644 --- a/docs/pvacsplice/output_files.rst +++ b/docs/pvacsplice/output_files.rst @@ -298,6 +298,10 @@ and ``%ile MT`` columns is controlled by the ``--top-score-metric`` parameter. - A list of positions in the Best Peptide that are problematic. ``None`` if the ``--problematic-pos`` parameter was not set during the pVACseq run + * - ``Num Included Peptides`` + - The number of included peptides according to the + ``--aggregate-inclusion-binding-threshold`` and + ``--aggregate-inclusion-count-limit`` * - ``Num Passing Peptides`` - The number of unique well-binding peptides for this mutation. * - ``IC50 MT`` diff --git a/pvactools/lib/aggregate_all_epitopes.py b/pvactools/lib/aggregate_all_epitopes.py index edb48bf3..ac111244 100644 --- a/pvactools/lib/aggregate_all_epitopes.py +++ b/pvactools/lib/aggregate_all_epitopes.py @@ -97,21 +97,18 @@ def get_best_mut_line(self, df, key, prediction_algorithms, el_algorithms, perce #these are all lines meeting the aggregate inclusion binding threshold included_df = self.get_included_df(df) - if len(included_df) > 0: - peptide_hla_counts = self.get_unique_peptide_hla_counts(included_df) - hla_counts = Counter(peptide_hla_counts["HLA Allele"]) - hla = dict(map(lambda x : (x, hla_counts[x]) if x in hla_counts else (x, ""), self.hla_types)) - #get a list of all unique gene/transcript/aa_change combinations - #store a count of all unique peptides that passed - (peptides, anno_count) = self.get_included_df_metrics(included_df, prediction_algorithms, el_algorithms, percentile_algorithms) - included_peptide_count = self.calculate_unique_peptide_count(included_df) - good_binder_count = self.calculate_good_binder_count(included_df) - else: - hla = dict(map(lambda x : (x, ""), self.hla_types)) - peptides = {} - anno_count = self.get_default_annotation_count() - included_peptide_count = 0 - good_binder_count = 0 + best_df = pd.DataFrame.from_dict([best]) + if not best_df.index.isin(included_df.index).all(): + included_df = pd.concat([included_df, best_df]) + best_df = best_df.to_dict() + peptide_hla_counts = self.get_unique_peptide_hla_counts(included_df) + hla_counts = Counter(peptide_hla_counts["HLA Allele"]) + hla = dict(map(lambda x : (x, hla_counts[x]) if x in hla_counts else (x, ""), self.hla_types)) + #get a list of all unique gene/transcript/aa_change combinations + #store a count of all unique peptides that passed + (peptides, anno_count) = self.get_included_df_metrics(included_df, prediction_algorithms, el_algorithms, percentile_algorithms) + included_peptide_count = self.calculate_unique_peptide_count(included_df) + good_binder_count = self.calculate_good_binder_count(included_df) #assemble the line out_dict = self.assemble_result_line(best, key, vaf_clonal, hla, anno_count, included_peptide_count, good_binder_count) @@ -362,7 +359,6 @@ def calculate_clonal_vaf(self): def read_input_file(self, used_columns, dtypes): df = pd.read_csv(self.input_file, delimiter='\t', float_precision='high', low_memory=False, na_values="NA", keep_default_na=False, usecols=used_columns, dtype=dtypes) - df = df.dropna(subset=["{} MT IC50 Score".format(self.mt_top_score_metric)]).reset_index() df = df.astype({"{} MT IC50 Score".format(self.mt_top_score_metric):'float'}) return df @@ -409,7 +405,7 @@ def get_best_binder(self, df): "Transcript Support Level", "Transcript Length", ], inplace=True, ascending=[True, True, False]) - return anchor_residue_pass_df.iloc[0].to_dict() + return anchor_residue_pass_df.iloc[0] def is_anchor_residue_pass(self, mutation): if self.use_allele_specific_binding_thresholds and mutation['HLA Allele'] in self.allele_specific_binding_thresholds: diff --git a/tests/test_aggregate_all_epitopes.py b/tests/test_aggregate_all_epitopes.py index 51f9dfde..f898577c 100644 --- a/tests/test_aggregate_all_epitopes.py +++ b/tests/test_aggregate_all_epitopes.py @@ -8,7 +8,7 @@ from pvactools.lib.aggregate_all_epitopes import PvacseqAggregateAllEpitopes, PvacfuseAggregateAllEpitopes, PvacbindAggregateAllEpitopes, PvacspliceAggregateAllEpitopes from tests.utils import * -class AggregateAllEptiopesTests(unittest.TestCase): +class AggregateAllEpitopesTests(unittest.TestCase): @classmethod def setUpClass(cls): #locate the bin and test_data directories diff --git a/tests/test_data/aggregate_all_epitopes/HCC1395.output.metrics.json b/tests/test_data/aggregate_all_epitopes/HCC1395.output.metrics.json index 597ebfcb..25d0b803 100644 --- a/tests/test_data/aggregate_all_epitopes/HCC1395.output.metrics.json +++ b/tests/test_data/aggregate_all_epitopes/HCC1395.output.metrics.json @@ -34,6 +34,216 @@ "good_binders": { "Transcript Set 1": { "peptides": { + "HLTRVTPMGW": { + "ic50s_MT": [ + 11111.0693359375, + "X", + "X", + "X" + ], + "percentiles_MT": [ + 13.0, + "X", + "X", + "X" + ], + "ic50s_WT": [ + 25893.689, + "X", + "X", + "X" + ], + "percentiles_WT": [ + 48.0, + "X", + "X", + "X" + ], + "hla_types": [ + "HLA-A*29:02", + "HLA-B*45:01", + "HLA-B*82:02", + "HLA-C*06:02" + ], + "mutation_position": "10", + "problematic_positions": "None", + "anchor_fails": "None", + "individual_ic50_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "NetMHC", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC" + ], + "MT": { + "HLA-A*29:02": [ + 10039.137390422107, + 5945.57, + 26680.83, + 12183.0, + 15519.07, + 13797.25, + 5312.27, + 4251.38 + ] + }, + "WT": { + "HLA-A*29:02": [ + 28595.11881805995, + 5969.79, + 37579.84, + 31060.99, + 33592.01, + 23192.26, + 7434.98, + 12838.96 + ] + } + }, + "individual_ic50_percentile_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "NetMHC", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC" + ], + "MT": { + "HLA-A*29:02": [ + 5.19712495803833, + 69.69999694824219, + 29.0, + 14.0, + 8.800000190734863, + 15.0, + 14.0, + 12.0 + ] + }, + "WT": { + "HLA-A*29:02": [ + 30.891874999999995, + 83.98, + 65.0, + 56.0, + 40.0, + 26.0, + 18.0, + 25.0 + ] + } + }, + "individual_el_calls": { + "algorithms": [ + "MHCflurryEL Processing", + "MHCflurryEL Presentation", + "NetMHCpanEL", + "BigMHC_EL", + "BigMHC_IM", + "DeepImmuno" + ], + "MT": { + "HLA-A*29:02": [ + 0.3148910235613584, + 0.0289657178985192, + 0.00182, + 0.000724664, + 0.15687987, + "NA" + ] + }, + "WT": { + "HLA-A*29:02": [ + 0.007340261596255, + 0.0036217768592992, + 1.1e-05, + 0.0002928419, + 0.027665546, + "NA" + ] + } + }, + "individual_el_percentile_calls": { + "algorithms": [ + "MHCflurryEL Processing", + "MHCflurryEL Presentation", + "NetMHCpanEL", + "BigMHC_EL", + "BigMHC_IM", + "DeepImmuno" + ], + "MT": { + "HLA-A*29:02": [ + "NA", + 8.545326086956507, + 7.2, + "NA", + "NA", + "NA" + ] + }, + "WT": { + "HLA-A*29:02": [ + "NA", + 99.28660326086955, + 58.0, + "NA", + "NA", + "NA" + ] + } + }, + "individual_percentile_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "NetMHC", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC", + "MHCflurryEL Presentation", + "NetMHCpanEL" + ], + "MT": { + "HLA-A*29:02": [ + 5.19712495803833, + 69.69999694824219, + 29.0, + 14.0, + 8.800000190734863, + 15.0, + 14.0, + 12.0, + 8.545326086956507, + 7.2 + ] + }, + "WT": { + "HLA-A*29:02": [ + 30.891874999999995, + 83.98, + 65.0, + 56.0, + 40.0, + 26.0, + 18.0, + 25.0, + 99.28660326086955, + 58.0 + ] + } + }, + "wt_peptide": "HLTRVTPMGG" + }, "TPMGWGCL": { "ic50s_MT": [ "X", @@ -261,7 +471,7 @@ 169 ], "transcript_count": 1, - "peptide_count": 1, + "peptide_count": 2, "total_expr": 0.082 } }, @@ -272,7 +482,7 @@ 1 ], "peptide_counts": [ - 1 + 2 ], "set_expr": [ 0.082 @@ -752,27 +962,27 @@ "good_binders": { "Transcript Set 1": { "peptides": { - "GTCKETFKLYY": { + "TFKLYYLES": { "ic50s_MT": [ - 414.66900634765625, + 7694.52001953125, "X", "X", "X" ], "percentiles_MT": [ - 0.6949999928474426, + 10.899999618530273, "X", "X", "X" ], "ic50s_WT": [ - 229.772, + 4817.84, "X", "X", "X" ], "percentiles_WT": [ - 0.616, + 6.45, "X", "X", "X" @@ -783,8 +993,8 @@ "HLA-B*82:02", "HLA-C*06:02" ], - "mutation_position": "8", - "problematic_positions": "3", + "mutation_position": "3", + "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { "algorithms": [ @@ -799,26 +1009,26 @@ ], "MT": { "HLA-A*29:02": [ - 248.96835423189663, - 4146.14, - 2943.98, - 57.51, - 580.37, - 2904.96, - 110.57, - 105.89 + 27527.076914576617, + 5629.59, + 4857.55, + 11417.23, + 13842.56, + 9759.45, + 4805.74, + 5369.95 ] }, "WT": { "HLA-A*29:02": [ - 152.79432927531116, - 3654.37, - 1727.08, - 47.34, - 306.75, - 2416.9, - 147.11, - 112.69 + 23361.6704809502, + 4857.16, + 2344.8, + 6095.65, + 8602.71, + 4778.52, + 1944.29, + 2274.94 ] } }, @@ -835,26 +1045,26 @@ ], "MT": { "HLA-A*29:02": [ - 0.8687499761581421, - 0.9700000286102295, - 3.0, - 0.25, - 0.699999988079071, - 1.2999999523162842, - 0.4, - 0.4 + 25.54487419128418, + 8.739999771118164, + 4.300000190734863, + 14.0, + 7.599999904632568, + 26.0, + 9.8, + 12.0 ] }, "WT": { "HLA-A*29:02": [ - 0.6319999999999997, - 0.72, - 2.3, - 0.2, - 0.45, - 0.9, - 0.6, - 0.4 + 15.483874999999996, + 1.85, + 2.6, + 7.3, + 4.6, + 12.0, + 5.2, + 5.9 ] } }, @@ -869,21 +1079,21 @@ ], "MT": { "HLA-A*29:02": [ - 0.6290885582566261, - 0.766819503992353, - 0.159, - 0.45457336, - 0.96785134, + 0.0240136757784057, + 0.0039851228795116, + 0.00124, + 0.0231885, + 0.46585923, "NA" ] }, "WT": { "HLA-A*29:02": [ - 0.3625158732756972, - 0.6729409187522049, - 0.167, - 0.3427218, - 0.97667897, + 0.023071428091498, + 0.0046549673570918, + 0.00188, + 0.024450062, + 0.60252845, "NA" ] } @@ -900,8 +1110,8 @@ "MT": { "HLA-A*29:02": [ "NA", - 0.3301902173912765, - 0.69, + 99.28660326086955, + 8.6, "NA", "NA", "NA" @@ -910,8 +1120,218 @@ "WT": { "HLA-A*29:02": [ "NA", - 0.484456521739105, - 0.66, + 62.74467391304348, + 7.0, + "NA", + "NA", + "NA" + ] + } + }, + "individual_percentile_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "NetMHC", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC", + "MHCflurryEL Presentation", + "NetMHCpanEL" + ], + "MT": { + "HLA-A*29:02": [ + 25.54487419128418, + 8.739999771118164, + 4.300000190734863, + 14.0, + 7.599999904632568, + 26.0, + 9.8, + 12.0, + 99.28660326086955, + 8.6 + ] + }, + "WT": { + "HLA-A*29:02": [ + 15.483874999999996, + 1.85, + 2.6, + 7.3, + 4.6, + 12.0, + 5.2, + 5.9, + 62.74467391304348, + 7.0 + ] + } + }, + "wt_peptide": "TFNLYYLES" + }, + "GTCKETFKLYY": { + "ic50s_MT": [ + 414.66900634765625, + "X", + "X", + "X" + ], + "percentiles_MT": [ + 0.6949999928474426, + "X", + "X", + "X" + ], + "ic50s_WT": [ + 229.772, + "X", + "X", + "X" + ], + "percentiles_WT": [ + 0.616, + "X", + "X", + "X" + ], + "hla_types": [ + "HLA-A*29:02", + "HLA-B*45:01", + "HLA-B*82:02", + "HLA-C*06:02" + ], + "mutation_position": "8", + "problematic_positions": "3", + "anchor_fails": "None", + "individual_ic50_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "NetMHC", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC" + ], + "MT": { + "HLA-A*29:02": [ + 248.96835423189663, + 4146.14, + 2943.98, + 57.51, + 580.37, + 2904.96, + 110.57, + 105.89 + ] + }, + "WT": { + "HLA-A*29:02": [ + 152.79432927531116, + 3654.37, + 1727.08, + 47.34, + 306.75, + 2416.9, + 147.11, + 112.69 + ] + } + }, + "individual_ic50_percentile_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "NetMHC", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC" + ], + "MT": { + "HLA-A*29:02": [ + 0.8687499761581421, + 0.9700000286102295, + 3.0, + 0.25, + 0.699999988079071, + 1.2999999523162842, + 0.4, + 0.4 + ] + }, + "WT": { + "HLA-A*29:02": [ + 0.6319999999999997, + 0.72, + 2.3, + 0.2, + 0.45, + 0.9, + 0.6, + 0.4 + ] + } + }, + "individual_el_calls": { + "algorithms": [ + "MHCflurryEL Processing", + "MHCflurryEL Presentation", + "NetMHCpanEL", + "BigMHC_EL", + "BigMHC_IM", + "DeepImmuno" + ], + "MT": { + "HLA-A*29:02": [ + 0.6290885582566261, + 0.766819503992353, + 0.159, + 0.45457336, + 0.96785134, + "NA" + ] + }, + "WT": { + "HLA-A*29:02": [ + 0.3625158732756972, + 0.6729409187522049, + 0.167, + 0.3427218, + 0.97667897, + "NA" + ] + } + }, + "individual_el_percentile_calls": { + "algorithms": [ + "MHCflurryEL Processing", + "MHCflurryEL Presentation", + "NetMHCpanEL", + "BigMHC_EL", + "BigMHC_IM", + "DeepImmuno" + ], + "MT": { + "HLA-A*29:02": [ + "NA", + 0.3301902173912765, + 0.69, + "NA", + "NA", + "NA" + ] + }, + "WT": { + "HLA-A*29:02": [ + "NA", + 0.484456521739105, + 0.66, "NA", "NA", "NA" @@ -1819,7 +2239,7 @@ 495 ], "transcript_count": 1, - "peptide_count": 5, + "peptide_count": 6, "total_expr": 0.0 }, "Transcript Set 2": { @@ -2274,7 +2694,7 @@ 1 ], "peptide_counts": [ - 5, + 6, 2 ], "set_expr": [ @@ -2292,6 +2712,216 @@ "good_binders": { "Transcript Set 1": { "peptides": { + "ATQKITFSA": { + "ic50s_MT": [ + "X", + 6294.759765625, + "X", + "X" + ], + "percentiles_MT": [ + "X", + 4.771999835968018, + "X", + "X" + ], + "ic50s_WT": [ + "X", + 5577.395, + "X", + "X" + ], + "percentiles_WT": [ + "X", + 5.01, + "X", + "X" + ], + "hla_types": [ + "HLA-A*29:02", + "HLA-B*45:01", + "HLA-B*82:02", + "HLA-C*06:02" + ], + "mutation_position": "6", + "problematic_positions": "None", + "anchor_fails": "None", + "individual_ic50_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "NetMHC", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC" + ], + "MT": { + "HLA-B*45:01": [ + 17800.490642115667, + 14412.84, + 2026.14, + 13141.57, + 10563.38, + 1824.25, + 456.26, + 584.28 + ] + }, + "WT": { + "HLA-B*45:01": [ + 18045.003608532377, + 9481.96, + 1159.58, + 12449.51, + 9290.63, + 1864.16, + 394.65, + 456.69 + ] + } + }, + "individual_ic50_percentile_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "NetMHC", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC" + ], + "MT": { + "HLA-B*45:01": [ + 5.044000148773193, + 15.079999923706055, + 2.200000047683716, + 6.900000095367432, + 3.9000000953674316, + 5.800000190734863, + 1.6, + 2.1 + ] + }, + "WT": { + "HLA-B*45:01": [ + 5.12, + 9.93, + 1.5, + 6.7, + 3.5, + 6.0, + 1.4, + 1.6 + ] + } + }, + "individual_el_calls": { + "algorithms": [ + "MHCflurryEL Processing", + "MHCflurryEL Presentation", + "NetMHCpanEL", + "BigMHC_EL", + "BigMHC_IM", + "DeepImmuno" + ], + "MT": { + "HLA-B*45:01": [ + 0.4862415082752704, + 0.030403672493413, + 0.00585, + 0.016126314, + 0.29042682, + "NA" + ] + }, + "WT": { + "HLA-B*45:01": [ + 0.4643194917589426, + 0.0278377054540816, + 0.00489, + 0.006729617, + 0.1976529, + "NA" + ] + } + }, + "individual_el_percentile_calls": { + "algorithms": [ + "MHCflurryEL Processing", + "MHCflurryEL Presentation", + "NetMHCpanEL", + "BigMHC_EL", + "BigMHC_IM", + "DeepImmuno" + ], + "MT": { + "HLA-B*45:01": [ + "NA", + 8.01565217391304, + 4.5, + "NA", + "NA", + "NA" + ] + }, + "WT": { + "HLA-B*45:01": [ + "NA", + 8.839293478260856, + 4.9, + "NA", + "NA", + "NA" + ] + } + }, + "individual_percentile_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "NetMHC", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC", + "MHCflurryEL Presentation", + "NetMHCpanEL" + ], + "MT": { + "HLA-B*45:01": [ + 5.044000148773193, + 15.079999923706055, + 2.200000047683716, + 6.900000095367432, + 3.9000000953674316, + 5.800000190734863, + 1.6, + 2.1, + 8.01565217391304, + 4.5 + ] + }, + "WT": { + "HLA-B*45:01": [ + 5.12, + 9.93, + 1.5, + 6.7, + 3.5, + 6.0, + 1.4, + 1.6, + 8.839293478260856, + 4.9 + ] + } + }, + "wt_peptide": "ATQKIAFSA" + }, "ITFSATRTI": { "ic50s_MT": [ "X", @@ -2519,7 +3149,7 @@ 251 ], "transcript_count": 1, - "peptide_count": 1, + "peptide_count": 2, "total_expr": 0.0 } }, @@ -2530,7 +3160,7 @@ 1 ], "peptide_counts": [ - 1 + 2 ], "set_expr": [ 0.0 @@ -10532,6 +11162,216 @@ "good_binders": { "Transcript Set 1": { "peptides": { + "LQVQQDHLN": { + "ic50s_MT": [ + 26189.26171875, + "X", + "X", + "X" + ], + "percentiles_MT": [ + 39.0, + "X", + "X", + "X" + ], + "ic50s_WT": [ + 23718.146, + "X", + "X", + "X" + ], + "percentiles_WT": [ + 39.9, + "X", + "X", + "X" + ], + "hla_types": [ + "HLA-A*29:02", + "HLA-B*45:01", + "HLA-B*82:02", + "HLA-C*06:02" + ], + "mutation_position": "1", + "problematic_positions": "None", + "anchor_fails": "None", + "individual_ic50_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "NetMHC", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC" + ], + "MT": { + "HLA-A*29:02": [ + 24802.811910107383, + 5941.78, + 29359.13, + 27575.71, + 34454.1, + 27875.69, + 15092.46, + 12105.15 + ] + }, + "WT": { + "HLA-A*29:02": [ + 24244.03207941355, + 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0.1533815246075391, + 0.0079751111087216, + 7.3e-05, + 0.009980634, + 0.29646373, + "NA" + ] + }, + "WT": { + "HLA-C*06:02": [ + 0.1374410334974527, + 0.007335698806628, + 9.1e-05, + 0.0073716855, + 0.20356573, + "NA" + ] + } + }, + "individual_el_percentile_calls": { + "algorithms": [ + "MHCflurryEL Processing", + "MHCflurryEL Presentation", + "NetMHCpanEL", + "BigMHC_EL", + "BigMHC_IM", + "DeepImmuno" + ], + "MT": { + "HLA-C*06:02": [ + "NA", + 31.64317934782608, + 26.0, + "NA", + "NA", + "NA" + ] + }, + "WT": { + "HLA-C*06:02": [ + "NA", + 31.64317934782608, + 24.0, + "NA", + "NA", + "NA" + ] + } + }, + "individual_percentile_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "NetMHC", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC", + "MHCflurryEL Presentation", + "NetMHCpanEL" + ], + "MT": { + "HLA-C*06:02": [ + 42.87062454223633, + 15.359999656677246, + 13.0, + 9.300000190734863, + 14.0, + 5.300000190734863, + "NA", + "NA", + 31.64317934782608, + 26.0 + ] + }, + "WT": { + "HLA-C*06:02": [ + 44.88862499999999, + 17.95, + 14.0, + 9.5, + 14.0, + 5.7, + "NA", + "NA", + 31.64317934782608, + 24.0 + ] + } + }, + "wt_peptide": "YSSAIIPQMLA" + }, "CFSSAIIPQM": { "ic50s_MT": [ 3573.4150390625, @@ -40665,7 +45202,7 @@ 314 ], "transcript_count": 1, - "peptide_count": 1, + "peptide_count": 2, "total_expr": 0.008 } }, @@ -40676,7 +45213,7 @@ 1 ], "peptide_counts": [ - 1 + 2 ], "set_expr": [ 0.008 @@ -49353,6 +53890,216 @@ "good_binders": { "Transcript Set 1": { "peptides": { + "LLNSLSVDL": { + "ic50s_MT": [ + "X", + "X", + "X", + 5793.85986328125 + ], + "percentiles_MT": [ + "X", + "X", + "X", + 9.350000381469727 + ], + "ic50s_WT": [ + "X", + "X", + "X", + 20782.765 + ], + "percentiles_WT": [ + "X", + "X", + "X", + 50.859 + ], + "hla_types": [ + "HLA-A*29:02", + "HLA-B*45:01", + "HLA-B*82:02", + "HLA-C*06:02" + ], + "mutation_position": "9", + "problematic_positions": "None", + "anchor_fails": "None", + "individual_ic50_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "NetMHC", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC" + ], + "MT": { + "HLA-C*06:02": [ + 3453.5809819284395, + 785.3, + 20331.13, + 14963.56, + 19279.63, + 7692.16, + 3497.92, + 3895.56 + ] + }, + "WT": { + "HLA-C*06:02": [ + 23410.01904324579, + 18155.51, + 39246.2, + 41599.44, + 43020.27, + 16404.99, + 11989.75, + 12751.76 + ] + } + }, + "individual_ic50_percentile_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "NetMHC", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC" + ], + "MT": { + "HLA-C*06:02": [ + 6.698999881744385, + 3.5799999237060547, + 8.800000190734863, + 16.0, + 7.5, + 27.0, + 20.0, + 22.0 + ] + }, + "WT": { + "HLA-C*06:02": [ + 50.71774999999999, + 33.67, + 40.0, + 77.0, + 71.0, + 51.0, + 36.0, + 37.0 + ] + } + }, + "individual_el_calls": { + "algorithms": [ + "MHCflurryEL Processing", + "MHCflurryEL Presentation", + "NetMHCpanEL", + "BigMHC_EL", + "BigMHC_IM", + "DeepImmuno" + ], + "MT": { + "HLA-C*06:02": [ + 0.0212356689153239, + 0.0288960593629738, + 0.000795, + 0.0006750826, + 0.012569367, + 0.98502254 + ] + }, + "WT": { + "HLA-C*06:02": [ + 0.0022862036603328, + 0.0043177077986462, + 2e-06, + 0.00010387441, + 0.0065268553, + 0.98747575 + ] + } + }, + "individual_el_percentile_calls": { + "algorithms": [ + "MHCflurryEL Processing", + "MHCflurryEL Presentation", + "NetMHCpanEL", + "BigMHC_EL", + "BigMHC_IM", + "DeepImmuno" + ], + "MT": { + "HLA-C*06:02": [ + "NA", + 8.545326086956507, + 9.9, + "NA", + "NA", + "NA" + ] + }, + "WT": { + "HLA-C*06:02": [ + "NA", + 62.74467391304348, + 73.0, + "NA", + "NA", + "NA" + ] + } + }, + "individual_percentile_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "NetMHC", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC", + "MHCflurryEL Presentation", + "NetMHCpanEL" + ], + "MT": { + "HLA-C*06:02": [ + 6.698999881744385, + 3.5799999237060547, + 8.800000190734863, + 16.0, + 7.5, + 27.0, + 20.0, + 22.0, + 8.545326086956507, + 9.9 + ] + }, + "WT": { + "HLA-C*06:02": [ + 50.71774999999999, + 33.67, + 40.0, + 77.0, + 71.0, + 51.0, + 36.0, + 37.0, + 62.74467391304348, + 73.0 + ] + } + }, + "wt_peptide": "LLNSLSVDP" + }, "SVDLDAECKY": { "ic50s_MT": [ 1355.64501953125, @@ -49985,27 +54732,22 @@ } }, "transcripts": [ - "ENST00000355303.10-ANO1-P/L-45", - "ENST00000531604.5-ANO1-P/L-45" + "ENST00000355303.10-ANO1-P/L-45" ], "transcript_expr": [ - 0.065, - 0.0 + 0.065 ], "tsl": [ - 1, - 3 + 1 ], "biotype": [ - "protein_coding", "protein_coding" ], "transcript_length": [ - 986, - 251 + 986 ], - "transcript_count": 2, - "peptide_count": 3, + "transcript_count": 1, + "peptide_count": 4, "total_expr": 0.065 }, "Transcript Set 2": { @@ -50220,27 +54962,27 @@ }, "wt_peptide": "SVDPDAECKY" }, - "LSVDLDAECKY": { + "DLDAECKYGLY": { "ic50s_MT": [ - 2382.330078125, + 2898.68994140625, "X", "X", "X" ], "percentiles_MT": [ - 1.7999999523162842, + 2.6500000953674316, "X", "X", "X" ], "ic50s_WT": [ - 3498.39, + 8340.196, "X", "X", "X" ], "percentiles_WT": [ - 2.45, + 7.346, "X", "X", "X" @@ -50251,8 +54993,8 @@ "HLA-B*82:02", "HLA-C*06:02" ], - "mutation_position": "5", - "problematic_positions": "9", + "mutation_position": "2", + "problematic_positions": "6", "anchor_fails": "None", "individual_ic50_calls": { "algorithms": [ @@ -50267,26 +55009,26 @@ ], "MT": { "HLA-A*29:02": [ - 140.56230194922912, - 5558.52, - 5332.11, - 605.05, - 4159.61, - 12790.86, - 422.31, - 142.19 + 920.4479611303162, + 5616.15, + 4397.92, + 1399.46, + 5546.66, + 17695.75, + 239.68, + 219.72 ] }, "WT": { "HLA-A*29:02": [ - 101.25226049108204, - 5411.89, - 7394.86, - 1584.89, - 7508.46, - 12249.09, - 630.42, - 416.74 + 6209.862057673519, + 5768.12, + 10839.76, + 10470.53, + 14227.03, + 50000.0, + 239.68, + 517.45 ] } }, @@ -50303,26 +55045,26 @@ ], "MT": { "HLA-A*29:02": [ - 0.5892500281333923, - 6.900000095367432, - 4.5, - 1.5, - 2.5999999046325684, - 14.0, - 1.9, - 0.6 + 1.6448750495910645, + 8.329999923706055, + 3.9000000953674316, + 2.200000047683716, + 3.0999999046325684, + 19.0, + 1.1, + 1.0 ] }, "WT": { "HLA-A*29:02": [ - 0.4392499999999997, - 4.62, - 5.8, - 2.3, - 4.0, - 13.0, - 2.6, - 1.8 + 3.810624999999999, + 16.16, + 8.0, + 9.2, + 7.9, + 47.0, + 1.1, + 2.2 ] } }, @@ -50337,21 +55079,21 @@ ], "MT": { "HLA-A*29:02": [ - 0.0936763293575495, - 0.4629130413931976, - 0.0393, - 0.0436849, - 0.7010426, + 0.2751555279828608, + 0.2088452111357986, + 0.0107, + 0.025989415, + 0.66756964, "NA" ] }, "WT": { "HLA-A*29:02": [ - 0.4554567625746131, - 0.8100051794764376, - 0.0534, - 0.03793961, - 0.462683, + 0.2533201510086655, + 0.03684471240955, + 0.00632, + 0.018689457, + 0.44080475, "NA" ] } @@ -50368,8 +55110,8 @@ "MT": { "HLA-A*29:02": [ "NA", - 0.903559782608582, - 1.7, + 1.7838858695651538, + 3.1, "NA", "NA", "NA" @@ -50378,8 +55120,8 @@ "WT": { "HLA-A*29:02": [ "NA", - 0.2619565217391226, - 1.4, + 6.792608695652163, + 4.0, "NA", "NA", "NA" @@ -50401,78 +55143,56 @@ ], "MT": { "HLA-A*29:02": [ - 0.5892500281333923, - 6.900000095367432, - 4.5, - 1.5, - 2.5999999046325684, - 14.0, - 1.9, - 0.6, - 0.903559782608582, - 1.7 + 1.6448750495910645, + 8.329999923706055, + 3.9000000953674316, + 2.200000047683716, + 3.0999999046325684, + 19.0, + 1.1, + 1.0, + 1.7838858695651538, + 3.1 ] }, "WT": { "HLA-A*29:02": [ - 0.4392499999999997, - 4.62, - 5.8, - 2.3, - 4.0, - 13.0, - 2.6, - 1.8, - 0.2619565217391226, - 1.4 + 3.810624999999999, + 16.16, + 8.0, + 9.2, + 7.9, + 47.0, + 1.1, + 2.2, + 6.792608695652163, + 4.0 ] } }, - "wt_peptide": "LSVDPDAECKY" - } - }, - "transcripts": [ - "ENST00000316296.9-ANO1-P/L-17" - ], - "transcript_expr": [ - 0.0 - ], - "tsl": [ - 2 - ], - "biotype": [ - "protein_coding" - ], - "transcript_length": [ - 642 - ], - "transcript_count": 1, - "peptide_count": 2, - "total_expr": 0.0 - }, - "Transcript Set 3": { - "peptides": { - "LDAECKYGLY": { + "wt_peptide": "DPDAECKYGLY" + }, + "VDLDAECKY": { "ic50s_MT": [ - 1185.83203125, + 4960.1298828125, "X", "X", "X" ], "percentiles_MT": [ - 2.1500000953674316, + 4.400000095367432, "X", "X", "X" ], "ic50s_WT": [ - 4118.843, + 9704.285, "X", "X", "X" ], "percentiles_WT": [ - 6.4, + 9.1, "X", "X", "X" @@ -50483,8 +55203,8 @@ "HLA-B*82:02", "HLA-C*06:02" ], - "mutation_position": "1", - "problematic_positions": "5", + "mutation_position": "3", + "problematic_positions": "7", "anchor_fails": "None", "individual_ic50_calls": { "algorithms": [ @@ -50499,26 +55219,26 @@ ], "MT": { "HLA-A*29:02": [ - 1404.4349455665078, - 5631.94, - 697.11, - 474.31, - 1553.24, - 10992.95, - 478.94, - 967.23 + 206.74077625975352, + 5590.51, + 4329.75, + 7366.35, + 7025.17, + 13212.86, + 1748.88, + 1709.9 ] }, "WT": { "HLA-A*29:02": [ - 5529.596718725659, - 5764.07, - 2708.09, - 2621.2, - 12106.79, - 29745.37, - 682.78, - 2044.23 + 527.365419757011, + 5552.83, + 13855.74, + 15044.73, + 17231.89, + 36141.06, + 4403.11, + 4385.0 ] } }, @@ -50535,26 +55255,26 @@ ], "MT": { "HLA-A*29:02": [ - 1.9594999551773071, - 8.819999694824219, - 1.399999976158142, - 2.0, - 1.399999976158142, - 12.0, - 2.1, - 3.7 + 0.7735000252723694, + 7.639999866485596, + 3.9000000953674316, + 8.5, + 3.799999952316284, + 34.0, + 4.9, + 4.9 ] }, "WT": { "HLA-A*29:02": [ - 3.573999999999999, - 15.81, - 2.9, - 4.1, - 6.5, - 32.0, - 2.8, - 6.3 + 1.2801250000000002, + 6.79, + 12.0, + 19.0, + 11.0, + 62.0, + 9.1, + 9.1 ] } }, @@ -50569,21 +55289,21 @@ ], "MT": { "HLA-A*29:02": [ - 0.1038067035842686, - 0.087178680498477, - 0.0216, - 0.16269088, - 0.8683477, + 0.0354273578850552, + 0.3253097817084458, + 0.0576, + 0.04872786, + 0.75704896, "NA" ] }, "WT": { "HLA-A*29:02": [ - 0.0662135537713766, - 0.0216087819885557, - 0.00115, - 0.060722344, - 0.6799751, + 0.0526074136141687, + 0.1710373932023114, + 0.0285, + 0.011653869, + 0.38437778, "NA" ] } @@ -50600,8 +55320,8 @@ "MT": { "HLA-A*29:02": [ "NA", - 3.2120380434781595, - 2.2, + 1.2795923913042344, + 1.4, "NA", "NA", "NA" @@ -50610,8 +55330,682 @@ "WT": { "HLA-A*29:02": [ "NA", - 11.115788043478249, - 8.9, + 2.04293478260864, + 1.9, + "NA", + "NA", + "NA" + ] + } + }, + "individual_percentile_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "NetMHC", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC", + "MHCflurryEL Presentation", + "NetMHCpanEL" + ], + "MT": { + "HLA-A*29:02": [ + 0.7735000252723694, + 7.639999866485596, + 3.9000000953674316, + 8.5, + 3.799999952316284, + 34.0, + 4.9, + 4.9, + 1.2795923913042344, + 1.4 + ] + }, + "WT": { + "HLA-A*29:02": [ + 1.2801250000000002, + 6.79, + 12.0, + 19.0, + 11.0, + 62.0, + 9.1, + 9.1, + 2.04293478260864, + 1.9 + ] + } + }, + "wt_peptide": "VDPDAECKY" + } + }, + "transcripts": [ + "ENST00000531604.5-ANO1-P/L-45" + ], + "transcript_expr": [ + 0.0 + ], + "tsl": [ + 3 + ], + "biotype": [ + "protein_coding" + ], + "transcript_length": [ + 251 + ], + "transcript_count": 1, + "peptide_count": 3, + "total_expr": 0.0 + }, + "Transcript Set 3": { 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0.0005199099, + "NA" + ] + } + }, + "individual_el_percentile_calls": { + "algorithms": [ + "MHCflurryEL Processing", + "MHCflurryEL Presentation", + "NetMHCpanEL", + "BigMHC_EL", + "BigMHC_IM", + "DeepImmuno" + ], + "MT": { + "HLA-B*45:01": [ + "NA", + 62.74467391304348, + 25.0, + "NA", + "NA", + "NA" + ] + }, + "WT": { + "HLA-B*45:01": [ + "NA", + 46.22467391304348, + 14.0, + "NA", + "NA", + "NA" + ] + } + }, + "individual_percentile_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "NetMHC", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC", + "MHCflurryEL Presentation", + "NetMHCpanEL" + ], + "MT": { + "HLA-B*45:01": [ + 6.276249885559082, + 22.059999465942383, + 6.599999904632568, + 4.5, + 4.0, + 4.699999809265137, + 24.0, + 15.0, + 62.74467391304348, + 25.0 + ] + }, + "WT": { + "HLA-B*45:01": [ + 5.2856250000000005, + 20.07, + 6.5, + 4.2, + 4.8, + 4.0, + 24.0, + 14.0, + 46.22467391304348, + 14.0 + ] + } + }, + "wt_peptide": "LEGLNFNLTE" + } + }, + "transcripts": [ + "ENST00000393087.9-SERPINA1-E/D-110" + ], + "transcript_expr": [ + 0.0 + ], + "tsl": [ + 1 + ], + "biotype": [ + "protein_coding" + ], + "transcript_length": [ + 418 + ], + "transcript_count": 1, + "peptide_count": 1, + "total_expr": 0.0 + } + }, + "sets": [ + "Transcript Set 1" + ], + "transcript_counts": [ + 1 + ], + "peptide_counts": [ + 1 + ], + "set_expr": [ + 0.0 + ], "DNA VAF": 0.18, "RNA VAF": 0.0, "gene_expr": 4.892, @@ -82696,19 +89945,255 @@ "transcript_count": 2, "peptide_count": 3, "total_expr": 7.857 + }, + "Transcript Set 2": { + "peptides": { + "SFLSEEGTAK": { + "ic50s_MT": [ + 9099.4541015625, + "X", + "X", + "X" + ], + "percentiles_MT": [ + 11.593999862670898, + "X", + "X", + "X" + ], + "ic50s_WT": [ + 10147.926, + "X", + "X", + "X" + ], + "percentiles_WT": [ + 11.403, + "X", + "X", + "X" + ], + "hla_types": [ + "HLA-A*29:02", + "HLA-B*45:01", + "HLA-B*82:02", + "HLA-C*06:02" + ], + "mutation_position": "4", + "problematic_positions": "None", + "anchor_fails": "None", + "individual_ic50_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "NetMHC", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC" + ], + "MT": { + "HLA-A*29:02": [ + 8094.058386713167, + 5155.89, + 26532.02, + 16228.45, + 17240.09, + 6062.77, + 7911.89, + 10104.85 + ] + }, + "WT": { + "HLA-A*29:02": [ + 9342.9311507542, + 5103.96, + 25877.93, + 15967.2, + 17126.68, + 5869.13, + 7911.89, + 10952.92 + ] + } + }, + "individual_ic50_percentile_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "NetMHC", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC" + ], + "MT": { + "HLA-A*29:02": [ + 4.453249931335449, + 2.7899999618530273, + 28.0, + 19.0, + 11.0, + 4.5, + 18.0, + 22.0 + ] + }, + "WT": { + "HLA-A*29:02": [ + 4.937249999999999, + 2.5700000000000003, + 27.0, + 19.0, + 10.0, + 4.3, + 18.0, + 23.0 + ] + } + }, + "individual_el_calls": { + "algorithms": [ + "MHCflurryEL Processing", + "MHCflurryEL Presentation", + "NetMHCpanEL", + "BigMHC_EL", + "BigMHC_IM", + "DeepImmuno" + ], + "MT": { + "HLA-A*29:02": [ + 0.1441455826861784, + 0.0197012224274007, + 0.00271, + 0.008885548, + 0.021217223, + "NA" + ] + }, + "WT": { + "HLA-A*29:02": [ + 0.16382881073514, + 0.0183985383356125, + 0.00286, + 0.0075540734, + 0.019803224, + "NA" + ] + } + }, + "individual_el_percentile_calls": { + "algorithms": [ + "MHCflurryEL Processing", + "MHCflurryEL Presentation", + "NetMHCpanEL", + "BigMHC_EL", + "BigMHC_IM", + "DeepImmuno" + ], + "MT": { + "HLA-A*29:02": [ + "NA", + 12.187228260869546, + 5.9, + "NA", + "NA", + "NA" + ] + }, + "WT": { + "HLA-A*29:02": [ + "NA", + 12.805461956521723, + 5.8, + "NA", + "NA", + "NA" + ] + } + }, + "individual_percentile_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "NetMHC", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC", + "MHCflurryEL Presentation", + "NetMHCpanEL" + ], + "MT": { + "HLA-A*29:02": [ + 4.453249931335449, + 2.7899999618530273, + 28.0, + 19.0, + 11.0, + 4.5, + 18.0, + 22.0, + 12.187228260869546, + 5.9 + ] + }, + "WT": { + "HLA-A*29:02": [ + 4.937249999999999, + 2.5700000000000003, + 27.0, + 19.0, + 10.0, + 4.3, + 18.0, + 23.0, + 12.805461956521723, + 5.8 + ] + } + }, + "wt_peptide": "SFLAEEGTAK" + } + }, + "transcripts": [ + "ENST00000560031.6-GALK2-A/S-197" + ], + "transcript_expr": [ + 0.717 + ], + "tsl": [ + 1 + ], + "biotype": [ + "protein_coding" + ], + "transcript_length": [ + 458 + ], + "transcript_count": 1, + "peptide_count": 1, + "total_expr": 0.717 } }, "sets": [ - "Transcript Set 1" + "Transcript Set 1", + "Transcript Set 2" ], "transcript_counts": [ - 2 + 2, + 1 ], "peptide_counts": [ - 3 + 3, + 1 ], "set_expr": [ - 7.857 + 7.857, + 0.717 ], "DNA VAF": 1.0, "RNA VAF": 1.0, @@ -86635,29 +94120,29 @@ "good_binders": { "Transcript Set 1": { "peptides": { - "KPFSWRHCL": { + "VQKKKPFSW": { "ic50s_MT": [ "X", "X", - 382.46600341796875, + 24437.931640625, "X" ], "percentiles_MT": [ "X", "X", - 0.10000000149011612, + 38.0, "X" ], "ic50s_WT": [ "X", "X", - 413.52, + 30726.73, "X" ], "percentiles_WT": [ "X", "X", - 0.132, + 38.0, "X" ], "hla_types": [ @@ -86666,8 +94151,8 @@ "HLA-B*82:02", "HLA-C*06:02" ], - "mutation_position": "3", - "problematic_positions": "8", + "mutation_position": "7", + "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { "algorithms": [ @@ -86682,24 +94167,24 @@ ], "MT": { "HLA-B*82:02": [ - 382.4657233339892, - 12.62, + 24437.931932660296, + 33037.57, "NA", - 688.93, - 464.34, - 238.6, + 23957.42, + 34672.12, + 21970.92, "NA", "NA" ] }, "WT": { "HLA-B*82:02": [ - 491.8012119062004, - 12.32, + 21900.08460879904, + 29898.46, "NA", - 543.0, - 413.52, - 249.16, + 30726.73, + 34474.24, + 33144.32, "NA", "NA" ] @@ -86718,24 +94203,24 @@ ], "MT": { "HLA-B*82:02": [ - 0.1002499982714653, - 0.0, + 9.203499794006348, + 62.060001373291016, "NA", - 0.6000000238418579, - 0.029999999329447746, - 0.6000000238418579, + 49.0, + 38.0, + 54.0, "NA", "NA" ] }, "WT": { "HLA-B*82:02": [ - 0.132, - 0.0, + 6.058624999999998, + 46.23, "NA", - 0.35, - 0.03, - 0.6, + 63.0, + 38.0, + 71.0, "NA", "NA" ] @@ -86752,21 +94237,21 @@ ], "MT": { "HLA-B*82:02": [ - 0.8464413210749626, - 0.8238200251626376, - 0.485, - 0.28383243, - 0.07994232, + 0.6994412466883659, + 0.0467162655835412, + 0.00744, + 0.00044804352, + 0.00037791024, "NA" ] }, "WT": { "HLA-B*82:02": [ - 0.8157897964119911, - 0.7666988941217268, - 0.511, - 0.44828296, - 0.21458468, + 0.7210933864116669, + 0.0555821236449682, + 0.0128, + 0.0013910106, + 0.00068415364, "NA" ] } @@ -86783,8 +94268,8 @@ "MT": { "HLA-B*82:02": [ "NA", - 0.2409510869564997, - 0.05, + 5.44942934782604, + 8.0, "NA", "NA", "NA" @@ -86793,8 +94278,218 @@ "WT": { "HLA-B*82:02": [ "NA", - 0.3317663043477949, - 0.04, + 4.657581521739076, + 5.7, + "NA", + "NA", + "NA" + ] + } + }, + "individual_percentile_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "NetMHC", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC", + "MHCflurryEL Presentation", + "NetMHCpanEL" + ], + "MT": { + "HLA-B*82:02": [ + 9.203499794006348, + 62.060001373291016, + "NA", + 49.0, + 38.0, + 54.0, + "NA", + "NA", + 5.44942934782604, + 8.0 + ] + }, + "WT": { + "HLA-B*82:02": [ + 6.058624999999998, + 46.23, + "NA", + 63.0, + 38.0, + 71.0, + "NA", + "NA", + 4.657581521739076, + 5.7 + ] + } + }, + "wt_peptide": "VQKKKPISW" + }, + "KPFSWRHCL": { + "ic50s_MT": [ + "X", + "X", + 382.46600341796875, + "X" + ], + "percentiles_MT": [ + "X", + "X", + 0.10000000149011612, + "X" + ], + "ic50s_WT": [ + "X", + "X", + 413.52, + "X" + ], + "percentiles_WT": [ + "X", + "X", + 0.132, + "X" + ], + "hla_types": [ + "HLA-A*29:02", + "HLA-B*45:01", + "HLA-B*82:02", + "HLA-C*06:02" + ], + "mutation_position": "3", + "problematic_positions": "8", + "anchor_fails": "None", + "individual_ic50_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "NetMHC", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC" + ], + "MT": { + "HLA-B*82:02": [ + 382.4657233339892, + 12.62, + "NA", + 688.93, + 464.34, + 238.6, + "NA", + "NA" + ] + }, + "WT": { + "HLA-B*82:02": [ + 491.8012119062004, + 12.32, + "NA", + 543.0, + 413.52, + 249.16, + "NA", + "NA" + ] + } + }, + "individual_ic50_percentile_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "NetMHC", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC" + ], + "MT": { + "HLA-B*82:02": [ + 0.1002499982714653, + 0.0, + "NA", + 0.6000000238418579, + 0.029999999329447746, + 0.6000000238418579, + "NA", + "NA" + ] + }, + "WT": { + "HLA-B*82:02": [ + 0.132, + 0.0, + "NA", + 0.35, + 0.03, + 0.6, + "NA", + "NA" + ] + } + }, + "individual_el_calls": { + "algorithms": [ + "MHCflurryEL Processing", + "MHCflurryEL Presentation", + "NetMHCpanEL", + "BigMHC_EL", + "BigMHC_IM", + "DeepImmuno" + ], + "MT": { + "HLA-B*82:02": [ + 0.8464413210749626, + 0.8238200251626376, + 0.485, + 0.28383243, + 0.07994232, + "NA" + ] + }, + "WT": { + "HLA-B*82:02": [ + 0.8157897964119911, + 0.7666988941217268, + 0.511, + 0.44828296, + 0.21458468, + "NA" + ] + } + }, + "individual_el_percentile_calls": { + "algorithms": [ + "MHCflurryEL Processing", + "MHCflurryEL Presentation", + "NetMHCpanEL", + "BigMHC_EL", + "BigMHC_IM", + "DeepImmuno" + ], + "MT": { + "HLA-B*82:02": [ + "NA", + 0.2409510869564997, + 0.05, + "NA", + "NA", + "NA" + ] + }, + "WT": { + "HLA-B*82:02": [ + "NA", + 0.3317663043477949, + 0.04, "NA", "NA", "NA" @@ -86862,7 +94557,7 @@ 1691 ], "transcript_count": 1, - "peptide_count": 1, + "peptide_count": 2, "total_expr": 0.0 } }, @@ -86873,7 +94568,7 @@ 1 ], "peptide_counts": [ - 1 + 2 ], "set_expr": [ 0.0 @@ -93595,11 +101290,252 @@ "best_hla_allele": "HLA-A*29:02" }, "chr16-49281350-49281351-C-T": { - "good_binders": {}, - "sets": [], - "transcript_counts": [], - "peptide_counts": [], - "set_expr": [], + "good_binders": { + "Transcript Set 1": { + "peptides": { + "NSNPTSDPT": { + "ic50s_MT": [ + "X", + "X", + "X", + 17484.130859375 + ], + "percentiles_MT": [ + "X", + "X", + "X", + 33.69200134277344 + ], + "ic50s_WT": [ + "X", + "X", + "X", + 25848.948 + ], + "percentiles_WT": [ + "X", + "X", + "X", + 47.5 + ], + "hla_types": [ + "HLA-A*29:02", + "HLA-B*45:01", + "HLA-B*82:02", + "HLA-C*06:02" + ], + "mutation_position": "1", + "problematic_positions": "None", + "anchor_fails": "None", + "individual_ic50_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "NetMHC", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC" + ], + "MT": { + "HLA-C*06:02": [ + 18954.472353661426, + 16013.79, + 37626.2, + 38150.11, + 35174.29, + 6262.79, + 994.97, + 1881.78 + ] + }, + "WT": { + "HLA-C*06:02": [ + 21336.356567298622, + 30361.54, + 41676.93, + 41151.77, + 40030.16, + 9759.45, + 3671.22, + 8801.77 + ] + } + }, + "individual_ic50_percentile_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "NetMHC", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC" + ], + "MT": { + "HLA-C*06:02": [ + 33.38462448120117, + 29.790000915527344, + 35.0, + 60.0, + 34.0, + 22.0, + 9.1, + 15.0 + ] + }, + "WT": { + "HLA-C*06:02": [ + 41.92649999999999, + 60.61, + 51.0, + 74.0, + 53.0, + 34.0, + 21.0, + 31.0 + ] + } + }, + "individual_el_calls": { + "algorithms": [ + "MHCflurryEL Processing", + "MHCflurryEL Presentation", + "NetMHCpanEL", + "BigMHC_EL", + "BigMHC_IM", + "DeepImmuno" + ], + "MT": { + "HLA-C*06:02": [ + 0.0008114783013297, + 0.0052678815530951, + 3.1e-05, + 1.9985984e-05, + 0.00605011, + 0.96872836 + ] + }, + "WT": { + "HLA-C*06:02": [ + 0.0015205521485768, + 0.0047101325240077, + 1.4e-05, + 1.8074661e-05, + 0.005028888, + 0.9816414 + ] + } + }, + "individual_el_percentile_calls": { + "algorithms": [ + "MHCflurryEL Processing", + "MHCflurryEL Presentation", + "NetMHCpanEL", + "BigMHC_EL", + "BigMHC_IM", + "DeepImmuno" + ], + "MT": { + "HLA-C*06:02": [ + "NA", + 46.22467391304348, + 35.0, + "NA", + "NA", + "NA" + ] + }, + "WT": { + "HLA-C*06:02": [ + "NA", + 62.74467391304348, + 44.0, + "NA", + "NA", + "NA" + ] + } + }, + "individual_percentile_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "NetMHC", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC", + "MHCflurryEL Presentation", + "NetMHCpanEL" + ], + "MT": { + "HLA-C*06:02": [ + 33.38462448120117, + 29.790000915527344, + 35.0, + 60.0, + 34.0, + 22.0, + 9.1, + 15.0, + 46.22467391304348, + 35.0 + ] + }, + "WT": { + "HLA-C*06:02": [ + 41.92649999999999, + 60.61, + 51.0, + 74.0, + 53.0, + 34.0, + 21.0, + 31.0, + 62.74467391304348, + 44.0 + ] + } + }, + "wt_peptide": "DSNPTSDPT" + } + }, + "transcripts": [ + "ENST00000219197.11-CBLN1-D/N-39" + ], + "transcript_expr": [ + 0.331 + ], + "tsl": [ + 1 + ], + "biotype": [ + "protein_coding" + ], + "transcript_length": [ + 193 + ], + "transcript_count": 1, + "peptide_count": 1, + "total_expr": 0.331 + } + }, + "sets": [ + "Transcript Set 1" + ], + "transcript_counts": [ + 1 + ], + "peptide_counts": [ + 1 + ], + "set_expr": [ + 0.331 + ], "DNA VAF": 0.215, "RNA VAF": 0.4, "gene_expr": 0.713, @@ -99027,6 +106963,216 @@ }, "Transcript Set 2": { "peptides": { + "DEIVAHKQG": { + "ic50s_MT": [ + "X", + 12633.4853515625, + "X", + "X" + ], + "percentiles_MT": [ + "X", + 8.649999618530273, + "X", + "X" + ], + "ic50s_WT": [ + "X", + 42366.415, + "X", + "X" + ], + "percentiles_WT": [ + "X", + 69.0, + "X", + "X" + ], + "hla_types": [ + "HLA-A*29:02", + "HLA-B*45:01", + "HLA-B*82:02", + "HLA-C*06:02" + ], + "mutation_position": "4-5", + "problematic_positions": "None", + "anchor_fails": "None", + "individual_ic50_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "NetMHC", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC" + ], + "MT": { + "HLA-B*45:01": [ + 953.6223154478864, + 28760.79, + 24321.77, + 15044.73, + 12815.8, + 3343.7, + 12451.17, + 6786.1 + ] + }, + "WT": { + "HLA-B*45:01": [ + 30145.63999101526, + 37059.96, + 46458.86, + 44150.12, + 40582.71, + 33869.37, + 61689.32, + 70245.74 + ] + } + }, + "individual_ic50_percentile_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "NetMHC", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC" + ], + "MT": { + "HLA-B*45:01": [ + 1.1148749589920044, + 40.630001068115234, + 18.0, + 7.400000095367432, + 4.800000190734863, + 9.899999618530273, + 25.0, + 18.0 + ] + }, + "WT": { + "HLA-B*45:01": [ + 35.63949999999999, + 77.48, + 86.0, + 80.0, + 62.0, + 68.0, + 66.0, + 70.0 + ] + } + }, + "individual_el_calls": { + "algorithms": [ + "MHCflurryEL Processing", + "MHCflurryEL Presentation", + "NetMHCpanEL", + "BigMHC_EL", + "BigMHC_IM", + "DeepImmuno" + ], + "MT": { + "HLA-B*45:01": [ + 0.1221874745097011, + 0.1292604016410015, + 0.0257, + 0.0004418902, + 9.486738e-05, + "NA" + ] + }, + "WT": { + "HLA-B*45:01": [ + 0.0075966296863043, + 0.0034444291687035, + 3.3e-05, + 4.3773096e-05, + 0.0010458113, + "NA" + ] + } + }, + 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3.8986413043477626, + 6.8 + ] + } + }, + "wt_peptide": "QHMTEVVRR" + } + }, + "transcripts": [ + "ENST00000269305.9-TP53-R/H-175" + ], + "transcript_expr": [ + 141.682 + ], + "tsl": [ + 1 + ], + "biotype": [ + "protein_coding" + ], + "transcript_length": [ + 393 + ], + "transcript_count": 1, + "peptide_count": 1, + "total_expr": 141.682 } }, "sets": [ - "Transcript Set 1" + "Transcript Set 1", + "Transcript Set 2" ], "transcript_counts": [ - 10 + 10, + 1 ], "peptide_counts": [ + 1, 1 ], "set_expr": [ - 15.309999999999999 + 15.309999999999999, + 141.682 ], "DNA VAF": 0.989, "RNA VAF": 1.0, @@ -100535,45 +108917,32 @@ "best_hla_allele": "HLA-A*29:02" }, "chr17-10499040-10499041-G-A": { - "good_binders": {}, - "sets": [], - "transcript_counts": [], - "peptide_counts": [], - "set_expr": [], - "DNA VAF": 0.988, - "RNA VAF": 0.0, - "gene_expr": 0.009, - "best_peptide_mt": "DEKDTLVSQLL", - "best_peptide_wt": "DEKDTLVSQLS", - "best_hla_allele": "HLA-B*45:01" - }, - 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42899.87, + 12449.51, + 41176.27, + 12930.01, + 421.01, + 3932.24 + ] + } + }, + "individual_ic50_percentile_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "NetMHC", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC" + ], + "MT": { + "HLA-B*45:01": [ + 2.635499954223633, + 25.479999542236328, + 35.0, + 4.5, + 44.0, + 8.300000190734863, + 0.4, + 8.8 + ] + }, + "WT": { + "HLA-B*45:01": [ + 2.3044999999999995, + 29.28, + 56.0, + 6.4, + 67.0, + 18.0, + 0.4, + 8.8 + ] + } + }, + "individual_el_calls": { + "algorithms": [ + "MHCflurryEL Processing", + "MHCflurryEL Presentation", + "NetMHCpanEL", + "BigMHC_EL", + "BigMHC_IM", + "DeepImmuno" + ], + "MT": { + "HLA-B*45:01": [ + 0.0003937882902391, + 0.0128932288775055, + 0.000288, + 8.692084e-05, + 7.442206e-05, + "NA" + ] + }, + "WT": { + "HLA-B*45:01": [ + 0.0003334330504003, + 0.0170629018126828, + 0.0002, + 6.779871e-05, + 9.640105e-05, + "NA" + ] + } + }, + "individual_el_percentile_calls": { + "algorithms": [ + "MHCflurryEL Processing", + "MHCflurryEL Presentation", + "NetMHCpanEL", + "BigMHC_EL", + "BigMHC_IM", + "DeepImmuno" + ], + "MT": { + "HLA-B*45:01": [ + "NA", + 18.61798913043478, + 17.0, + "NA", + "NA", + "NA" + ] + }, + "WT": { + "HLA-B*45:01": [ + "NA", + 13.500896739130424, + 20.0, + "NA", + "NA", + "NA" + ] + } + }, + "individual_percentile_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "NetMHC", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC", + "MHCflurryEL Presentation", + "NetMHCpanEL" + ], + "MT": { + "HLA-B*45:01": [ + 2.635499954223633, + 25.479999542236328, + 35.0, + 4.5, + 44.0, + 8.300000190734863, + 0.4, + 8.8, + 18.61798913043478, + 17.0 + ] + }, + "WT": { + "HLA-B*45:01": [ + 2.3044999999999995, + 29.28, + 56.0, + 6.4, + 67.0, + 18.0, + 0.4, + 8.8, + 13.500896739130424, + 20.0 + ] + } + }, + "wt_peptide": "EEDEDDDHGHN" + } + }, + "transcripts": [ + "ENST00000398571.7-USP34-D/H-624" + ], + "transcript_expr": [ + 33.212 + ], + "tsl": [ + 5 + ], + "biotype": [ + "protein_coding" + ], + "transcript_length": [ + 3546 + ], + "transcript_count": 1, + "peptide_count": 1, + "total_expr": 33.212 + } + }, + "sets": [ + "Transcript Set 1" + ], + "transcript_counts": [ + 1 + ], + "peptide_counts": [ + 1 + ], + "set_expr": [ + 33.212 + ], "DNA VAF": 0.284, "RNA VAF": 0.355, "gene_expr": 47.363, @@ -142825,27 +152889,27 @@ "good_binders": { "Transcript Set 1": { "peptides": { - "LIGVVLLCF": { + "FWKLLVSFH": { "ic50s_MT": [ - 3903.840087890625, + 5265.27490234375, "X", "X", "X" ], "percentiles_MT": [ - 5.5, + 7.699999809265137, "X", "X", "X" ], "ic50s_WT": [ - 14464.345, + 8196.635, "X", "X", "X" ], "percentiles_WT": [ - 22.0, + 12.5, "X", "X", "X" @@ -142856,8 +152920,8 @@ "HLA-B*82:02", "HLA-C*06:02" ], - "mutation_position": "9", - "problematic_positions": "8", + "mutation_position": "1", + "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { "algorithms": [ @@ -142872,26 +152936,26 @@ ], "MT": { "HLA-A*29:02": [ - 843.4872172316107, - 3972.57, - 3835.11, - 5182.46, - 9559.73, - 5932.98, - 2487.48, - 2290.71 + 6584.417493130829, + 5734.05, + 4796.5, + 4701.59, + 7918.3, + 7287.08, + 4536.91, + 4753.02 ] }, "WT": { "HLA-A*29:02": [ - 17556.469543607956, - 5603.3, - 16490.42, - 21970.92, - 26387.14, - 11233.42, - 12438.27, - 11694.19 + 10484.210580510462, + 5819.17, + 8358.56, + 7945.94, + 9223.42, + 8853.9, + 7866.11, + 8034.71 ] } }, @@ -142908,26 +152972,26 @@ ], "MT": { "HLA-A*29:02": [ - 1.5802500247955322, - 0.8600000143051147, - 3.5999999046325684, - 6.5, - 5.099999904632568, - 16.0, - 6.2, - 5.9 + 3.927999973297119, + 13.539999961853027, + 4.199999809265137, + 6.0, + 4.199999809265137, + 19.0, + 9.4, + 9.7 ] }, "WT": { "HLA-A*29:02": [ - 9.323624999999996, - 7.969999999999999, - 14.0, - 33.0, - 23.0, - 29.0, - 21.0, - 21.0 + 5.3787499999999975, + 22.33, + 6.4, + 9.0, + 4.9, + 24.0, + 16.0, + 16.0 ] } }, @@ -142942,21 +153006,21 @@ ], "MT": { "HLA-A*29:02": [ - 0.0089618864876683, - 0.1007504941744888, - 0.00238, - 0.02149165, - 0.5903574, + 0.0054747102840337, + 0.0148133660985927, + 0.0165, + 0.01324126, + 0.2288325, "NA" ] }, "WT": { "HLA-A*29:02": [ - 0.0083234935300424, - 0.0058244794698552, - 4e-05, - 0.0030343109, - 0.21341991, + 0.0117416006760322, + 0.0096895817578121, + 0.0112, + 0.0032385406, + 0.09203427, "NA" ] } @@ -142973,8 +153037,8 @@ "MT": { "HLA-A*29:02": [ "NA", - 2.910570652173845, - 6.3, + 16.15755434782608, + 2.5, "NA", "NA", "NA" @@ -142983,8 +153047,450 @@ "WT": { "HLA-A*29:02": [ "NA", - 46.22467391304348, - 38.0, + 24.57923913043477, + 3.0, + "NA", + "NA", + "NA" + ] + } + }, + "individual_percentile_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "NetMHC", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC", + "MHCflurryEL Presentation", + "NetMHCpanEL" + ], + "MT": { + "HLA-A*29:02": [ + 3.927999973297119, + 13.539999961853027, + 4.199999809265137, + 6.0, + 4.199999809265137, + 19.0, + 9.4, + 9.7, + 16.15755434782608, + 2.5 + ] + }, + "WT": { + "HLA-A*29:02": [ + 5.3787499999999975, + 22.33, + 6.4, + 9.0, + 4.9, + 24.0, + 16.0, + 16.0, + 24.57923913043477, + 3.0 + ] + } + }, + "wt_peptide": "IWKLLVSFH" + }, + "LIGVVLLCF": { + "ic50s_MT": [ + 3903.840087890625, + "X", + "X", + "X" + ], + "percentiles_MT": [ + 5.5, + "X", + "X", + "X" + ], + "ic50s_WT": [ + 14464.345, + "X", + "X", + "X" + ], + "percentiles_WT": [ + 22.0, + "X", + "X", + "X" + ], + "hla_types": [ + "HLA-A*29:02", + "HLA-B*45:01", + "HLA-B*82:02", + "HLA-C*06:02" + ], + "mutation_position": "9", + "problematic_positions": "8", + "anchor_fails": "None", + "individual_ic50_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "NetMHC", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC" + ], + "MT": { + "HLA-A*29:02": [ + 843.4872172316107, + 3972.57, + 3835.11, + 5182.46, + 9559.73, + 5932.98, + 2487.48, + 2290.71 + ] + }, + "WT": { + "HLA-A*29:02": [ 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}, + "WT": { + "HLA-A*29:02": [ + 17556.469543607956, + 5603.3, + 16490.42, + 21970.92, + 26387.14, + 11233.42, + 12438.27, + 11694.19 + ] + } + }, + "individual_ic50_percentile_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "NetMHC", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC" + ], + "MT": { + "HLA-A*29:02": [ + 1.5802500247955322, + 0.8600000143051147, + 3.5999999046325684, + 6.5, + 5.099999904632568, + 16.0, + 6.2, + 5.9 + ] + }, + "WT": { + "HLA-A*29:02": [ + 9.323624999999996, + 7.969999999999999, + 14.0, + 33.0, + 23.0, + 29.0, + 21.0, + 21.0 + ] + } + }, + "individual_el_calls": { + "algorithms": [ + "MHCflurryEL Processing", + "MHCflurryEL Presentation", + "NetMHCpanEL", + "BigMHC_EL", + "BigMHC_IM", + "DeepImmuno" + ], + "MT": { + "HLA-A*29:02": [ + 0.0089618864876683, + 0.1007504941744888, + 0.00238, + 0.02149165, + 0.5903574, + "NA" + ] + }, + "WT": { + "HLA-A*29:02": [ + 0.0083234935300424, + 0.0058244794698552, + 4e-05, + 0.0030343109, + 0.21341991, + "NA" + ] + } + }, + "individual_el_percentile_calls": { + "algorithms": [ + "MHCflurryEL Processing", + "MHCflurryEL Presentation", + "NetMHCpanEL", + "BigMHC_EL", + "BigMHC_IM", + "DeepImmuno" + ], + "MT": { + "HLA-A*29:02": [ + "NA", + 2.910570652173845, + 6.3, + "NA", + "NA", + "NA" + ] + }, + "WT": { + "HLA-A*29:02": [ + "NA", + 46.22467391304348, + 38.0, "NA", "NA", "NA" @@ -143037,30 +153543,25 @@ } }, "transcripts": [ - "ENST00000409872.1-ITGB6-I/F-729", "ENST00000428609.6-ITGB6-I/F-687" ], "transcript_expr": [ - 0.054, 0.0 ], "tsl": [ - 1, 2 ], "biotype": [ - "protein_coding", "protein_coding" ], "transcript_length": [ - 788, 746 ], - "transcript_count": 2, + "transcript_count": 1, "peptide_count": 1, - "total_expr": 0.054 + "total_expr": 0.0 }, - "Transcript Set 2": { + "Transcript Set 3": { "peptides": { "CFWKLLVSF": { "ic50s_MT": [ @@ -143725,18 +154226,22 @@ }, "sets": [ "Transcript Set 1", - "Transcript Set 2" + "Transcript Set 2", + "Transcript Set 3" ], "transcript_counts": [ - 2, + 1, + 1, 3 ], "peptide_counts": [ + 2, 1, 3 ], "set_expr": [ 0.054, + 0.0, 0.022 ], "DNA VAF": 0.225, @@ -144234,6 +154739,216 @@ "good_binders": { "Transcript Set 1": { "peptides": { + "RNLSFFLTPA": { + "ic50s_MT": [ + "X", + 5226.5, + "X", + "X" + ], + "percentiles_MT": [ + "X", + 5.75, + "X", + "X" + ], + "ic50s_WT": [ + "X", + 21147.735, + "X", + "X" + ], + "percentiles_WT": [ + "X", + 26.525, + "X", + "X" + ], + "hla_types": [ + "HLA-A*29:02", + "HLA-B*45:01", + "HLA-B*82:02", + "HLA-C*06:02" + ], + "mutation_position": "10", + "problematic_positions": "None", + "anchor_fails": "None", + "individual_ic50_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "NetMHC", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC" + ], + "MT": { + "HLA-B*45:01": [ + 26840.478508036183, + 332.87, + 7797.49, + 9865.62, + 7516.43, + 2936.57, + 1616.93, + 1321.08 + ] + }, + "WT": { + "HLA-B*45:01": [ + 29810.200887277813, 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"HLA-B*82:02", "HLA-C*06:02" ], - "mutation_position": "4", + "mutation_position": "1", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -194090,24 +209155,24 @@ ], "MT": { "HLA-B*82:02": [ - 20422.31354620228, - 3537.51, + 24385.121734252, + 7594.25, "NA", - 4701.59, - 15931.82, - 2443.19, + 12930.01, + 18749.3, + 11355.63, "NA", "NA" ] }, "WT": { "HLA-B*82:02": [ - 22016.36245678829, - 2410.53, + 25169.795706199144, + 14145.36, "NA", - 4909.54, - 16972.65, - 2781.92, + 9654.43, + 18315.4, + 9972.95, "NA", "NA" ] @@ -194126,24 +209191,24 @@ ], "MT": { "HLA-B*82:02": [ - 4.919250011444092, - 5.090000152587891, + 9.203499794006348, + 8.649999618530273, "NA", - 3.0999999046325684, - 4.900000095367432, - 3.5999999046325684, + 12.0, + 6.800000190734863, + 13.0, "NA", "NA" ] }, "WT": { "HLA-B*82:02": [ - 6.279624999999999, - 3.99, + 10.708625, + 14.7, "NA", - 3.3, - 5.6, - 4.0, + 7.2, + 6.5, + 9.8, "NA", "NA" ] @@ -194160,21 +209225,21 @@ ], "MT": { 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"MHCflurryEL Processing", + "MHCflurryEL Presentation", + "NetMHCpanEL", + "BigMHC_EL", + "BigMHC_IM", + "DeepImmuno" + ], + "MT": { + "HLA-B*45:01": [ + 0.0770270437933504, + 0.155674587439247, + 0.0125, + 0.002497816, + 0.00013024689, + "NA" + ] + }, + "WT": { + "HLA-B*45:01": [ + 0.0632124486146494, + 0.1615921064611665, + 0.0129, + 0.002795273, + 7.429353e-05, + "NA" + ] + } + }, + "individual_el_percentile_calls": { + "algorithms": [ + "MHCflurryEL Processing", + "MHCflurryEL Presentation", + "NetMHCpanEL", + "BigMHC_EL", + "BigMHC_IM", + "DeepImmuno" + ], + "MT": { + "HLA-B*45:01": [ + "NA", + 2.1733967391303537, + 3.2, + "NA", + "NA", + "NA" + ] + }, + "WT": { + "HLA-B*45:01": [ + "NA", + 2.1200543478259988, + 3.2, + "NA", + "NA", + "NA" + ] + } + }, + "individual_percentile_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "NetMHC", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC", + "MHCflurryEL Presentation", + "NetMHCpanEL" + ], + "MT": { + "HLA-B*45:01": [ + 0.9427499771118164, + 8.130000114440918, + 2.5999999046325684, + 2.0, + 2.0999999046325684, + 1.600000023841858, + 2.7, + 2.2, + 2.1733967391303537, + 3.2 + ] + }, + "WT": { + "HLA-B*45:01": [ + 0.9023749999999992, + 5.69, + 1.9, + 2.2, + 2.4, + 1.6, + 2.7, + 2.5, + 2.1200543478259988, + 3.2 + ] + } + }, + "wt_peptide": "AELDGRCPSD" + }, + "AELDGRCLSDS": { + "ic50s_MT": [ + "X", + 3664.02490234375, + "X", + "X" + ], + "percentiles_MT": [ + "X", + 3.8450000286102295, + "X", + "X" + ], + "ic50s_WT": [ + "X", + 3143.875, + "X", + "X" + ], + "percentiles_WT": [ + "X", + 3.205, + "X", + "X" + ], + "hla_types": [ + "HLA-A*29:02", + "HLA-B*45:01", + "HLA-B*82:02", + "HLA-C*06:02" + ], + "mutation_position": "8", + "problematic_positions": "7", + "anchor_fails": "None", + "individual_ic50_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "NetMHC", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC" + ], + "MT": { + "HLA-B*45:01": [ + 2797.571854459549, + 3564.13, + 6826.6, + 1145.59, + 5771.71, + 2054.82, + 4573.94, + 3763.92 ] }, "WT": { "HLA-B*45:01": [ - 628.4147187275536, - 891.74, - 11788.16, - 711.66, - 3145.69, - 1746.99, - 850.06, - 1067.19 + 2532.48926731774, + 2412.06, + 9316.6, + 1340.18, + 5687.96, + 1925.66, + 4563.42, + 3755.26 ] } }, @@ -264581,26 +284054,26 @@ ], "MT": { "HLA-B*45:01": [ - 1.0583750009536743, - 9.199999809265137, - 5.900000095367432, - 1.399999976158142, - 2.9000000953674316, - 1.2000000476837158, - 0.9, - 2.3 + 1.725250005722046, + 4.590000152587891, + 5.199999809265137, + 1.7999999523162842, + 2.299999952316284, + 3.0999999046325684, + 9.5, + 8.6 ] }, "WT": { "HLA-B*45:01": [ - 0.9273749999999992, - 1.84, - 8.1, - 1.4, - 1.5, - 2.6, - 0.3, - 0.4 + 1.6573749999999985, + 3.51, + 6.7, + 2.1, + 2.3, + 2.9, + 9.5, + 8.6 ] } }, @@ -264615,21 +284088,21 @@ ], "MT": { "HLA-B*45:01": [ - 0.396499564871192, - 0.3053443174788817, - 0.0852, - 0.0022422315, - 0.00032410285, + 0.0799511909717693, + 0.0430100093498705, + 0.0264, + 0.002500877, + 0.00022965665, "NA" ] }, "WT": { "HLA-B*45:01": [ - 0.1158901765011251, - 0.1787741489647438, - 0.221, - 0.019096816, - 0.0024072179, + 0.0348352441797032, + 0.0404930672442368, + 0.0164, + 0.00038403907, + 5.2841002e-05, "NA" ] } @@ -264646,8 +284119,8 @@ "MT": { "HLA-B*45:01": [ "NA", - 1.3454076086955666, - 1.2, + 5.913749999999965, + 2.2, "NA", "NA", "NA" @@ -264656,8 +284129,8 @@ "WT": { "HLA-B*45:01": [ "NA", - 1.9827717391303563, - 0.53, + 6.18413043478256, + 2.9, "NA", "NA", "NA" @@ -264679,57 +284152,79 @@ ], "MT": { "HLA-B*45:01": [ - 1.0583750009536743, - 9.199999809265137, - 5.900000095367432, - 1.399999976158142, - 2.9000000953674316, - 1.2000000476837158, - 0.9, - 2.3, - 1.3454076086955666, - 1.2 + 1.725250005722046, + 4.590000152587891, + 5.199999809265137, + 1.7999999523162842, + 2.299999952316284, + 3.0999999046325684, + 9.5, + 8.6, + 5.913749999999965, + 2.2 ] }, "WT": { "HLA-B*45:01": [ - 0.9273749999999992, - 1.84, - 8.1, - 1.4, - 1.5, - 2.6, - 0.3, - 0.4, - 1.9827717391303563, - 0.53 + 1.6573749999999985, + 3.51, + 6.7, + 2.1, + 2.3, + 2.9, + 9.5, + 8.6, + 6.18413043478256, + 2.9 ] } }, - "wt_peptide": "AELDGRCP" - }, - "AELDGRCLS": { + "wt_peptide": "AELDGRCPSDS" + } + }, + "transcripts": [ + "ENST00000373896.8-PHF19-P/L-499" + ], + "transcript_expr": [ + 3.291 + ], + "tsl": [ + 2 + ], + "biotype": [ + "protein_coding" + ], + "transcript_length": [ + 580 + ], + "transcript_count": 1, + "peptide_count": 2, + "total_expr": 3.291 + }, + "Transcript Set 3": { + "peptides": { + "LSDSSAEGA": { "ic50s_MT": [ "X", - 915.625, + 22354.609375, "X", "X" ], "percentiles_MT": [ "X", - 1.5499999523162842, + 25.5, "X", "X" ], "ic50s_WT": [ "X", - 495.47, + 25167.187, "X", "X" ], "percentiles_WT": [ "X", - 0.91, + 43.575, "X", "X" ], @@ -264739,9 +284234,9 @@ "HLA-B*82:02", "HLA-C*06:02" ], - "mutation_position": "8", - "problematic_positions": "7", - "anchor_fails": "HLA-B*45:01", + "mutation_position": "1", + "problematic_positions": "None", + "anchor_fails": "None", "individual_ic50_calls": { "algorithms": [ "MHCflurry", @@ -264755,26 +284250,26 @@ ], "MT": { "HLA-B*45:01": [ - 102.5664708198418, - 2072.67, - 1204.66, - 888.39, - 206.06, - 942.86, - 881.48, - 1744.3 + 16280.84093741836, + 28428.38, + 41345.03, + 37739.56, + 33008.68, + 8387.64, + 6519.44, + 9091.17 ] }, "WT": { "HLA-B*45:01": [ - 108.4726278205287, - 282.71, - 672.7, - 508.87, - 208.44, - 482.07, - 705.03, - 1157.76 + 22109.01490525834, + 28225.36, + 44690.8, + 42971.89, + 41785.74, + 19505.61, + 8713.85, + 13696.83 ] } }, @@ -264791,26 +284286,26 @@ ], "MT": { "HLA-B*45:01": [ - 0.25075000524520874, - 3.1600000858306885, - 1.5, - 1.600000023841858, - 0.1899999976158142, - 3.0, - 3.3, - 6.7 + 4.531125068664551, + 39.689998626708984, + 48.0, + 35.0, + 27.0, + 24.0, + 18.0, + 21.0 ] }, "WT": { "HLA-B*45:01": [ - 0.2686249999999998, - 0.8999999999999999, - 0.92, - 1.1, - 0.19, - 1.4, - 2.5, - 4.4 + 7.653875, + 39.15, + 69.0, + 68.0, + 71.0, + 48.0, + 21.0, + 26.0 ] } }, @@ -264825,21 +284320,21 @@ ], "MT": { "HLA-B*45:01": [ - 0.1020555621944367, - 0.5466484460505325, - 0.423, - 0.01131933, - 0.0019371504, + 0.0042773936147568, + 0.0061760130808522, + 0.000214, + 0.0007066003, + 0.015515787, "NA" ] }, "WT": { "HLA-B*45:01": [ - 0.0648125784937292, - 0.5002461459028515, - 0.277, - 0.07298648, - 0.0064345696, + 0.0002551340567151, + 0.0045306492722463, + 4e-05, + 0.00024201178, + 0.0027004345, "NA" ] } @@ -264856,8 +284351,8 @@ "MT": { "HLA-B*45:01": [ "NA", - 0.7226358695651243, - 0.24, + 37.35904891304347, + 19.0, "NA", "NA", "NA" @@ -264866,8 +284361,8 @@ "WT": { "HLA-B*45:01": [ "NA", - 0.8208423913042395, - 0.42, + 62.74467391304348, + 39.0, "NA", "NA", "NA" @@ -264889,57 +284384,35 @@ ], "MT": { "HLA-B*45:01": [ - 0.25075000524520874, - 3.1600000858306885, - 1.5, - 1.600000023841858, - 0.1899999976158142, - 3.0, - 3.3, - 6.7, - 0.7226358695651243, - 0.24 + 4.531125068664551, + 39.689998626708984, + 48.0, + 35.0, + 27.0, + 24.0, + 18.0, + 21.0, + 37.35904891304347, + 19.0 ] }, "WT": { "HLA-B*45:01": [ - 0.2686249999999998, - 0.8999999999999999, - 0.92, - 1.1, - 0.19, - 1.4, - 2.5, - 4.4, - 0.8208423913042395, - 0.42 + 7.653875, + 39.15, + 69.0, + 68.0, + 71.0, + 48.0, + 21.0, + 26.0, + 62.74467391304348, + 39.0 ] } }, - "wt_peptide": "AELDGRCPS" - } - }, - "transcripts": [ - "ENST00000419155.5-PHF19-P/L-290" - ], - "transcript_expr": [ - 3.274 - ], - "tsl": [ - 2 - ], - "biotype": [ - "protein_coding" - ], - "transcript_length": [ - 371 - ], - "transcript_count": 1, - "peptide_count": 2, - "total_expr": 3.274 - }, - "Transcript Set 2": { - "peptides": { + "wt_peptide": "PSDSSAEGA" + }, "AELDGRCLSD": { "ic50s_MT": [ "X", @@ -265362,45 +284835,44 @@ } }, "transcripts": [ - "ENST00000616568.5-PHF19-P/L-518", - "ENST00000373896.8-PHF19-P/L-499" + "ENST00000616568.5-PHF19-P/L-518" ], "transcript_expr": [ - 0.658, - 3.291 + 0.658 ], "tsl": [ - 1, - 2 + 1 ], 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"MT": { - "HLA-B*45:01": [ - 812.7775430120497, - 13008.01, - 19773.36, - 3705.68, - 8321.02, - 2781.92, - 5428.63, - 4196.91 + "HLA-B*82:02": [ + 21269.31841910777, + 7076.29, + "NA", + 13284.53, + 29007.7, + 10301.97, + "NA", + "NA" ] }, "WT": { - "HLA-B*45:01": [ - 15574.842725984963, - 36006.94, - 44338.24, - 25152.75, - 29784.35, - 33504.88, - 21962.92, - 12131.93 + "HLA-B*82:02": [ + 18098.167451933725, + 6564.9, + "NA", + 13797.25, + 29030.92, + 10757.62, + "NA", + "NA" ] } }, @@ -280788,27 +301227,27 @@ "SMMPMBEC" ], "MT": { - "HLA-B*45:01": [ - 1.0378750562667847, - 13.510000228881836, - 15.0, - 3.299999952316284, - 3.0999999046325684, - 4.099999904632568, - 20.0, - 16.0 + "HLA-B*82:02": [ + 5.641749858856201, + 8.210000038146973, + "NA", + 12.0, + 22.0, + 11.0, + "NA", + "NA" ] }, "WT": { - "HLA-B*45:01": [ - 4.3225, - 70.92, - 66.0, - 15.0, - 20.0, - 40.0, - 48.0, - 34.0 + "HLA-B*82:02": [ + 3.583, + 7.77, + "NA", + 13.0, + 22.0, + 12.0, + "NA", + "NA" ] } }, @@ -280822,22 +301261,22 @@ "DeepImmuno" ], "MT": { - "HLA-B*45:01": [ - 0.0325762745924294, - 0.1121129397621659, - 0.000966, - 0.00046642387, - 0.000863388, + "HLA-B*82:02": [ + 0.0002092353365696, + 0.0047027180527955, + 0.000961, + 3.5963538e-05, + 0.00016184917, "NA" ] }, "WT": { - "HLA-B*45:01": [ - 0.0071141267690109, - 0.0065106219699329, - 3.1e-05, - 0.0030283313, - 0.035890456, + "HLA-B*82:02": [ + 0.0002997757078446, + 0.0054985849875194, + 0.00117, + 4.468943e-05, + 0.00015047283, "NA" ] } @@ -280852,20 +301291,20 @@ "DeepImmuno" ], "MT": { - "HLA-B*45:01": [ + "HLA-B*82:02": [ "NA", - 2.6922554347825383, - 9.7, + 62.74467391304348, + 22.0, "NA", "NA", "NA" ] }, "WT": { - "HLA-B*45:01": [ + "HLA-B*82:02": [ "NA", - 37.35904891304347, - 43.0, + 46.22467391304348, + 21.0, "NA", "NA", "NA" @@ -280886,55 +301325,55 @@ "NetMHCpanEL" ], "MT": { - "HLA-B*45:01": [ - 1.0378750562667847, - 13.510000228881836, - 15.0, - 3.299999952316284, - 3.0999999046325684, - 4.099999904632568, - 20.0, - 16.0, - 2.6922554347825383, - 9.7 + "HLA-B*82:02": [ + 5.641749858856201, + 8.210000038146973, + "NA", + 12.0, + 22.0, + 11.0, + "NA", + "NA", + 62.74467391304348, + 22.0 ] }, "WT": { - "HLA-B*45:01": [ - 4.3225, - 70.92, - 66.0, - 15.0, - 20.0, - 40.0, - 48.0, - 34.0, - 37.35904891304347, - 43.0 + "HLA-B*82:02": [ + 3.583, + 7.77, + "NA", + 13.0, + 22.0, + 12.0, + "NA", + "NA", + 46.22467391304348, + 21.0 ] } }, - "wt_peptide": "FDVVVIGGGI" + "wt_peptide": "AATSAGGSGA" } }, "transcripts": [ - "ENST00000693128.1-MAOA-D/E-15" + "ENST00000374597.3-STARD8-G/S-188" ], "transcript_expr": [ - 0.0 + 0.038 ], "tsl": [ - "NA" + 1 ], "biotype": [ "protein_coding" ], "transcript_length": [ - 492 + 1023 ], "transcript_count": 1, - "peptide_count": 3, - "total_expr": 0.0 + "peptide_count": 1, + "total_expr": 0.038 } }, "sets": [ @@ -280944,26 +301383,13 @@ 1 ], "peptide_counts": [ - 3 + 1 ], "set_expr": [ - 0.0 + 0.038 ], "DNA VAF": 1.0, "RNA VAF": 1.0, - "gene_expr": 0.784, - "best_peptide_mt": "FEVVVIGG", - "best_peptide_wt": "FDVVVIGG", - "best_hla_allele": "HLA-B*45:01" - }, - "chrX-68717715-68717716-G-A": { - "good_binders": {}, - "sets": [], - "transcript_counts": [], - "peptide_counts": [], - "set_expr": [], - "DNA VAF": 1.0, - "RNA VAF": 1.0, "gene_expr": 0.753, "best_peptide_mt": "AATSASGSGA", "best_peptide_wt": "AATSAGGSGA", @@ -286015,11 +306441,252 @@ "best_hla_allele": "HLA-B*45:01" }, "chrX-154349376-154349377-C-G": { - "good_binders": {}, - "sets": [], - "transcript_counts": [], - "peptide_counts": [], - "set_expr": [], + "good_binders": { + "Transcript Set 1": { + "peptides": { + "YVGQKSSFTVH": { + "ic50s_MT": [ + 11846.7646484375, + "X", + "X", + "X" + ], + "percentiles_MT": [ + 11.322999954223633, + "X", + "X", + "X" + ], + "ic50s_WT": [ + 30563.774, + "X", + "X", + "X" + ], + "percentiles_WT": [ + 50.382, + "X", + "X", + "X" + ], + "hla_types": [ + "HLA-A*29:02", + "HLA-B*45:01", + "HLA-B*82:02", + "HLA-C*06:02" + ], + "mutation_position": "11", + "problematic_positions": "None", + "anchor_fails": "None", + "individual_ic50_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "NetMHC", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC" + ], + "MT": { + "HLA-A*29:02": [ + 21338.455759969173, + 5499.02, + 26291.39, + 10246.39, + 22684.98, + 9972.95, + 13447.14, + 3538.91 + ] + }, + "WT": { + "HLA-A*29:02": [ + 31382.177204102543, + 5888.44, + 34090.69, + 34423.54, + 37081.02, + 29745.37, + 13447.14, + 4244.92 + ] + } + }, + "individual_ic50_percentile_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "NetMHC", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC" + ], + "MT": { + "HLA-A*29:02": [ + 12.845624923706055, + 5.800000190734863, + 28.0, + 9.0, + 17.0, + 8.800000190734863, + 42.0, + 9.8 + ] + }, + "WT": { + "HLA-A*29:02": [ + 50.764875, + 39.69, + 50.0, + 67.0, + 53.0, + 32.0, + 42.0, + 13.0 + ] + } + }, + "individual_el_calls": { + "algorithms": [ + "MHCflurryEL Processing", + "MHCflurryEL Presentation", + "NetMHCpanEL", + "BigMHC_EL", + "BigMHC_IM", + "DeepImmuno" + ], + "MT": { + "HLA-A*29:02": [ + 0.1322458824142813, + 0.0074586784505917, + 0.00172, + 0.001694218, + 0.04995152, + "NA" + ] + }, + "WT": { + "HLA-A*29:02": [ + 0.0026227210910292, + 0.0032553550225559, + 6e-06, + 0.0013578404, + 0.05012742, + "NA" + ] + } + }, + "individual_el_percentile_calls": { + "algorithms": [ + "MHCflurryEL Processing", + "MHCflurryEL Presentation", + "NetMHCpanEL", + "BigMHC_EL", + "BigMHC_IM", + "DeepImmuno" + ], + "MT": { + "HLA-A*29:02": [ + "NA", + 31.64317934782608, + 7.4, + "NA", + "NA", + "NA" + ] + }, + "WT": { + "HLA-A*29:02": [ + "NA", + 99.28660326086955, + 68.0, + "NA", + "NA", + "NA" + ] + } + }, + "individual_percentile_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "NetMHC", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC", + "MHCflurryEL Presentation", + "NetMHCpanEL" + ], + "MT": { + "HLA-A*29:02": [ + 12.845624923706055, + 5.800000190734863, + 28.0, + 9.0, + 17.0, + 8.800000190734863, + 42.0, + 9.8, + 31.64317934782608, + 7.4 + ] + }, + "WT": { + "HLA-A*29:02": [ + 50.764875, + 39.69, + 50.0, + 67.0, + 53.0, + 32.0, + 42.0, + 13.0, + 99.28660326086955, + 68.0 + ] + } + }, + "wt_peptide": "YVGQKSSFTVD" + } + }, + "transcripts": [ + "ENST00000369850.10-FLNA-D/H-2581" + ], + "transcript_expr": [ + 21.322 + ], + "tsl": [ + 1 + ], + "biotype": [ + "protein_coding" + ], + "transcript_length": [ + 2647 + ], + "transcript_count": 1, + "peptide_count": 1, + "total_expr": 21.322 + } + }, + "sets": [ + "Transcript Set 1" + ], + "transcript_counts": [ + 1 + ], + "peptide_counts": [ + 1 + ], + "set_expr": [ + 21.322 + ], "DNA VAF": 0.992, "RNA VAF": 0.998, "gene_expr": 706.463, diff --git a/tests/test_data/aggregate_all_epitopes/HCC1395.output.tsv b/tests/test_data/aggregate_all_epitopes/HCC1395.output.tsv index 04e91d6c..3bcaaa54 100644 --- a/tests/test_data/aggregate_all_epitopes/HCC1395.output.tsv +++ b/tests/test_data/aggregate_all_epitopes/HCC1395.output.tsv @@ -91,8 +91,8 @@ chr1-27793606-27793607-C-G 10.STX12.ENST00000373943.9.missense.88P/R 3 1 STX12 chr12-49526214-49526215-G-A 685.SPATS2.ENST00000321898.10.missense.533R/H 3 SPATS2 R533H 3 LPQHKPRTSQT ENST00000321898.10 1 HLA-B*82:02 4 None 3 0 3325.660 3472.750 6.800 6.900 23.424 1.000 23.424 334.000 0.968 Poor Pending chr6-3723707-3723708-C-G 327.PXDC1.ENST00000380283.5.missense.203E/Q 1 3 PXDC1 E203Q 2 SEFPSQLED ENST00000380283.5 1 HLA-B*45:01 6 None 4 0 2200.855 2216.300 2.250 2.400 22.483 0.539 12.118 406.000 0.418 Poor Pending chr16-74391670-74391671-C-T 846.NPIPB15.ENST00000429990.1.missense.308P/L 1 2 4 NPIPB15 P308L 2 VPLPLSPL ENST00000429990.1 5 HLA-B*82:02 5 None 7 0 685.220 546.914 0.400 0.330 10.432 0.015 0.156 68.000 0.409 Poor Pending -chr8-133256733-133256734-C-G 517.NDRG1.ENST00000674925.1.missense.44E/Q NDRG1 E44Q 0 QEQGQISGWTQ ENST00000674925.1 NA HLA-B*45:01 3 None 0 0 5688.845 5464.350 6.046 7.450 678.195 0.274 185.825 223.000 0.402 Poor Pending -chr2-190982493-190982494-G-C 171.STAT1.ENST00000361099.8.missense.491P/A 2 4 STAT1 P491A 16 RNLSFFLTPA ENST00000361099.8 1 HLA-B*45:01 10 None 6 1 5226.500 21147.735 5.750 26.525 172.622 0.520 89.763 1475.000 0.583 Poor Pending +chr8-133256733-133256734-C-G 517.NDRG1.ENST00000674925.1.missense.44E/Q 1 NDRG1 E44Q 1 QEQGQISGWTQ ENST00000674925.1 NA HLA-B*45:01 3 None 1 0 5688.845 5464.350 6.046 7.450 678.195 0.274 185.825 223.000 0.402 Poor Pending +chr2-190982493-190982494-G-C 171.STAT1.ENST00000361099.8.missense.491P/A 2 1 4 STAT1 P491A 16 RNLSFFLTPA ENST00000361099.8 1 HLA-B*45:01 10 None 7 1 5226.500 21147.735 5.750 26.525 172.622 0.520 89.763 1475.000 0.583 Poor Pending chr1-16972417-16972418-C-G 2.CROCC.ENST00000375541.10.missense.2009S/C 2 CROCC S2009C 1 APFCPPSGPP ENST00000375541.10 5 HLA-B*82:02 4 4 2 0 2250.430 2788.070 3.720 2.700 11.754 1.000 11.754 56.000 0.988 Poor Pending chr10-32567832-32567833-C-T 571.CCDC7.ENST00000277657.12.missense.454S/L 3 2 CCDC7 S454L 5 IPLEKETRKL ENST00000277657.12 1 HLA-B*82:02 10 None 5 0 1612.378 12612.410 1.749 12.000 20.750 0.208 4.316 226.000 0.359 Poor Pending chr4-154491218-154491219-G-C 279.DCHS2.ENST00000357232.10.missense.46S/C 5 DCHS2 S46C 1 ARTQRCLLW ENST00000357232.10 1 HLA-C*06:02 6 6 5 0 1237.637 748.136 1.584 0.923 2.425 1.000 2.425 17.000 0.963 Poor Pending @@ -108,9 +108,9 @@ chr20-41165771-41165772-C-G 987.PLCG1.ENST00000373271.5.missense.582S/C 2 PLC chr9-35750917-35750918-C-T 537.RGP1.ENST00000378078.5.missense.139T/I 1 RGP1 T139I 1 VKYVYKLII ENST00000378078.5 1 HLA-C*06:02 8 None 1 0 2947.106 1809.150 5.343 2.485 12.548 0.995 12.485 194.000 0.979 Poor Pending chrX-15355261-15355262-C-T 1044.VEGFD.ENST00000297904.4.missense.177E/K 3 VEGFD E177K 1 VPLTSVPKL ENST00000297904.4 1 HLA-B*82:02 8 None 3 0 1151.800 735.140 0.310 0.235 0.674 1.000 0.674 5.000 0.987 Poor Pending chr15-45133932-45133933-G-A 802.DUOX1.ENST00000321429.8.missense.43R/K 2 DUOX1 R43K 3 MEHKWGSKG ENST00000321429.8 1 HLA-B*45:01 4 None 2 0 1211.600 1253.160 1.550 1.906 0.947 1.000 0.947 2.000 1.000 Poor Pending -chr17-29286059-29286060-C-G 885.NUFIP2.ENST00000225388.9.missense.645R/T NUFIP2 R645T 0 KEQRYQTG ENST00000225388.9 1 HLA-B*45:01 7 None 0 0 5171.661 12225.944 5.520 11.500 31.008 0.998 30.946 661.000 1.000 Poor Pending +chr17-29286059-29286060-C-G 885.NUFIP2.ENST00000225388.9.missense.645R/T 1 NUFIP2 R645T 1 KEQRYQTG ENST00000225388.9 1 HLA-B*45:01 7 None 1 0 5171.661 12225.944 5.520 11.500 31.008 0.998 30.946 661.000 1.000 Poor Pending chrX-71378281-71378287-GAGATAT-G 1082.TAF1.ENST00000373790.9.inframe_del.306-308GDI/G 1 TAF1 GDI306-308G 3 FSQSTGDKV ENST00000373790.9 1 HLA-C*06:02 7-8 None 1 0 3070.838 14438.772 6.393 28.057 18.137 0.745 13.512 153.000 0.894 Poor Pending -chr11-862686-862687-C-G 612.TSPAN4.ENST00000397397.7.missense.67I/M 3 2 1 TSPAN4 I67M 12 ITGAFVMAMGF ENST00000397397.7 1 HLA-A*29:02 9 None 5 0 6751.405 7629.320 8.894 8.300 72.214 0.996 71.925 550.000 1.000 Poor Pending +chr11-862686-862687-C-G 612.TSPAN4.ENST00000397397.7.missense.67I/M 4 2 1 TSPAN4 I67M 12 ITGAFVMAMGF ENST00000397397.7 1 HLA-A*29:02 9 None 6 0 6751.405 7629.320 8.894 8.300 72.214 0.996 71.925 550.000 1.000 Poor Pending chr11-6401000-6401001-C-T 626.APBB1.ENST00000311051.7.missense.552A/T 1 2 1 APBB1 A552T 11 VPVTKPVGVDV ENST00000311051.7 1 HLA-B*82:02 4 None 4 0 2327.080 2122.020 2.300 2.100 6.678 1.000 6.678 85.000 0.990 Poor Pending chr7-77600798-77600799-C-T 391.PTPN12.ENST00000248594.11.missense.230H/Y 1 3 PTPN12 H230Y 4 VPICIYCSAGC ENST00000248594.11 1 HLA-B*82:02 6 4,7,11 4 0 4358.650 4062.650 3.620 3.330 128.676 0.161 20.717 732.000 0.203 Poor Pending chr20-23354058-23354059-C-G 977.NXT1.ENST00000254998.3.missense.6F/L 1 NXT1 F6L 1 ASVDLKTYV ENST00000254998.3 1 HLA-C*06:02 5 None 1 0 3683.760 1487.160 7.600 3.125 38.946 0.422 16.435 519.000 0.375 Poor Pending @@ -119,33 +119,33 @@ chr2-31366060-31366061-G-C 119.XDH.ENST00000379416.4.missense.791R/G 1 XDH R7 chr9-4286160-4286161-G-T 533.GLIS3.ENST00000481827.5.missense.89Q/K 1 4 1 GLIS3 Q89K 4 LPALSPRRKML ENST00000481827.5 1 HLA-B*82:02 9 None 6 0 1067.790 719.410 1.085 0.485 2.761 0.043 0.119 23.000 0.153 Poor Pending chr19-14049194-14049195-C-T 931.IL27RA.ENST00000263379.4.missense.428A/V 1 3 IL27RA A428V 1 GPTLWRLQDV ENST00000263379.4 1 HLA-B*82:02 10 None 4 0 2277.270 3343.700 2.500 4.600 13.617 0.305 4.153 197.000 0.262 Poor Pending chr19-6755017-6755018-T-C 922.SH2D3A.ENST00000245908.11.missense.265E/G 4 SH2D3A E265G 2 AEEDEGEEN ENST00000245908.11 1 HLA-B*45:01 6 None 4 0 2187.524 1879.948 4.253 5.173 3.820 1.000 3.820 5.000 0.985 Poor Pending -chr12-48693119-48693120-G-C 684.CCNT1.ENST00000261900.8.missense.698I/M CCNT1 I698M 0 NPRSGGMSSRS ENST00000261900.8 1 HLA-B*82:02 7 None 0 0 5267.250 5182.460 3.800 3.600 23.125 1.000 23.125 230.000 1.000 Poor Pending -chrX-154349376-154349377-C-G 1111.FLNA.ENST00000369850.10.missense.2581D/H FLNA D2581H 0 YVGQKSSFTVH ENST00000369850.10 1 HLA-A*29:02 11 None 0 0 11846.765 30563.774 11.323 50.382 706.463 0.998 705.050 5609.000 0.992 Poor Pending +chr12-48693119-48693120-G-C 684.CCNT1.ENST00000261900.8.missense.698I/M 1 CCNT1 I698M 1 NPRSGGMSSRS ENST00000261900.8 1 HLA-B*82:02 7 None 1 0 5267.250 5182.460 3.800 3.600 23.125 1.000 23.125 230.000 1.000 Poor Pending +chrX-154349376-154349377-C-G 1111.FLNA.ENST00000369850.10.missense.2581D/H 1 FLNA D2581H 1 YVGQKSSFTVH ENST00000369850.10 1 HLA-A*29:02 11 None 1 0 11846.765 30563.774 11.323 50.382 706.463 0.998 705.050 5609.000 0.992 Poor Pending chr7-140024672-140024681-TCAAAGATCA-T 446.PARP12.ENST00000263549.8.inframe_del.662-665VIFE/E 1 PARP12 VIFE662-665E 1 PSIFEKHQVY ENST00000263549.8 1 HLA-A*29:02 4-5 None 1 0 2389.355 196.392 4.000 0.355 29.767 0.153 4.554 307.000 0.108 Poor Pending chr1-27359862-27359863-T-G 9.MAP3K6.ENST00000374040.7.missense.764I/L 1 MAP3K6 I764L 1 HRDLKGDNV ENST00000374040.7 1 HLA-C*06:02 4 None 1 0 3392.751 1148.258 2.465 3.000 32.590 0.315 10.266 295.000 0.260 Poor Pending chr1-36179726-36179728-GG-AA 14.MAP7D1.ENST00000373151.6.missense.764-765EE/EK 3 1 MAP7D1 EE764-765EK 4 KPIPQEPQWSL ENST00000373151.6 1 HLA-B*82:02 1 None 4 0 1091.150 733.791 0.670 0.300 93.193 NA NA NA 0.361 Poor Pending -chr8-125102410-125102411-G-C 501.NSMCE2.ENST00000520866.5.missense.27L/F NSMCE2 L27F 0 VESALSSFK ENST00000520866.5 2 HLA-B*45:01 8 None 0 0 5585.211 5058.075 6.500 5.950 78.578 0.242 19.016 996.000 0.262 Poor Pending -chr1-168179177-168179178-A-T 68.TIPRL.ENST00000367830.3.missense.34E/V TIPRL E34V 0 MKSADVVKL ENST00000367830.3 1 HLA-C*06:02 7 None 0 0 5157.295 4532.155 2.495 2.950 55.746 0.332 18.508 927.000 0.273 Poor Pending +chr8-125102410-125102411-G-C 501.NSMCE2.ENST00000520866.5.missense.27L/F 1 NSMCE2 L27F 1 VESALSSFK ENST00000520866.5 2 HLA-B*45:01 8 None 1 0 5585.211 5058.075 6.500 5.950 78.578 0.242 19.016 996.000 0.262 Poor Pending +chr1-168179177-168179178-A-T 68.TIPRL.ENST00000367830.3.missense.34E/V 1 TIPRL E34V 1 MKSADVVKL ENST00000367830.3 1 HLA-C*06:02 7 None 1 0 5157.295 4532.155 2.495 2.950 55.746 0.332 18.508 927.000 0.273 Poor Pending chr10-125729432-125729433-C-G 583.EDRF1.ENST00000356792.9.missense.324P/A 7 EDRF1 P324A 6 AIFGGGRY ENST00000356792.9 1 HLA-A*29:02 1 None 7 2 2363.550 4259.324 1.231 3.170 17.377 0.185 3.215 205.000 0.155 Poor Pending chr9-137199427-137199428-T-A 556.TPRN.ENST00000409012.6.missense.428E/D 1 1 TPRN E428D 1 LPAASDEAEPA ENST00000409012.6 1 HLA-B*82:02 6 None 2 0 2642.762 3801.707 5.000 5.300 10.805 0.333 3.598 93.000 0.296 Poor Pending -chr2-669669-669670-C-T 115.TMEM18.ENST00000355654.6.missense.98M/I TMEM18 M98I 0 MIIVVIWVW ENST00000355654.6 1 HLA-A*29:02 6 None 0 0 5621.880 5872.154 8.750 6.900 55.263 0.306 16.910 980.000 0.262 Poor Pending -chr12-112043094-112043095-A-C 688.NAA25.ENST00000261745.9.missense.789S/R NAA25 S789R 0 YELDTRGLED ENST00000261745.9 1 HLA-B*45:01 6 None 0 0 7553.065 8834.680 5.350 5.516 23.927 1.000 23.927 192.000 1.000 Poor Pending -chr17-7675087-7675088-C-T 862.TP53.ENST00000269305.9.missense.175R/H 1 TP53 R175H 10 QHMTEVVRH ENST00000269305.9 1 HLA-A*29:02 9 None 1 0 18290.766 27172.470 22.885 22.500 165.032 1.000 165.032 1415.000 0.989 Poor Pending -chr13-98431277-98431278-G-T 719.FARP1.ENST00000595437.5.missense.714R/L 2 1 3 FARP1 R714L 5 LAALAEITEM ENST00000595437.5 1 HLA-B*82:02 1 None 6 0 8075.950 8950.220 5.700 4.500 26.190 0.994 26.033 169.000 1.000 Poor Pending -chr20-17659330-17659331-C-T 976.RRBP1.ENST00000377813.6.missense.393E/K RRBP1 E393K 0 NQGKKVKGA ENST00000377813.6 1 HLA-B*45:01 7 None 0 0 15310.574 12423.337 8.700 7.800 153.904 0.493 75.875 676.000 0.574 Poor Pending +chr2-669669-669670-C-T 115.TMEM18.ENST00000355654.6.missense.98M/I 1 TMEM18 M98I 1 MIIVVIWVW ENST00000355654.6 1 HLA-A*29:02 6 None 1 0 5621.880 5872.154 8.750 6.900 55.263 0.306 16.910 980.000 0.262 Poor Pending +chr12-112043094-112043095-A-C 688.NAA25.ENST00000261745.9.missense.789S/R 1 NAA25 S789R 1 YELDTRGLED ENST00000261745.9 1 HLA-B*45:01 6 None 1 0 7553.065 8834.680 5.350 5.516 23.927 1.000 23.927 192.000 1.000 Poor Pending +chr17-7675087-7675088-C-T 862.TP53.ENST00000269305.9.missense.175R/H 1 1 TP53 R175H 11 QHMTEVVRH ENST00000269305.9 1 HLA-A*29:02 9 None 2 0 18290.766 27172.470 22.885 22.500 165.032 1.000 165.032 1415.000 0.989 Poor Pending +chr13-98431277-98431278-G-T 719.FARP1.ENST00000595437.5.missense.714R/L 2 2 3 FARP1 R714L 5 LAALAEITEM ENST00000595437.5 1 HLA-B*82:02 1 None 7 0 8075.950 8950.220 5.700 4.500 26.190 0.994 26.033 169.000 1.000 Poor Pending +chr20-17659330-17659331-C-T 976.RRBP1.ENST00000377813.6.missense.393E/K 1 RRBP1 E393K 1 NQGKKVKGA ENST00000377813.6 1 HLA-B*45:01 7 None 1 0 15310.574 12423.337 8.700 7.800 153.904 0.493 75.875 676.000 0.574 Poor Pending chr6-43587456-43587457-G-A 351.POLH.ENST00000372236.9.missense.153G/D 2 3 POLH G153D 2 IEGLPQDPT ENST00000372236.9 1 HLA-B*45:01 7 None 5 0 2977.985 3031.475 2.900 2.898 12.570 0.291 3.658 237.000 0.230 Poor Pending -chr5-134893641-134893642-T-C 302.TXNDC15.ENST00000358387.9.missense.248S/P 1 4 TXNDC15 S248P 1 DAPQHSSLS ENST00000358387.9 1 HLA-C*06:02 3 None 5 0 12894.035 16771.027 21.131 30.500 42.950 0.996 42.778 447.000 0.993 Poor Pending +chr5-134893641-134893642-T-C 302.TXNDC15.ENST00000358387.9.missense.248S/P 1 4 1 TXNDC15 S248P 2 DAPQHSSLS ENST00000358387.9 1 HLA-C*06:02 3 None 6 0 12894.035 16771.027 21.131 30.500 42.950 0.996 42.778 447.000 0.993 Poor Pending chr7-112821984-112821985-G-T 428.BMT2.ENST00000297145.9.missense.326T/K 2 2 BMT2 T326K 1 KTKSDLVSRNY ENST00000297145.9 1 HLA-A*29:02 3 None 4 0 3684.145 2780.635 4.480 2.500 34.269 0.188 6.443 224.000 0.179 Poor Pending -chr15-49282070-49282071-G-T 810.GALK2.ENST00000560031.6.missense.197A/S 3 GALK2 A197S 2 SFLSEEGTAK ENST00000560031.6 1 HLA-A*29:02 4 None 3 0 9099.454 10147.926 11.594 11.403 24.473 1.000 24.473 184.000 1.000 Poor Pending +chr15-49282070-49282071-G-T 810.GALK2.ENST00000560031.6.missense.197A/S 1 3 GALK2 A197S 3 SFLSEEGTAK ENST00000560031.6 1 HLA-A*29:02 4 None 4 0 9099.454 10147.926 11.594 11.403 24.473 1.000 24.473 184.000 1.000 Poor Pending chr14-91783159-91783160-T-A 756.TC2N.ENST00000360594.9.missense.471K/N 4 1 TC2N K471N 5 IEAVNQWNET ENST00000360594.9 1 HLA-B*45:01 8 None 5 0 1901.265 3255.500 2.750 3.450 1.985 0.125 0.248 16.000 0.151 Poor Pending chrX-78015862-78015863-G-C 1092.ATP7A.ENST00000341514.11.missense.870D/H 5 1 ATP7A D870H 13 HESLITGEAM ENST00000341514.11 1 HLA-B*45:01 1 None 6 1 3531.850 8772.635 2.250 3.700 5.153 0.951 4.901 41.000 0.982 Poor Pending chr7-128815875-128815876-C-G 441.CCDC136.ENST00000494552.5.missense.980S/C 7 CCDC136 S980C 2 SEEEEDDADC ENST00000494552.5 1 HLA-B*45:01 10 10 7 0 2356.280 2591.061 4.350 5.425 4.998 0.250 1.250 32.000 0.200 Poor Pending chr20-10054508-10054509-G-C 974.ANKEF1.ENST00000378392.6.missense.694K/N 2 1 ANKEF1 K694N 2 SEGNKVQKG ENST00000378392.6 1 HLA-B*45:01 4 None 3 0 2509.040 2375.340 3.300 3.600 3.908 0.382 1.493 34.000 0.521 Poor Pending -chr2-61348284-61348285-C-G 127.USP34.ENST00000398571.7.missense.624D/H USP34 D624H 0 EEHEDDDHGHN ENST00000398571.7 5 HLA-B*45:01 3 None 0 0 6867.255 12689.760 12.900 15.750 47.363 0.355 16.814 591.000 0.284 Poor Pending +chr2-61348284-61348285-C-G 127.USP34.ENST00000398571.7.missense.624D/H 1 USP34 D624H 1 EEHEDDDHGHN ENST00000398571.7 5 HLA-B*45:01 3 None 1 0 6867.255 12689.760 12.900 15.750 47.363 0.355 16.814 591.000 0.284 Poor Pending chr10-37957500-37957501-C-T 576.ZNF25.ENST00000302609.8.missense.21E/K 2 1 ZNF25 E21K 1 KEKWKLLTPAQ ENST00000302609.8 1 HLA-B*45:01 3 None 3 0 3908.060 3664.590 6.525 5.143 13.090 0.471 6.165 187.000 0.485 Poor Pending chr16-87417563-87417564-G-C 848.ZCCHC14.ENST00000268616.9.missense.290L/V 4 ZCCHC14 L290V 4 MPSSVQTPQT ENST00000268616.9 1 HLA-B*82:02 5 None 4 0 3364.322 4416.246 0.700 0.810 12.705 0.248 3.151 153.000 0.277 Poor Pending chr13-25541936-25541938-GA-CT 695.ATP8A2.ENST00000381655.7.missense.224D/L 1 1 5 ATP8A2 D224L 6 IRQGLSHTAL ENST00000381655.7 1 HLA-C*06:02 10 None 5 0 1743.110 25171.981 0.774 34.000 0.145 NA NA NA 0.319 Poor Pending -chr9-37784015-37784016-T-A 538.EXOSC3.ENST00000327304.10.missense.124K/N EXOSC3 K124N 0 VTANSGDIF ENST00000327304.10 1 HLA-A*29:02 4 None 0 0 6920.210 9886.520 9.825 15.230 28.784 0.533 15.342 255.000 0.480 Poor Pending +chr9-37784015-37784016-T-A 538.EXOSC3.ENST00000327304.10.missense.124K/N 1 EXOSC3 K124N 1 VTANSGDIF ENST00000327304.10 1 HLA-A*29:02 4 None 1 0 6920.210 9886.520 9.825 15.230 28.784 0.533 15.342 255.000 0.480 Poor Pending chr11-46728135-46728136-T-C 641.F2.ENST00000311907.10.missense.424V/A 3 2 F2 V424A 2 TENDLLARIG ENST00000311907.10 1 HLA-B*45:01 7 None 5 0 1973.235 1743.915 2.600 2.300 0.048 1.000 0.048 1.000 0.357 Poor Pending chr19-17052841-17052842-C-G 945.HAUS8.ENST00000253669.10.missense.304K/N 1 HAUS8 K304N 2 SELKDVTAKN ENST00000253669.10 1 HLA-B*45:01 10 None 1 0 4520.046 7503.075 5.050 3.950 10.348 0.602 6.229 98.000 0.548 Poor Pending chr19-14049194-14049196-CC-TT 932.IL27RA.ENST00000263379.4.missense.428A/V 1 IL27RA A428V 1 VPPGTPAI ENST00000263379.4 1 HLA-B*82:02 1 None 1 0 1844.100 1610.820 1.400 1.400 13.617 NA NA NA 0.268 Poor Pending @@ -154,50 +154,50 @@ chr15-40622779-40622780-C-T 787.KNL1.ENST00000399668.7.missense.839P/L 1 KNL1 chr15-40622778-40622779-C-T 783.KNL1.ENST00000399668.7.missense.839P/S 1 KNL1 P839S 1 KPKFLKEKQNV ENST00000399668.7 1 HLA-B*82:02 5 None 1 0 4676.230 4830.500 5.600 3.200 13.527 0.492 6.655 128.000 0.444 Poor Pending chr2-102015965-102015966-C-T 144.IL1R2.ENST00000393414.6.missense.143T/I 1 3 5 IL1R2 T143I 4 YPQILILST ENST00000393414.6 1 HLA-B*82:02 6 None 8 0 2171.320 1218.890 0.660 0.350 0.517 0.300 0.155 10.000 0.200 Poor Pending chr9-129102403-129102404-T-C 547.CRAT.ENST00000318080.7.missense.209Y/C 5 CRAT Y209C 6 HNCQFFELDVY ENST00000318080.7 1 HLA-A*29:02 3 3 5 0 2350.677 907.740 2.296 1.800 11.624 0.018 0.209 169.000 0.275 Poor Pending -chr3-56617278-56617279-G-C 219.CCDC66.ENST00000326595.11.missense.637E/Q CCDC66 E637Q 0 TQDKGASLQ ENST00000326595.11 1 HLA-C*06:02 9 None 0 0 19218.256 18459.346 24.000 25.500 24.974 1.000 24.974 133.000 1.000 Poor Pending +chr3-56617278-56617279-G-C 219.CCDC66.ENST00000326595.11.missense.637E/Q 1 CCDC66 E637Q 1 TQDKGASLQ ENST00000326595.11 1 HLA-C*06:02 9 None 1 0 19218.256 18459.346 24.000 25.500 24.974 1.000 24.974 133.000 1.000 Poor Pending chr19-13765994-13765995-G-C 928.MRI1.ENST00000040663.8.missense.138R/T 1 MRI1 R138T 1 TEDMLEKDLT ENST00000040663.8 1 HLA-B*45:01 10 None 1 0 4861.945 18342.410 4.750 9.100 24.532 0.201 4.931 389.000 0.224 Poor Pending chr1-183880710-183880711-A-C 74.RGL1.ENST00000360851.4.missense.174Y/S 1 1 RGL1 Y174S 2 LLDSLTRMM ENST00000360851.4 1 HLA-C*06:02 4 None 2 0 2323.900 3763.694 3.350 6.549 0.461 0.286 0.132 7.000 0.300 Poor Pending chr17-7588499-7588500-G-C 861.SOX15.ENST00000538513.6.missense.194Q/E 3 SOX15 Q194E 2 LPESDPRL ENST00000538513.6 1 HLA-B*82:02 3 None 3 0 2751.900 1269.610 1.796 1.400 0.580 0.692 0.401 13.000 0.722 Poor Pending -chr7-92077866-92077867-G-C 408.AKAP9.ENST00000491695.2.missense.528D/H AKAP9 D528H 0 KITTHNKVI ENST00000491695.2 1 HLA-C*06:02 5 None 0 0 9351.740 21632.225 6.300 23.000 36.250 0.408 14.790 238.000 0.412 Poor Pending +chr7-92077866-92077867-G-C 408.AKAP9.ENST00000491695.2.missense.528D/H 1 AKAP9 D528H 1 KITTHNKVI ENST00000491695.2 1 HLA-C*06:02 5 None 1 0 9351.740 21632.225 6.300 23.000 36.250 0.408 14.790 238.000 0.412 Poor Pending chrX-107601385-107601386-G-T 1105.FRMPD3.ENST00000276185.9.missense.1116S/I 3 FRMPD3 S1116I 4 KRIKLEETSLV ENST00000276185.9 5 HLA-C*06:02 3 None 3 0 2279.417 3902.688 3.939 4.660 0.100 0.500 0.050 4.000 0.391 Poor Pending -chr9-120858190-120858191-G-A 546.PHF19.ENST00000616568.5.missense.518P/L 4 PHF19 P518L 3 LSDSSAEGA ENST00000616568.5 1 HLA-B*45:01 1 None 4 0 22354.609 25167.187 25.500 43.575 47.989 0.447 21.451 103.000 0.517 Poor Pending +chr9-120858190-120858191-G-A 546.PHF19.ENST00000616568.5.missense.518P/L 5 PHF19 P518L 3 LSDSSAEGA ENST00000616568.5 1 HLA-B*45:01 1 None 5 0 22354.609 25167.187 25.500 43.575 47.989 0.447 21.451 103.000 0.517 Poor Pending chr9-137436071-137436072-C-T 558.ENTPD8.ENST00000344119.6.missense.331G/S 1 1 ENTPD8 G331S 1 SQEDCAFDGVY ENST00000344119.6 1 HLA-A*29:02 1 5 2 0 2406.120 4042.055 2.300 3.150 0.236 0.500 0.118 4.000 0.346 Poor Pending -chr18-80138228-80138229-G-T 909.ADNP2.ENST00000262198.9.missense.939R/I ADNP2 R939I 0 ISAPKDSSSDL ENST00000262198.9 1 HLA-B*82:02 1 None 0 0 17401.420 18929.995 18.340 4.950 19.521 0.959 18.721 122.000 1.000 Poor Pending +chr18-80138228-80138229-G-T 909.ADNP2.ENST00000262198.9.missense.939R/I 1 ADNP2 R939I 1 ISAPKDSSSDL ENST00000262198.9 1 HLA-B*82:02 1 None 1 0 17401.420 18929.995 18.340 4.950 19.521 0.959 18.721 122.000 1.000 Poor Pending chr16-25246937-25246938-C-T 838.ZKSCAN2.ENST00000328086.12.missense.420E/K 2 ZKSCAN2 E420K 1 AFFKDMDALL ENST00000328086.12 1 HLA-A*29:02 4 None 2 0 4084.325 2526.062 3.150 3.000 4.925 0.441 2.172 68.000 0.454 Poor Pending chr15-43149136-43149137-G-C 789.TMEM62.ENST00000564494.1.missense.216W/C 1 TMEM62 W216C 1 LELEVGDCK ENST00000564494.1 1 HLA-B*45:01 8 8 1 0 4702.850 5491.988 6.810 12.094 3.179 1.000 3.179 39.000 0.960 Poor Pending chr6-152325133-152325134-C-T 371.SYNE1.ENST00000367255.10.missense.5203E/K 1 SYNE1 E5203K 1 VAQDQKKIL ENST00000367255.10 1 HLA-C*06:02 6 None 1 0 4076.190 4698.510 4.800 7.200 5.739 0.286 1.641 7.000 0.323 Poor Pending chrX-9967396-9967397-G-A 1043.CLDN34.ENST00000445307.4.missense.14V/I 2 3 1 1 CLDN34 V14I 1 FSIFALTTI ENST00000445307.4 NA HLA-C*06:02 3 None 7 0 2706.140 5120.060 2.700 4.500 0.013 1.000 0.013 1.000 0.989 Poor Pending chr4-176120050-176120052-AG-GA 283.WDR17.ENST00000508596.6.missense.164-165KV/KI 2 WDR17 KV164-165KI 2 HTHQKGKIV ENST00000508596.6 1 HLA-C*06:02 8 None 2 0 2657.255 2338.375 2.510 2.105 0.514 NA NA NA 0.508 Poor Pending -chr5-7886679-7886680-G-C 292.MTRR.ENST00000264668.6.missense.402E/Q 3 1 MTRR E402Q 2 QIRAIPKKAF ENST00000264668.6 1 HLA-B*82:02 1 None 3 1 12930.010 14145.360 9.204 9.800 64.271 0.204 13.111 372.000 0.194 Poor Pending +chr5-7886679-7886680-G-C 292.MTRR.ENST00000264668.6.missense.402E/Q 3 1 1 MTRR E402Q 2 QIRAIPKKAF ENST00000264668.6 1 HLA-B*82:02 1 None 4 1 12930.010 14145.360 9.204 9.800 64.271 0.204 13.111 372.000 0.194 Poor Pending chr3-52395054-52395055-C-T 216.DNAH1.ENST00000420323.7.missense.3655P/L 4 2 1 DNAH1 P3655L 2 EPRFIELQTA ENST00000420323.7 1 HLA-B*82:02 7 None 7 0 4621.260 7640.539 1.500 1.500 3.000 0.550 1.650 20.000 0.263 Poor Pending chr7-97006043-97006044-G-C 423.DLX6.ENST00000518156.3.missense.23E/Q 1 1 DLX6 E23Q 1 SSKSAFMQF ENST00000518156.3 1 HLA-C*06:02 8 None 1 0 4357.515 3597.800 15.000 12.000 2.584 0.424 1.096 33.000 0.411 Poor Pending -chr22-26540809-26540810-G-T 1003.TPST2.ENST00000338754.9.missense.274P/H TPST2 P274H 0 HEDLIGKHGGV ENST00000338754.9 1 HLA-B*45:01 8 None 0 0 7623.420 7558.075 4.750 4.300 28.333 0.210 5.950 371.000 0.203 Poor Pending -chr11-6410863-6410864-C-T 637.APBB1.ENST00000311051.7.missense.162E/K 1 APBB1 E162K 2 EEKDDDDEEEE ENST00000311051.7 1 HLA-B*45:01 3 None 1 0 8521.320 6728.640 6.750 7.200 6.678 1.000 6.678 65.000 1.000 Poor Pending -chr6-43340177-43340178-C-G 349.ZNF318.ENST00000361428.3.missense.1274G/R ZNF318 G1274R 0 KESPTSSSFR ENST00000361428.3 1 HLA-B*45:01 10 None 0 0 7306.472 3565.075 6.600 3.850 12.831 0.377 4.837 106.000 0.347 Poor Pending -chr4-103145955-103145956-C-G 268.CENPE.ENST00000380026.8.missense.1404R/T 2 CENPE R1404T 1 TLQESHDEM ENST00000380026.8 1 HLA-A*29:02 1 None 2 0 9704.430 13996.040 17.500 16.080 29.958 0.242 7.250 380.000 0.239 Poor Pending +chr22-26540809-26540810-G-T 1003.TPST2.ENST00000338754.9.missense.274P/H 1 TPST2 P274H 1 HEDLIGKHGGV ENST00000338754.9 1 HLA-B*45:01 8 None 1 0 7623.420 7558.075 4.750 4.300 28.333 0.210 5.950 371.000 0.203 Poor Pending +chr11-6410863-6410864-C-T 637.APBB1.ENST00000311051.7.missense.162E/K 2 APBB1 E162K 3 EEKDDDDEEEE ENST00000311051.7 1 HLA-B*45:01 3 None 2 0 8521.320 6728.640 6.750 7.200 6.678 1.000 6.678 65.000 1.000 Poor Pending +chr6-43340177-43340178-C-G 349.ZNF318.ENST00000361428.3.missense.1274G/R 1 ZNF318 G1274R 1 KESPTSSSFR ENST00000361428.3 1 HLA-B*45:01 10 None 1 0 7306.472 3565.075 6.600 3.850 12.831 0.377 4.837 106.000 0.347 Poor Pending +chr4-103145955-103145956-C-G 268.CENPE.ENST00000380026.8.missense.1404R/T 1 2 CENPE R1404T 2 TLQESHDEM ENST00000380026.8 1 HLA-A*29:02 1 None 3 0 9704.430 13996.040 17.500 16.080 29.958 0.242 7.250 380.000 0.239 Poor Pending chr3-186164997-186164998-C-T 257.DGKG.ENST00000265022.8.missense.706E/K 1 DGKG E706K 2 LSDQLLKVV ENST00000265022.8 1 HLA-C*06:02 7 None 1 0 4161.525 2990.115 5.550 8.150 0.612 1.000 0.612 2.000 0.518 Poor Pending chr8-132141242-132141243-C-G 510.KCNQ3.ENST00000388996.10.missense.451D/H 2 1 KCNQ3 D451H 5 FTPLNVHAI ENST00000388996.10 1 HLA-C*06:02 7 None 3 0 3125.170 6156.960 1.240 3.000 0.019 1.000 0.019 2.000 0.291 Poor Pending -chr19-12580947-12580948-G-A 926.ZNF490.ENST00000311437.11.missense.376S/F 1 1 ZNF490 S376F 1 GEAFKSSSFCE ENST00000311437.11 1 HLA-B*45:01 9 10 2 0 7964.055 6623.933 7.800 9.800 15.981 0.257 4.107 167.000 0.351 Poor Pending -chr12-31697921-31697922-G-T 680.AMN1.ENST00000281471.11.missense.118H/N 1 2 1 AMN1 H118N 2 SYLNEASLKR ENST00000281471.11 1 HLA-A*29:02 4 None 3 0 6424.453 7813.180 6.150 5.900 15.000 0.178 2.670 73.000 0.453 Poor Pending -chr1-223264671-223264672-G-C 91.SUSD4.ENST00000344029.6.missense.228L/V 1 SUSD4 L228V 6 VIWSSSPPR ENST00000344029.6 1 HLA-A*29:02 1 None 1 0 9344.650 8282.775 5.539 6.352 24.362 0.203 4.945 236.000 0.374 Poor Pending +chr19-12580947-12580948-G-A 926.ZNF490.ENST00000311437.11.missense.376S/F 2 1 ZNF490 S376F 2 GEAFKSSSFCE ENST00000311437.11 1 HLA-B*45:01 9 10 3 0 7964.055 6623.933 7.800 9.800 15.981 0.257 4.107 167.000 0.351 Poor Pending +chr12-31697921-31697922-G-T 680.AMN1.ENST00000281471.11.missense.118H/N 2 2 1 AMN1 H118N 3 SYLNEASLKR ENST00000281471.11 1 HLA-A*29:02 4 None 4 0 6424.453 7813.180 6.150 5.900 15.000 0.178 2.670 73.000 0.453 Poor Pending +chr1-223264671-223264672-G-C 91.SUSD4.ENST00000344029.6.missense.228L/V 1 1 SUSD4 L228V 7 VIWSSSPPR ENST00000344029.6 1 HLA-A*29:02 1 None 2 0 9344.650 8282.775 5.539 6.352 24.362 0.203 4.945 236.000 0.374 Poor Pending chr2-71611503-71611504-C-G 135.DYSF.ENST00000409651.5.missense.1381L/V 1 1 2 DYSF L1381V 11 RNMKSYQVA ENST00000409651.5 1 HLA-B*45:01 8 None 4 1 3710.915 5311.435 3.650 5.100 0.119 1.000 0.119 2.000 1.000 Poor Pending -chr8-123220246-123220247-C-A 492.C8orf76.ENST00000276704.6.missense.333E/D 2 1 C8orf76 E333D 1 KIKDEVHPDV ENST00000276704.6 1 HLA-C*06:02 9 None 3 0 15392.495 9103.385 17.216 7.382 45.915 0.173 7.943 352.000 0.129 Poor Pending -chr20-59944225-59944226-A-G 997.FAM217B.ENST00000360816.8.missense.95S/G 1 FAM217B S95G 1 DEDSAGDLS ENST00000360816.8 1 HLA-B*45:01 6 None 1 0 14353.965 14805.790 9.900 9.350 16.580 0.446 7.395 130.000 0.578 Poor Pending -chrX-43656385-43656386-C-A 1076.MAOA.ENST00000338702.4.missense.15D/E 1 2 1 MAOA D15E 1 FEVVVIGG ENST00000338702.4 1 HLA-B*45:01 2 None 3 0 6252.771 35265.750 6.500 45.112 0.784 1.000 0.784 2.000 1.000 Poor Pending +chr8-123220246-123220247-C-A 492.C8orf76.ENST00000276704.6.missense.333E/D 2 2 C8orf76 E333D 1 KIKDEVHPDV ENST00000276704.6 1 HLA-C*06:02 9 None 4 0 15392.495 9103.385 17.216 7.382 45.915 0.173 7.943 352.000 0.129 Poor Pending +chr20-59944225-59944226-A-G 997.FAM217B.ENST00000360816.8.missense.95S/G 2 FAM217B S95G 2 DEDSAGDLS ENST00000360816.8 1 HLA-B*45:01 6 None 2 0 14353.965 14805.790 9.900 9.350 16.580 0.446 7.395 130.000 0.578 Poor Pending +chrX-43656385-43656386-C-A 1076.MAOA.ENST00000338702.4.missense.15D/E 1 3 1 MAOA D15E 2 FEVVVIGG ENST00000338702.4 1 HLA-B*45:01 2 None 4 0 6252.771 35265.750 6.500 45.112 0.784 1.000 0.784 2.000 1.000 Poor Pending chr4-40808808-40808809-A-G 263.NSUN7.ENST00000381782.7.missense.676Y/C 1 1 NSUN7 Y676C 1 MPTQHLCCRW ENST00000381782.7 1 HLA-B*82:02 7 7,8 2 1 4772.830 3869.790 2.719 4.619 0.405 0.333 0.135 6.000 0.471 Poor Pending -chr7-27130623-27130624-C-T 382.HOXA4.ENST00000360046.10.missense.37G/D HOXA4 G37D 0 GPDGGPGYQQ ENST00000360046.10 1 HLA-B*82:02 3 None 0 0 6539.790 7818.020 5.140 5.500 1.689 0.375 0.633 16.000 0.375 Poor Pending +chr7-27130623-27130624-C-T 382.HOXA4.ENST00000360046.10.missense.37G/D 1 HOXA4 G37D 1 GPDGGPGYQQ ENST00000360046.10 1 HLA-B*82:02 3 None 1 0 6539.790 7818.020 5.140 5.500 1.689 0.375 0.633 16.000 0.375 Poor Pending chr6-33723018-33723020-CA-TG 346.IP6K3.ENST00000293756.5.missense.311-312SV/SI 4 1 IP6K3 SV311-312SI 2 LRALLSII ENST00000293756.5 1 HLA-C*06:02 7 None 5 1 4377.809 3064.893 4.353 3.036 0.009 NA NA NA 0.718 Poor Pending -chr19-422192-422193-G-C 910.SHC2.ENST00000264554.11.missense.525H/D SHC2 H525D 0 GMDAGQPKH ENST00000264554.11 1 HLA-A*29:02 3 None 0 0 6285.960 4157.485 5.800 5.158 8.139 0.070 0.570 115.000 0.110 Poor Pending -chr14-32773880-32773881-G-T 737.AKAP6.ENST00000280979.9.missense.1192M/I AKAP6 M1192I 0 IGKESETL ENST00000280979.9 1 HLA-C*06:02 1 None 0 0 11339.865 8491.965 11.295 9.744 2.905 1.000 2.905 6.000 0.607 Poor Pending +chr19-422192-422193-G-C 910.SHC2.ENST00000264554.11.missense.525H/D 1 SHC2 H525D 1 GMDAGQPKH ENST00000264554.11 1 HLA-A*29:02 3 None 1 0 6285.960 4157.485 5.800 5.158 8.139 0.070 0.570 115.000 0.110 Poor Pending +chr14-32773880-32773881-G-T 737.AKAP6.ENST00000280979.9.missense.1192M/I 1 AKAP6 M1192I 1 IGKESETL ENST00000280979.9 1 HLA-C*06:02 1 None 1 0 11339.865 8491.965 11.295 9.744 2.905 1.000 2.905 6.000 0.607 Poor Pending chr15-40622778-40622780-CC-TT 785.KNL1.ENST00000399668.7.missense.839P/L 1 KNL1 P839L 1 KPKFLKEKQNV ENST00000399668.7 1 HLA-B*82:02 5 None 1 0 4676.230 4830.500 5.600 3.200 13.527 NA NA NA 0.450 Poor Pending -chr1-86453473-86453474-G-A 45.CLCA2.ENST00000370565.5.missense.754G/E CLCA2 G754E 0 LEVPAGPHPD ENST00000370565.5 1 HLA-B*45:01 2 None 0 0 10237.470 46657.880 8.066 84.000 0.509 1.000 0.509 2.000 0.575 Poor Pending -chr3-184239802-184239803-C-T 255.VWA5B2.ENST00000426955.6.missense.836A/V 7 VWA5B2 A836V 3 PPAVPPQVP ENST00000426955.6 1 HLA-B*82:02 8 None 7 0 7406.310 5743.490 9.300 6.700 0.083 1.000 0.083 2.000 0.429 Poor Pending -chr1-227091906-227091907-GC-G 103.CDC42BPA.ENST00000366764.8.FS.778GC/G CDC42BPA FS778 0 EKVLLTEENKN ENST00000366764.8 1 HLA-B*45:01 11 None 0 0 35971.633 34029.983 54.500 43.000 40.050 0.061 2.443 312.000 0.236 Poor Pending -chrX-68717715-68717716-G-A 1079.STARD8.ENST00000374597.3.missense.188G/S STARD8 G188S 0 AATSASGSGA ENST00000374597.3 1 HLA-B*82:02 6 None 0 0 13284.530 13797.250 12.000 13.000 0.753 1.000 0.753 3.000 1.000 Poor Pending -chr22-37570267-37570268-C-G 1008.LGALS2.ENST00000215886.6.missense.132E/Q LGALS2 E132Q 0 NMSSFKLKQ ENST00000215886.6 1 HLA-A*29:02 9 None 0 0 8035.340 10549.745 8.000 13.000 0.067 0.222 0.015 9.000 0.484 Poor Pending -chr17-4818361-4818376-TGGACAGAATCCTGAA-T 857.PLD2.ENST00000572940.5.inframe_del.662-667VDRILK/V 3 PLD2 VDRILK662-667V 3 DEIVAHKQG ENST00000572940.5 1 HLA-B*45:01 4-5 None 3 1 12633.485 42366.415 8.650 69.000 35.110 0.012 0.421 328.000 0.225 Poor Pending -chr16-49281350-49281351-C-T 839.CBLN1.ENST00000219197.11.missense.39D/N CBLN1 D39N 0 NSNPTSDPT ENST00000219197.11 1 HLA-C*06:02 1 None 0 0 17484.131 25848.948 33.692 47.500 0.713 0.400 0.285 5.000 0.215 Poor Pending -chr22-37374977-37374978-G-A 1007.ELFN2.ENST00000402918.7.missense.186P/L 1 2 ELFN2 P186L 1 ELAGNLFN ENST00000402918.7 4 HLA-A*29:02 6 None 3 0 32952.840 34777.658 56.000 62.531 0.890 0.368 0.328 19.000 0.168 Poor Pending +chr1-86453473-86453474-G-A 45.CLCA2.ENST00000370565.5.missense.754G/E 1 CLCA2 G754E 1 LEVPAGPHPD ENST00000370565.5 1 HLA-B*45:01 2 None 1 0 10237.470 46657.880 8.066 84.000 0.509 1.000 0.509 2.000 0.575 Poor Pending +chr3-184239802-184239803-C-T 255.VWA5B2.ENST00000426955.6.missense.836A/V 8 VWA5B2 A836V 3 PPAVPPQVP ENST00000426955.6 1 HLA-B*82:02 8 None 8 0 7406.310 5743.490 9.300 6.700 0.083 1.000 0.083 2.000 0.429 Poor Pending +chr1-227091906-227091907-GC-G 103.CDC42BPA.ENST00000366764.8.FS.778GC/G 1 CDC42BPA FS778 1 EKVLLTEENKN ENST00000366764.8 1 HLA-B*45:01 11 None 1 0 35971.633 34029.983 54.500 43.000 40.050 0.061 2.443 312.000 0.236 Poor Pending +chrX-68717715-68717716-G-A 1079.STARD8.ENST00000374597.3.missense.188G/S 1 STARD8 G188S 1 AATSASGSGA ENST00000374597.3 1 HLA-B*82:02 6 None 1 0 13284.530 13797.250 12.000 13.000 0.753 1.000 0.753 3.000 1.000 Poor Pending +chr22-37570267-37570268-C-G 1008.LGALS2.ENST00000215886.6.missense.132E/Q 1 LGALS2 E132Q 1 NMSSFKLKQ ENST00000215886.6 1 HLA-A*29:02 9 None 1 0 8035.340 10549.745 8.000 13.000 0.067 0.222 0.015 9.000 0.484 Poor Pending +chr17-4818361-4818376-TGGACAGAATCCTGAA-T 857.PLD2.ENST00000572940.5.inframe_del.662-667VDRILK/V 3 1 PLD2 VDRILK662-667V 3 DEIVAHKQG ENST00000572940.5 1 HLA-B*45:01 4-5 None 4 1 12633.485 42366.415 8.650 69.000 35.110 0.012 0.421 328.000 0.225 Poor Pending +chr16-49281350-49281351-C-T 839.CBLN1.ENST00000219197.11.missense.39D/N 1 CBLN1 D39N 1 NSNPTSDPT ENST00000219197.11 1 HLA-C*06:02 1 None 1 0 17484.131 25848.948 33.692 47.500 0.713 0.400 0.285 5.000 0.215 Poor Pending +chr22-37374977-37374978-G-A 1007.ELFN2.ENST00000402918.7.missense.186P/L 2 2 ELFN2 P186L 1 ELAGNLFN ENST00000402918.7 4 HLA-A*29:02 6 None 4 0 32952.840 34777.658 56.000 62.531 0.890 0.368 0.328 19.000 0.168 Poor Pending chr20-59301546-59301547-G-T 993.EDN3.ENST00000395654.3.missense.64G/W 4 4 1 EDN3 G64W 4 GEWTVAPTA ENST00000395654.3 1 HLA-B*45:01 3 None 9 1 42.900 80.960 0.050 0.095 0.019 0.000 0.000 0.000 0.220 NoExpr Pending chr11-59364558-59364559-T-A 646.OR5AN1.ENST00000313940.2.missense.34V/E 7 2 1 OR5AN1 V34E 3 VLFTIFLEIY ENST00000313940.2 NA HLA-A*29:02 8 None 9 4 53.390 63.505 0.290 0.240 0.154 0.000 0.000 0.000 0.116 NoExpr Pending chr16-25221522-25221523-G-C 837.AQP8.ENST00000566125.5.missense.103M/I 5 AQP8 M103I 2 LNLVILLPY ENST00000566125.5 1 HLA-A*29:02 5 None 5 2 67.053 74.412 0.400 0.485 0.000 0.000 0.000 0.000 0.247 NoExpr Pending @@ -286,35 +286,35 @@ chr1-119895935-119895936-C-T 49.ADAM30.ENST00000369400.2.missense.134R/Q 1 AD chr15-44767434-44767452-AAATGGACAGTTGGAGTTG-A 791.TRIM69.ENST00000338264.8.inframe_del.230-236KWTVGVV/I 1 1 TRIM69 KWTVGVV230-236I 3 WEVEVAKKTI ENST00000338264.8 1 HLA-B*45:01 9-10 None 2 0 4505.730 12791.895 3.400 9.481 21.208 0.000 0.000 3.000 0.299 NoExpr Pending chr6-43283594-43283595-A-T 348.TTBK1.ENST00000259750.9.missense.952E/V 1 TTBK1 E952V 1 MSSGGQALRSV ENST00000259750.9 1 HLA-C*06:02 11 None 1 0 4623.750 24809.270 7.486 38.310 0.015 0.000 0.000 0.000 0.267 NoExpr Pending chr11-124319973-124319974-G-A 670.OR8D2.ENST00000624618.2.missense.75S/F 4 1 OR8D2 S75F 1 FVITPKMLVNF ENST00000624618.2 NA HLA-A*29:02 1 None 5 0 4940.735 7927.620 3.581 3.700 0.000 0.000 0.000 0.000 1.000 NoExpr Pending -chr4-5988666-5988667-T-A 261.C4orf50.ENST00000531445.3.missense.1127M/L C4orf50 M1127L 0 REHLQGKAKL ENST00000531445.3 5 HLA-B*45:01 10 None 0 0 5147.705 7818.115 3.000 3.200 0.025 0.000 0.000 0.000 0.946 NoExpr Pending -chr2-160107761-160107762-T-A 157.ITGB6.ENST00000409872.1.missense.729I/F 4 ITGB6 I729F 5 FWKLLVSFH ENST00000409872.1 1 HLA-A*29:02 1 None 4 0 5265.275 8196.635 7.700 12.500 0.093 0.000 0.000 0.000 0.225 NoExpr Pending -chr7-47833094-47833095-G-A 387.PKD1L1.ENST00000289672.7.missense.2111T/I 1 PKD1L1 T2111I 1 HIQAPSSGL ENST00000289672.7 1 HLA-B*82:02 2 None 1 0 5670.880 6667.100 5.400 7.500 0.696 0.000 0.000 0.000 0.322 NoExpr Pending -chr8-138737576-138737577-C-A 518.COL22A1.ENST00000303045.11.missense.696G/W 1 COL22A1 G696W 1 LRWKKGDMG ENST00000303045.11 1 HLA-C*06:02 3 None 1 0 5695.865 12356.070 14.995 27.215 0.308 0.000 0.000 2.000 0.200 NoExpr Pending -chr11-70087776-70087777-C-T 665.ANO1.ENST00000355303.10.missense.45P/L 5 ANO1 P45L 4 LLNSLSVDL ENST00000355303.10 1 HLA-C*06:02 9 None 5 0 5793.860 20782.765 9.350 50.859 0.764 0.000 0.000 0.000 0.187 NoExpr Pending -chr3-58210851-58210852-G-C 222.DNASE1L3.ENST00000394549.7.missense.19L/V 1 DNASE1L3 L19V 2 LLLSIHSAVAM ENST00000394549.7 1 HLA-B*82:02 9 None 1 0 5837.470 5743.490 6.900 6.400 0.181 0.000 0.000 0.000 1.000 NoExpr Pending -chr17-10499040-10499041-G-A 882.MYH1.ENST00000226207.6.missense.1306S/L MYH1 S1306L 0 DEKDTLVSQLL ENST00000226207.6 5 HLA-B*45:01 11 None 0 0 6105.965 9722.242 6.000 6.850 0.009 0.000 0.000 0.000 0.988 NoExpr Pending -chr1-22660990-22660991-G-A 6.C1QB.ENST00000509305.6.missense.121A/T 1 C1QB A121T 1 ATQKITFSA ENST00000509305.6 1 HLA-B*45:01 6 None 1 1 6294.760 5577.395 4.772 5.010 0.000 0.000 0.000 0.000 0.984 NoExpr Pending -chrX-32389609-32389610-C-T 1045.DMD.ENST00000357033.9.missense.1470R/H 1 DMD R1470H 1 HLQESKMIL ENST00000357033.9 1 HLA-B*82:02 1 None 1 0 6599.580 7518.290 7.800 3.740 3.178 0.000 0.000 0.000 1.000 NoExpr Pending -chr1-196995755-196995756-A-G 75.CFHR5.ENST00000256785.5.missense.216N/S CFHR5 N216S 0 PPPQLSSGEV ENST00000256785.5 1 HLA-B*82:02 7 None 0 0 6682.850 6940.780 5.670 6.460 0.000 0.000 0.000 0.000 0.287 NoExpr Pending -chr9-138120681-138120682-G-A 563.CACNA1B.ENST00000371372.6.missense.2097G/D CACNA1B G2097D 0 LPPGEGPTD ENST00000371372.6 5 HLA-B*82:02 9 None 0 0 7518.077 6128.720 16.240 6.479 0.154 0.000 0.000 0.000 0.276 NoExpr Pending -chr1-22576425-22576426-C-A 4.EPHA8.ENST00000374644.8.missense.123N/K 5 2 EPHA8 N123K 2 TFKLYYLES ENST00000374644.8 1 HLA-A*29:02 3 None 7 1 7694.520 4817.840 10.900 6.450 0.001 0.000 0.000 0.000 0.272 NoExpr Pending -chr6-32223881-32223881-T-TAGCAGC 345.NOTCH4.ENST00000375023.3.inframe_ins.16L/LLL NOTCH4 L16LLL 0 LLLLLLLLLL ENST00000375023.3 1 HLA-A*29:02 10 None 0 0 8156.630 16576.905 12.958 29.680 1.260 0.000 0.000 0.000 0.187 NoExpr Pending -chr14-94382907-94382908-C-G 761.SERPINA1.ENST00000393087.9.missense.110E/D SERPINA1 E110D 0 LEGLNFNLTD ENST00000393087.9 1 HLA-B*45:01 10 None 0 0 8280.080 8248.135 10.800 10.250 4.892 0.000 0.000 0.000 0.180 NoExpr Pending -chr1-66834005-66834006-C-G 43.DNAI4.ENST00000371026.8.missense.626G/R 2 2 DNAI4 G626R 2 SKWVIRKRL ENST00000371026.8 1 HLA-C*06:02 8 None 4 0 8661.280 10706.560 3.755 16.000 7.011 0.000 0.000 0.000 0.605 NoExpr Pending -chr11-46876561-46876562-C-T 643.LRP4.ENST00000378623.6.missense.1147R/Q LRP4 R1147Q 0 DTGTNQIEV ENST00000378623.6 1 HLA-C*06:02 6 None 0 0 10325.625 8796.365 16.000 13.260 0.268 0.000 0.000 2.000 0.421 NoExpr Pending -chr21-44330789-44330813-AGGCAGCCGCGGCCCCTAGCGGCCC-A 1002.CFAP410.ENST00000397956.7.inframe_del.217-224GPLGAAAA/- CFAP410 GPLGAAAA217-224- 0 HRGRVSGSA ENST00000397956.7 1 HLA-C*06:02 7-8 None 0 0 10429.297 24458.045 11.886 34.500 6.570 0.000 0.000 18.000 0.376 NoExpr Pending -chr6-55351464-55351465-G-C 357.GFRAL.ENST00000340465.2.missense.195D/H GFRAL D195H 0 MLAFCDCAQSH ENST00000340465.2 1 HLA-A*29:02 11 5,7 0 0 10463.800 22065.710 11.700 43.500 0.013 0.000 0.000 0.000 0.511 NoExpr Pending -chr3-52517959-52517960-A-C 218.STAB1.ENST00000321725.10.missense.1573H/P 1 STAB1 H1573P 1 TAPTVGDGL ENST00000321725.10 1 HLA-B*82:02 3 None 1 0 10584.440 10844.771 10.232 8.800 0.090 0.000 0.000 0.000 1.000 NoExpr Pending -chr7-151181249-151181250-C-T 449.ASB10.ENST00000420175.3.missense.265D/N 1 1 ASB10 D265N 1 ITNAEATTA ENST00000420175.3 1 HLA-C*06:02 3 None 2 0 11080.185 16671.475 22.116 19.139 0.000 0.000 0.000 0.000 0.153 NoExpr Pending -chr1-16006133-16006134-G-T 1.SRARP.ENST00000329454.2.missense.100G/W 1 SRARP G100W 1 HLTRVTPMGW ENST00000329454.2 1 HLA-A*29:02 10 None 1 0 11111.069 25893.689 13.000 48.000 0.082 0.000 0.000 0.000 1.000 NoExpr Pending -chr7-39339738-39339739-G-C 386.POU6F2.ENST00000518318.7.missense.232Q/H POU6F2 Q232H 0 QPPPSTNHHP ENST00000518318.7 1 HLA-B*82:02 8 None 0 0 11112.540 12051.900 8.700 9.600 0.273 0.000 0.000 0.000 0.299 NoExpr Pending -chr11-1078020-1078022-CTA-C 623.MUC2.ENST00000675028.1.FS.178CTA/C MUC2 FS178 0 YNGLQSFRIPL ENST00000675028.1 NA HLA-B*82:02 7-11 None 0 0 11172.820 20529.260 8.700 23.000 0.001 0.000 0.000 0.000 0.918 NoExpr Pending -chr3-44242057-44242058-G-A 215.TOPAZ1.ENST00000309765.4.missense.2R/Q TOPAZ1 R2Q 0 QRPPPLGPT ENST00000309765.4 5 HLA-C*06:02 1 None 0 0 11791.070 8737.595 10.600 6.400 0.005 0.000 0.000 0.000 0.307 NoExpr Pending -chr1-207623001-207623002-C-G 88.CR1.ENST00000400960.7.missense.1979S/C 3 CR1 S1979C 3 TLCGTIFFI ENST00000400960.7 1 HLA-C*06:02 3 3 3 0 12588.990 6571.845 7.484 6.771 0.135 0.000 0.000 0.000 0.285 NoExpr Pending -chr8-132948805-132948806-C-G 515.TG.ENST00000220616.9.missense.1755P/R 2 TG P1755R 1 GLLSSRSVLL ENST00000220616.9 1 HLA-B*82:02 6 None 2 1 15290.890 15881.050 13.000 13.000 0.721 0.000 0.000 0.000 0.992 NoExpr Pending -chr11-58190707-58190708-A-T 645.OR9Q2.ENST00000641291.1.missense.73Y/F 1 OR9Q2 Y73F 1 FSSAIIPQMLA ENST00000641291.1 NA HLA-C*06:02 1 None 1 0 15845.410 16297.426 14.680 15.975 0.008 0.000 0.000 0.000 0.514 NoExpr Pending -chr22-37723212-37723213-GA-G 1013.TRIOBP.ENST00000644935.1.FS.219GA/G 1 TRIOBP FS219 1 GRSAGSTGQ ENST00000644935.1 NA HLA-C*06:02 6-9 None 1 0 16866.109 8900.005 16.579 5.600 35.473 0.000 0.000 5.000 0.289 NoExpr Pending -chr1-160876800-160876801-C-T 67.ITLN1.ENST00000326245.4.missense.269G/R ITLN1 G269R 0 GRGYFPEA ENST00000326245.4 1 HLA-B*45:01 2 None 0 0 19964.096 18750.188 18.000 21.850 0.000 0.000 0.000 0.000 0.250 NoExpr Pending -chr15-84036950-84036951-A-T 823.ADAMTSL3.ENST00000286744.10.missense.1645I/F 1 ADAMTSL3 I1645F 1 VQKKKPFSW ENST00000286744.10 1 HLA-B*82:02 7 None 1 1 24437.932 30726.730 38.000 38.000 2.043 0.000 0.000 0.000 0.366 NoExpr Pending -chr1-59858482-59858483-C-T 40.HOOK1.ENST00000371208.5.missense.433S/L 3 1 HOOK1 S433L 3 LQVQQDHLN ENST00000371208.5 1 HLA-A*29:02 1 None 4 0 26189.262 23718.146 39.000 39.900 0.230 0.000 0.000 0.000 0.394 NoExpr Pending -chr8-123220221-123220221-A-AGGGCTAC 491.C8orf76.ENST00000276704.6.FS.342A/AGGGCTAC C8orf76 FS342 0 GSVARSPD ENST00000276704.6 1 HLA-A*29:02 5-8 None 0 0 34694.453 28970.725 79.725 41.500 45.915 0.000 0.000 344.000 0.724 NoExpr Pending +chr4-5988666-5988667-T-A 261.C4orf50.ENST00000531445.3.missense.1127M/L 1 C4orf50 M1127L 1 REHLQGKAKL ENST00000531445.3 5 HLA-B*45:01 10 None 1 0 5147.705 7818.115 3.000 3.200 0.025 0.000 0.000 0.000 0.946 NoExpr Pending +chr2-160107761-160107762-T-A 157.ITGB6.ENST00000409872.1.missense.729I/F 5 ITGB6 I729F 5 FWKLLVSFH ENST00000409872.1 1 HLA-A*29:02 1 None 5 0 5265.275 8196.635 7.700 12.500 0.093 0.000 0.000 0.000 0.225 NoExpr Pending +chr7-47833094-47833095-G-A 387.PKD1L1.ENST00000289672.7.missense.2111T/I 2 PKD1L1 T2111I 2 HIQAPSSGL ENST00000289672.7 1 HLA-B*82:02 2 None 2 0 5670.880 6667.100 5.400 7.500 0.696 0.000 0.000 0.000 0.322 NoExpr Pending +chr8-138737576-138737577-C-A 518.COL22A1.ENST00000303045.11.missense.696G/W 2 COL22A1 G696W 2 LRWKKGDMG ENST00000303045.11 1 HLA-C*06:02 3 None 2 0 5695.865 12356.070 14.995 27.215 0.308 0.000 0.000 2.000 0.200 NoExpr Pending +chr11-70087776-70087777-C-T 665.ANO1.ENST00000355303.10.missense.45P/L 5 1 ANO1 P45L 4 LLNSLSVDL ENST00000355303.10 1 HLA-C*06:02 9 None 6 0 5793.860 20782.765 9.350 50.859 0.764 0.000 0.000 0.000 0.187 NoExpr Pending +chr3-58210851-58210852-G-C 222.DNASE1L3.ENST00000394549.7.missense.19L/V 2 DNASE1L3 L19V 3 LLLSIHSAVAM ENST00000394549.7 1 HLA-B*82:02 9 None 2 0 5837.470 5743.490 6.900 6.400 0.181 0.000 0.000 0.000 1.000 NoExpr Pending +chr17-10499040-10499041-G-A 882.MYH1.ENST00000226207.6.missense.1306S/L 1 MYH1 S1306L 1 DEKDTLVSQLL ENST00000226207.6 5 HLA-B*45:01 11 None 1 0 6105.965 9722.242 6.000 6.850 0.009 0.000 0.000 0.000 0.988 NoExpr Pending +chr1-22660990-22660991-G-A 6.C1QB.ENST00000509305.6.missense.121A/T 1 1 C1QB A121T 1 ATQKITFSA ENST00000509305.6 1 HLA-B*45:01 6 None 2 1 6294.760 5577.395 4.772 5.010 0.000 0.000 0.000 0.000 0.984 NoExpr Pending +chrX-32389609-32389610-C-T 1045.DMD.ENST00000357033.9.missense.1470R/H 2 DMD R1470H 2 HLQESKMIL ENST00000357033.9 1 HLA-B*82:02 1 None 2 0 6599.580 7518.290 7.800 3.740 3.178 0.000 0.000 0.000 1.000 NoExpr Pending +chr1-196995755-196995756-A-G 75.CFHR5.ENST00000256785.5.missense.216N/S 1 CFHR5 N216S 1 PPPQLSSGEV ENST00000256785.5 1 HLA-B*82:02 7 None 1 0 6682.850 6940.780 5.670 6.460 0.000 0.000 0.000 0.000 0.287 NoExpr Pending +chr9-138120681-138120682-G-A 563.CACNA1B.ENST00000371372.6.missense.2097G/D 1 CACNA1B G2097D 1 LPPGEGPTD ENST00000371372.6 5 HLA-B*82:02 9 None 1 0 7518.077 6128.720 16.240 6.479 0.154 0.000 0.000 0.000 0.276 NoExpr Pending +chr1-22576425-22576426-C-A 4.EPHA8.ENST00000374644.8.missense.123N/K 6 2 EPHA8 N123K 2 TFKLYYLES ENST00000374644.8 1 HLA-A*29:02 3 None 8 1 7694.520 4817.840 10.900 6.450 0.001 0.000 0.000 0.000 0.272 NoExpr Pending +chr6-32223881-32223881-T-TAGCAGC 345.NOTCH4.ENST00000375023.3.inframe_ins.16L/LLL 1 NOTCH4 L16LLL 1 LLLLLLLLLL ENST00000375023.3 1 HLA-A*29:02 10 None 1 0 8156.630 16576.905 12.958 29.680 1.260 0.000 0.000 0.000 0.187 NoExpr Pending +chr14-94382907-94382908-C-G 761.SERPINA1.ENST00000393087.9.missense.110E/D 1 SERPINA1 E110D 1 LEGLNFNLTD ENST00000393087.9 1 HLA-B*45:01 10 None 1 0 8280.080 8248.135 10.800 10.250 4.892 0.000 0.000 0.000 0.180 NoExpr Pending +chr1-66834005-66834006-C-G 43.DNAI4.ENST00000371026.8.missense.626G/R 2 3 DNAI4 G626R 2 SKWVIRKRL ENST00000371026.8 1 HLA-C*06:02 8 None 5 0 8661.280 10706.560 3.755 16.000 7.011 0.000 0.000 0.000 0.605 NoExpr Pending +chr11-46876561-46876562-C-T 643.LRP4.ENST00000378623.6.missense.1147R/Q 1 LRP4 R1147Q 1 DTGTNQIEV ENST00000378623.6 1 HLA-C*06:02 6 None 1 0 10325.625 8796.365 16.000 13.260 0.268 0.000 0.000 2.000 0.421 NoExpr Pending +chr21-44330789-44330813-AGGCAGCCGCGGCCCCTAGCGGCCC-A 1002.CFAP410.ENST00000397956.7.inframe_del.217-224GPLGAAAA/- 1 CFAP410 GPLGAAAA217-224- 1 HRGRVSGSA ENST00000397956.7 1 HLA-C*06:02 7-8 None 1 0 10429.297 24458.045 11.886 34.500 6.570 0.000 0.000 18.000 0.376 NoExpr Pending +chr6-55351464-55351465-G-C 357.GFRAL.ENST00000340465.2.missense.195D/H 1 GFRAL D195H 1 MLAFCDCAQSH ENST00000340465.2 1 HLA-A*29:02 11 5,7 1 0 10463.800 22065.710 11.700 43.500 0.013 0.000 0.000 0.000 0.511 NoExpr Pending +chr3-52517959-52517960-A-C 218.STAB1.ENST00000321725.10.missense.1573H/P 2 STAB1 H1573P 1 TAPTVGDGL ENST00000321725.10 1 HLA-B*82:02 3 None 2 0 10584.440 10844.771 10.232 8.800 0.090 0.000 0.000 0.000 1.000 NoExpr Pending +chr7-151181249-151181250-C-T 449.ASB10.ENST00000420175.3.missense.265D/N 1 2 ASB10 D265N 2 ITNAEATTA ENST00000420175.3 1 HLA-C*06:02 3 None 3 0 11080.185 16671.475 22.116 19.139 0.000 0.000 0.000 0.000 0.153 NoExpr Pending +chr1-16006133-16006134-G-T 1.SRARP.ENST00000329454.2.missense.100G/W 1 1 SRARP G100W 1 HLTRVTPMGW ENST00000329454.2 1 HLA-A*29:02 10 None 2 0 11111.069 25893.689 13.000 48.000 0.082 0.000 0.000 0.000 1.000 NoExpr Pending +chr7-39339738-39339739-G-C 386.POU6F2.ENST00000518318.7.missense.232Q/H 1 POU6F2 Q232H 1 QPPPSTNHHP ENST00000518318.7 1 HLA-B*82:02 8 None 1 0 11112.540 12051.900 8.700 9.600 0.273 0.000 0.000 0.000 0.299 NoExpr Pending +chr11-1078020-1078022-CTA-C 623.MUC2.ENST00000675028.1.FS.178CTA/C 1 MUC2 FS178 1 YNGLQSFRIPL ENST00000675028.1 NA HLA-B*82:02 7-11 None 1 0 11172.820 20529.260 8.700 23.000 0.001 0.000 0.000 0.000 0.918 NoExpr Pending +chr3-44242057-44242058-G-A 215.TOPAZ1.ENST00000309765.4.missense.2R/Q 1 TOPAZ1 R2Q 1 QRPPPLGPT ENST00000309765.4 5 HLA-C*06:02 1 None 1 0 11791.070 8737.595 10.600 6.400 0.005 0.000 0.000 0.000 0.307 NoExpr Pending +chr1-207623001-207623002-C-G 88.CR1.ENST00000400960.7.missense.1979S/C 3 1 CR1 S1979C 4 TLCGTIFFI ENST00000400960.7 1 HLA-C*06:02 3 3 3 0 12588.990 6571.845 7.484 6.771 0.135 0.000 0.000 0.000 0.285 NoExpr Pending +chr8-132948805-132948806-C-G 515.TG.ENST00000220616.9.missense.1755P/R 1 2 TG P1755R 2 GLLSSRSVLL ENST00000220616.9 1 HLA-B*82:02 6 None 3 1 15290.890 15881.050 13.000 13.000 0.721 0.000 0.000 0.000 0.992 NoExpr Pending +chr11-58190707-58190708-A-T 645.OR9Q2.ENST00000641291.1.missense.73Y/F 1 1 OR9Q2 Y73F 1 FSSAIIPQMLA ENST00000641291.1 NA HLA-C*06:02 1 None 2 0 15845.410 16297.426 14.680 15.975 0.008 0.000 0.000 0.000 0.514 NoExpr Pending +chr22-37723212-37723213-GA-G 1013.TRIOBP.ENST00000644935.1.FS.219GA/G 1 1 TRIOBP FS219 1 GRSAGSTGQ ENST00000644935.1 NA HLA-C*06:02 6-9 None 2 0 16866.109 8900.005 16.579 5.600 35.473 0.000 0.000 5.000 0.289 NoExpr Pending +chr1-160876800-160876801-C-T 67.ITLN1.ENST00000326245.4.missense.269G/R 1 ITLN1 G269R 1 GRGYFPEA ENST00000326245.4 1 HLA-B*45:01 2 None 1 0 19964.096 18750.188 18.000 21.850 0.000 0.000 0.000 0.000 0.250 NoExpr Pending +chr15-84036950-84036951-A-T 823.ADAMTSL3.ENST00000286744.10.missense.1645I/F 2 ADAMTSL3 I1645F 1 VQKKKPFSW ENST00000286744.10 1 HLA-B*82:02 7 None 2 1 24437.932 30726.730 38.000 38.000 2.043 0.000 0.000 0.000 0.366 NoExpr Pending +chr1-59858482-59858483-C-T 40.HOOK1.ENST00000371208.5.missense.433S/L 1 3 1 HOOK1 S433L 3 LQVQQDHLN ENST00000371208.5 1 HLA-A*29:02 1 None 5 0 26189.262 23718.146 39.000 39.900 0.230 0.000 0.000 0.000 0.394 NoExpr Pending +chr8-123220221-123220221-A-AGGGCTAC 491.C8orf76.ENST00000276704.6.FS.342A/AGGGCTAC 1 C8orf76 FS342 1 GSVARSPD ENST00000276704.6 1 HLA-A*29:02 5-8 None 1 0 34694.453 28970.725 79.725 41.500 45.915 0.000 0.000 344.000 0.724 NoExpr Pending diff --git a/tests/test_data/aggregate_all_epitopes/output.allele_specific_binding_thresholds.metrics.json b/tests/test_data/aggregate_all_epitopes/output.allele_specific_binding_thresholds.metrics.json index 7f617ce0..7aaed642 100644 --- a/tests/test_data/aggregate_all_epitopes/output.allele_specific_binding_thresholds.metrics.json +++ b/tests/test_data/aggregate_all_epitopes/output.allele_specific_binding_thresholds.metrics.json @@ -1960,11 +1960,194 @@ "best_hla_allele": "HLA-A*02:01" }, "22-18020271-18020272-G-A": { - "good_binders": {}, - "sets": [], - "transcript_counts": [], - "peptide_counts": [], - "set_expr": [], + "good_binders": { + "Transcript Set 1": { + "peptides": { + "SGGSHVWTH": { + "ic50s_MT": [ + "X", + 10761.9697265625 + ], + "percentiles_MT": [ + "X", + 24.0 + ], + "ic50s_WT": [ + "X", + 30462.795 + ], + "percentiles_WT": [ + "X", + 42.0 + ], + "hla_types": [ + "HLA-A*02:01", + "HLA-B*35:01" + ], + "mutation_position": "9", + "problematic_positions": "None", + "anchor_fails": "None", + "individual_ic50_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "NetMHC", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC" + ], + "MT": { + "HLA-B*35:01": [ + 12573.719007242402, + 6627.91, + 13543.0, + 16946.23, + 21020.53, + 8950.22, + 8195.59, + 8387.64 + ] + }, + "WT": { + "HLA-B*35:01": [ + 14851.530349766888, + 6509.93, + 29526.7, + 31398.89, + 35960.47, + 19088.05, + 42714.96, + 41175.61 + ] + } + }, + "individual_ic50_percentile_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "NetMHC", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC" + ], + "MT": { + "HLA-B*35:01": [ + 5.171750068664551, + "NA", + 9.699999809265137, + 24.0, + 12.0, + 27.0, + 26.0, + 26.0 + ] + }, + "WT": { + "HLA-B*35:01": [ + 6.084125000000004, + "NA", + 33.0, + 53.0, + 35.0, + 42.0, + 50.0, + 49.0 + ] + } + }, + "individual_el_calls": { + "algorithms": [], + "MT": { + "HLA-B*35:01": [] + }, + "WT": { + "HLA-B*35:01": [] + } + }, + "individual_el_percentile_calls": { + "algorithms": [], + "MT": { + "HLA-B*35:01": [] + }, + "WT": { + "HLA-B*35:01": [] + } + }, + "individual_percentile_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "NetMHC", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC" + ], + "MT": { + "HLA-B*35:01": [ + 5.171750068664551, + "NA", + 9.699999809265137, + 24.0, + 12.0, + 27.0, + 26.0, + 26.0 + ] + }, + "WT": { + "HLA-B*35:01": [ + 6.084125000000004, + "NA", + 33.0, + 53.0, + 35.0, + 42.0, + 50.0, + 49.0 + ] + } + }, + "wt_peptide": "SGGSHVWTR" + } + }, + "transcripts": [ + "ENST00000262608.8-CECR2-R/H-535" + ], + "transcript_expr": [ + "NA" + ], + "tsl": [ + "Not Supported" + ], + "biotype": [ + "protein_coding" + ], + "transcript_length": [ + 1443 + ], + "transcript_count": 1, + "peptide_count": 1, + "total_expr": 0 + } + }, + "sets": [ + "Transcript Set 1" + ], + "transcript_counts": [ + 1 + ], + "peptide_counts": [ + 1 + ], + "set_expr": [ + 0 + ], "DNA VAF": 0.071, "RNA VAF": "NA", "gene_expr": "NA", @@ -3125,57 +3308,31 @@ "best_hla_allele": "HLA-A*02:01" }, "22-20709231-20709232-G-C": { - "good_binders": {}, - "sets": [], - "transcript_counts": [], - "peptide_counts": [], - "set_expr": [], - "DNA VAF": 0.5, - "RNA VAF": "NA", - "gene_expr": "NA", - "best_peptide_mt": "IANQDAAQG", - "best_peptide_wt": "IANEDAAQG", - "best_hla_allele": "HLA-B*35:01" - }, - "22-22550449-22550450-C-G": { - "good_binders": {}, - "sets": [], - "transcript_counts": [], - "peptide_counts": [], - "set_expr": [], - "DNA VAF": 1.0, - "RNA VAF": "NA", - "gene_expr": "NA", - "best_peptide_mt": "ISCTGSSGSI", - "best_peptide_wt": "ISCTRSSGSI", - "best_hla_allele": "HLA-A*02:01" - }, - "22-22550509-22550510-T-G": { "good_binders": { "Transcript Set 1": { "peptides": { - "GSAPTTVIY": { + "IANQDAAQG": { "ic50s_MT": [ "X", - 567.0800170898438 + 5738.35009765625 ], "percentiles_MT": [ "X", - 3.4000000953674316 + 10.49899959564209 ], "ic50s_WT": [ "X", - 901.875 + 5541.375 ], "percentiles_WT": [ "X", - 4.1 + 7.674 ], "hla_types": [ "HLA-A*02:01", "HLA-B*35:01" ], - "mutation_position": "3", + "mutation_position": "4", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -3191,26 +3348,26 @@ ], "MT": { "HLA-B*35:01": [ - 107.29542054898047, - 4753.83, - 441.74, - 688.93, - 932.48, - 3000.81, - 445.23, - 358.62 + 21319.565474518397, + 5347.98, + 3830.88, + 9602.34, + 23286.3, + 6128.72, + 1407.93, + 952.01 ] }, "WT": { "HLA-B*35:01": [ - 129.3374595606424, - 4665.8, - 824.5, - 979.25, - 1008.87, - 3272.12, - 735.5, - 592.43 + 17720.666141659938, + 5213.62, + 2854.77, + 7326.61, + 19945.03, + 5869.13, + 989.87, + 670.87 ] } }, @@ -3227,26 +3384,26 @@ ], "MT": { "HLA-B*35:01": [ - 0.3167499899864197, + 10.498749732971191, "NA", - 0.6700000166893005, - 3.4000000953674316, - 0.7200000286102295, - 12.0, - 4.3, - 3.8 + 3.200000047683716, + 16.0, + 14.0, + 21.0, + 9.4, + 7.0 ] }, "WT": { "HLA-B*35:01": [ - 0.37775, + 7.674250000000002, "NA", - 1.2, - 4.1, - 0.76, - 12.0, - 6.0, - 5.2 + 2.6, + 13.0, + 9.5, + 20.0, + 7.2, + 5.7 ] } }, @@ -3281,41 +3438,433 @@ ], "MT": { "HLA-B*35:01": [ - 0.3167499899864197, + 10.498749732971191, "NA", - 0.6700000166893005, - 3.4000000953674316, - 0.7200000286102295, - 12.0, - 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"individual_el_calls": { "algorithms": [], "MT": { - "HLA-A*02:01": [] + "HLA-B*35:01": [] }, "WT": { - "HLA-A*02:01": [] + "HLA-B*35:01": [] } }, "individual_el_percentile_calls": { "algorithms": [], "MT": { - "HLA-A*02:01": [] + "HLA-B*35:01": [] }, "WT": { - "HLA-A*02:01": [] + "HLA-B*35:01": [] } }, "individual_percentile_calls": { @@ -3628,35 +4373,35 @@ "SMMPMBEC" ], "MT": { - "HLA-A*02:01": [ - 2.625, + "HLA-B*35:01": [ + 2.828000068664551, "NA", + 11.0, 26.0, - 19.0, - 15.0, - 4.699999809265137, 12.0, - 13.0 + 29.0, + 31.0, + 32.0 ] }, "WT": { - "HLA-A*02:01": [ - 1.8984999999999992, + "HLA-B*35:01": [ + 3.8806250000000015, "NA", - 19.0, - 17.0, - 15.0, - 5.1, - 7.6, - 7.7 + 14.0, + 50.0, + 18.0, + 41.0, + 32.0, + 46.0 ] } }, - "wt_peptide": "DLIGKPGGV" + "wt_peptide": "SPVKEEEKP" } }, "transcripts": [ - "ENST00000338754.4-TPST2-P/H-274" + "ENST00000310624.6-NEFH-P/T-830" ], "transcript_expr": [ "NA" @@ -3668,7 +4413,7 @@ "protein_coding" ], "transcript_length": [ - 377 + 1020 ], "transcript_count": 1, "peptide_count": 1, @@ -3687,19 +4432,6 @@ "set_expr": [ 0 ], - "DNA VAF": 0.179, - "RNA VAF": "NA", - "gene_expr": "NA", - "best_peptide_mt": "DLIGKHGGV", - "best_peptide_wt": "DLIGKPGGV", - "best_hla_allele": "HLA-A*02:01" - }, - "22-29886116-29886117-C-A": { - "good_binders": {}, - "sets": [], - "transcript_counts": [], - "peptide_counts": [], - "set_expr": [], "DNA VAF": 0.038, "RNA VAF": "NA", "gene_expr": "NA", @@ -4759,46 +5491,242 @@ "SMMPMBEC" ], "MT": { - "HLA-B*35:01": [ - 0.4976249933242798, + "HLA-B*35:01": [ + 0.4976249933242798, + "NA", + 2.4000000953674316, + 1.399999976158142, + 1.2999999523162842, + 1.2999999523162842, + 0.8, + 0.6 + ] + }, + "WT": { + "HLA-B*35:01": [ + 0.420625, + "NA", + 0.54, + 0.37, + 0.35, + 0.7, + 0.3, + 0.2 + ] + } + }, + "individual_el_calls": { + "algorithms": [], + "MT": { + "HLA-B*35:01": [] + }, + "WT": { + "HLA-B*35:01": [] + } + }, + "individual_el_percentile_calls": { + "algorithms": [], + "MT": { + 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+ 43.93412399291992, "NA", - 2.4000000953674316, - 1.399999976158142, - 1.2999999523162842, - 1.2999999523162842, - 0.8, - 0.6 + 33.0, + 48.0, + 19.0, + 52.0, + 33.0, + 29.0 ] }, "WT": { - "HLA-B*35:01": [ - 0.420625, + "HLA-A*02:01": [ + 43.934125, "NA", - 0.54, - 0.37, - 0.35, - 0.7, - 0.3, - 0.2 + 39.0, + 49.0, + 15.0, + 48.0, + 18.0, + 20.0 ] } }, - "wt_peptide": "MVCELAGNPF" + "wt_peptide": "FNMSSFKLKE" } }, "transcripts": [ - "ENST00000402918.2-ELFN2-P/L-186" + "ENST00000215886.4-LGALS2-E/Q-132" ], "transcript_expr": [ "NA" @@ -4853,10 +5781,10 @@ "protein_coding" ], "transcript_length": [ - 820 + 132 ], "transcript_count": 1, - "peptide_count": 7, + "peptide_count": 1, "total_expr": 0 } }, @@ -4867,24 +5795,11 @@ 1 ], "peptide_counts": [ - 7 + 1 ], "set_expr": [ 0 ], - "DNA VAF": 0.135, - "RNA VAF": "NA", - "gene_expr": "NA", - "best_peptide_mt": "NLFNCECDL", - "best_peptide_wt": "NPFNCECDL", - "best_hla_allele": "HLA-A*02:01" - }, - "22-37966274-37966275-C-G": { - "good_binders": {}, - "sets": [], - "transcript_counts": [], - "peptide_counts": [], - "set_expr": [], "DNA VAF": 0.496, "RNA VAF": "NA", "gene_expr": "NA", @@ -7660,15 +8575,211 @@ ] }, "WT": { - "HLA-B*35:01": [ - 31.13186469159585, - 4664.77, - 14.39, - 17.78, - 10.26, - 828.06, - 48.71, - 72.72 + "HLA-B*35:01": [ + 31.13186469159585, + 4664.77, + 14.39, + 17.78, + 10.26, + 828.06, + 48.71, + 72.72 + ] + } + }, + "individual_ic50_percentile_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "NetMHC", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC" + ], + "MT": { + "HLA-B*35:01": [ + 0.10249999910593033, + "NA", + 0.10000000149011612, + 0.8899999856948853, + 0.05999999865889549, + 3.299999952316284, + 1.3, + 1.7 + ] + }, + "WT": { + "HLA-B*35:01": [ + 0.02875, + "NA", + 0.04, + 0.43, + 0.03, + 2.4, + 0.8, + 1.1 + ] + } + }, + "individual_el_calls": { + "algorithms": [], + "MT": { + "HLA-B*35:01": [] + }, + "WT": { + "HLA-B*35:01": [] + } + }, + "individual_el_percentile_calls": { + "algorithms": [], + "MT": { + "HLA-B*35:01": [] + }, + "WT": { + "HLA-B*35:01": [] + } + }, + "individual_percentile_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "NetMHC", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC" + ], + "MT": { + "HLA-B*35:01": [ + 0.10249999910593033, + "NA", + 0.10000000149011612, + 0.8899999856948853, + 0.05999999865889549, + 3.299999952316284, + 1.3, + 1.7 + ] + }, + "WT": { + "HLA-B*35:01": [ + 0.02875, + "NA", + 0.04, + 0.43, + 0.03, + 2.4, + 0.8, + 1.1 + ] + } + }, + "wt_peptide": "YSYGLLHTY" + } + }, + "transcripts": [ + "ENST00000253255.5-PKDREJ-T/I-1875" + ], + "transcript_expr": [ + "NA" + ], + "tsl": [ + "Not Supported" + ], + "biotype": [ + "protein_coding" + ], + "transcript_length": [ + 2253 + ], + "transcript_count": 1, + "peptide_count": 6, + "total_expr": 0 + } + }, + "sets": [ + "Transcript Set 1" + ], + "transcript_counts": [ + 1 + ], + "peptide_counts": [ + 6 + ], + "set_expr": [ + 0 + ], + "DNA VAF": 0.233, + "RNA VAF": "NA", + "gene_expr": "NA", + "best_peptide_mt": "HIYGSGGYAL", + "best_peptide_wt": "HTYGSGGYAL", + "best_hla_allele": "HLA-A*02:01" + }, + "22-50555769-50555770-G-A": { + "good_binders": { + "Transcript Set 1": { + "peptides": { + "SAKTTVVVTT": { + "ic50s_MT": [ + 27206.9140625, + "X" + ], + "percentiles_MT": [ + 40.0, + "X" + ], + "ic50s_WT": [ + 17665.8, + "X" + ], + "percentiles_WT": [ + 26.0, + "X" + ], + "hla_types": [ + "HLA-A*02:01", + "HLA-B*35:01" + ], + "mutation_position": "10", + "problematic_positions": "None", + "anchor_fails": "None", + "individual_ic50_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "NetMHC", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC" + ], + "MT": { + "HLA-A*02:01": [ + 26688.54021438732, + 5622.88, + 21610.43, + 27725.29, + 21822.37, + 50000.0, + 38768.59, + 32123.29 + ] + }, + "WT": { + "HLA-A*02:01": [ + 21608.482651616418, + 5570.1, + 13904.4, + 18780.76, + 13905.31, + 26985.39, + 20159.51, + 16550.84 ] } }, @@ -7684,46 +8795,46 @@ "SMMPMBEC" ], "MT": { - "HLA-B*35:01": [ - 0.10249999910593033, + "HLA-A*02:01": [ + 25.389875411987305, "NA", - 0.10000000149011612, - 0.8899999856948853, - 0.05999999865889549, - 3.299999952316284, - 1.3, - 1.7 + 37.0, + 40.0, + 27.0, + 54.0, + 52.0, + 49.0 ] }, "WT": { - "HLA-B*35:01": [ - 0.02875, + "HLA-A*02:01": [ + 13.856625000000005, "NA", - 0.04, - 0.43, - 0.03, - 2.4, - 0.8, - 1.1 + 25.0, + 26.0, + 18.0, + 44.0, + 41.0, + 38.0 ] } }, "individual_el_calls": { "algorithms": [], "MT": { - "HLA-B*35:01": [] + "HLA-A*02:01": [] }, "WT": { - "HLA-B*35:01": [] + "HLA-A*02:01": [] } }, "individual_el_percentile_calls": { "algorithms": [], "MT": { - "HLA-B*35:01": [] + "HLA-A*02:01": [] }, "WT": { - "HLA-B*35:01": [] + "HLA-A*02:01": [] } }, "individual_percentile_calls": { @@ -7738,35 +8849,35 @@ "SMMPMBEC" ], "MT": { - "HLA-B*35:01": [ - 0.10249999910593033, + "HLA-A*02:01": [ + 25.389875411987305, "NA", - 0.10000000149011612, - 0.8899999856948853, - 0.05999999865889549, - 3.299999952316284, - 1.3, - 1.7 + 37.0, + 40.0, + 27.0, + 54.0, + 52.0, + 49.0 ] }, "WT": { - "HLA-B*35:01": [ - 0.02875, + "HLA-A*02:01": [ + 13.856625000000005, "NA", - 0.04, - 0.43, - 0.03, - 2.4, - 0.8, - 1.1 + 25.0, + 26.0, + 18.0, + 44.0, + 41.0, + 38.0 ] } }, - "wt_peptide": "YSYGLLHTY" + "wt_peptide": "SAKTTVVVTA" } }, "transcripts": [ - "ENST00000253255.5-PKDREJ-T/I-1875" + "ENST00000262794.5-MOV10L1-A/T-482" ], "transcript_expr": [ "NA" @@ -7778,10 +8889,10 @@ "protein_coding" ], "transcript_length": [ - 2253 + 1211 ], "transcript_count": 1, - "peptide_count": 6, + "peptide_count": 1, "total_expr": 0 } }, @@ -7792,24 +8903,11 @@ 1 ], "peptide_counts": [ - 6 + 1 ], "set_expr": [ 0 ], - "DNA VAF": 0.233, - "RNA VAF": "NA", - "gene_expr": "NA", - "best_peptide_mt": "HIYGSGGYAL", - "best_peptide_wt": "HTYGSGGYAL", - "best_hla_allele": "HLA-A*02:01" - }, - "22-50555769-50555770-G-A": { - "good_binders": {}, - "sets": [], - "transcript_counts": [], - "peptide_counts": [], - "set_expr": [], "DNA VAF": 0.042, "RNA VAF": "NA", "gene_expr": "NA", @@ -9858,11 +10956,194 @@ "best_hla_allele": "HLA-A*02:01" }, "22-50869713-50869714-C-A": { - "good_binders": {}, - "sets": [], - "transcript_counts": [], - "peptide_counts": [], - "set_expr": [], + "good_binders": { + "Transcript Set 1": { + "peptides": { + "YESRVEPPH": { + "ic50s_MT": [ + "X", + 6159.2998046875 + ], + "percentiles_MT": [ + "X", + 14.0 + ], + "ic50s_WT": [ + "X", + 18030.513 + ], + "percentiles_WT": [ + "X", + 33.0 + ], + "hla_types": [ + "HLA-A*02:01", + "HLA-B*35:01" + ], + "mutation_position": "1", + "problematic_positions": "None", + "anchor_fails": "None", + "individual_ic50_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "NetMHC", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC" + ], + "MT": { + "HLA-B*35:01": [ + 17558.295646686685, + 5987.68, + 5243.65, + 10699.58, + 13202.43, + 6330.92, + 4135.99, + 2538.87 + ] + }, + "WT": { + "HLA-B*35:01": [ + 18379.255660686867, + 6063.92, + 17681.77, + 23318.07, + 25776.49, + 12382.34, + 24466.96, + 15799.38 + ] + } + }, + "individual_ic50_percentile_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "NetMHC", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC" + ], + "MT": { + "HLA-B*35:01": [ + 7.555500030517578, + "NA", + 4.0, + 17.0, + 5.699999809265137, + 21.0, + 18.0, + 14.0 + ] + }, + "WT": { + "HLA-B*35:01": [ + 8.065000000000005, + "NA", + 15.0, + 33.0, + 16.0, + 33.0, + 40.0, + 34.0 + ] + } + }, + "individual_el_calls": { + "algorithms": [], + "MT": { + "HLA-B*35:01": [] + }, + "WT": { + "HLA-B*35:01": [] + } + }, + "individual_el_percentile_calls": { + "algorithms": [], + "MT": { + "HLA-B*35:01": [] + }, + "WT": { + "HLA-B*35:01": [] + } + }, + "individual_percentile_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "NetMHC", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC" + ], + "MT": { + "HLA-B*35:01": [ + 7.555500030517578, + "NA", + 4.0, + 17.0, + 5.699999809265137, + 21.0, + 18.0, + 14.0 + ] + }, + "WT": { + "HLA-B*35:01": [ + 8.065000000000005, + "NA", + 15.0, + 33.0, + 16.0, + 33.0, + 40.0, + 34.0 + ] + } + }, + "wt_peptide": "SESRVEPPH" + } + }, + "transcripts": [ + "ENST00000395741.3-PPP6R2-S/Y-414" + ], + "transcript_expr": [ + "NA" + ], + "tsl": [ + "Not Supported" + ], + "biotype": [ + "protein_coding" + ], + "transcript_length": [ + 933 + ], + "transcript_count": 1, + "peptide_count": 1, + "total_expr": 0 + } + }, + "sets": [ + "Transcript Set 1" + ], + "transcript_counts": [ + 1 + ], + "peptide_counts": [ + 1 + ], + "set_expr": [ + 0 + ], "DNA VAF": 0.043, "RNA VAF": "NA", "gene_expr": "NA", diff --git a/tests/test_data/aggregate_all_epitopes/output.allele_specific_binding_thresholds.tsv b/tests/test_data/aggregate_all_epitopes/output.allele_specific_binding_thresholds.tsv index 064abf6c..9d24132d 100644 --- a/tests/test_data/aggregate_all_epitopes/output.allele_specific_binding_thresholds.tsv +++ b/tests/test_data/aggregate_all_epitopes/output.allele_specific_binding_thresholds.tsv @@ -15,10 +15,10 @@ ID Index A*02:01 B*35:01 Gene AA Change Num Passing Transcripts Best Peptide Bes 22-41920894-41920895-G-C 19.ACO2.ENST00000216254.4.missense.510E/Q 1 ACO2 E510Q 1 NPQTDYLTG ENST00000216254.4 Not Supported HLA-B*35:01 3 None 1 0 3121.315 3595.485 6.600 6.500 NA NA NA NA 0.250 Poor Pending 22-41895790-41895791-C-A 18.ACO2.ENST00000216254.4.missense.33A/E 1 ACO2 A33E 1 EMSHFEPNEY ENST00000216254.4 Not Supported HLA-B*35:01 1 None 1 0 3903.700 4456.030 2.600 3.700 NA NA NA NA 0.044 Poor Pending 22-26936775-26936776-G-T 11.TPST2.ENST00000338754.4.missense.274P/H 1 TPST2 P274H 1 DLIGKHGGV ENST00000338754.4 Not Supported HLA-A*02:01 6 None 1 0 4145.685 3402.989 13.000 7.700 NA NA NA NA 0.179 Poor Pending -22-20709231-20709232-G-C 8.FAM230A.ENST00000434783.3.missense.322E/Q FAM230A E322Q 0 IANQDAAQG ENST00000434783.3 Not Supported HLA-B*35:01 4 None 0 0 5738.350 5541.375 10.499 7.674 NA NA NA NA 0.500 Poor Pending -22-50869713-50869714-C-A 24.PPP6R2.ENST00000395741.3.missense.414S/Y PPP6R2 S414Y 0 YESRVEPPH ENST00000395741.3 Not Supported HLA-B*35:01 1 None 0 0 6159.300 18030.513 14.000 33.000 NA NA NA NA 0.043 Poor Pending -22-22550449-22550450-C-G 9.IGLV6-57.ENST00000390285.3.missense.43R/G IGLV6-57 R43G 0 ISCTGSSGSI ENST00000390285.3 Not Supported HLA-A*02:01 5 None 0 0 9672.631 20663.370 30.000 34.000 NA NA NA NA 1.000 Poor Pending -22-18020271-18020272-G-A 5.CECR2.ENST00000262608.8.missense.535R/H CECR2 R535H 0 SGGSHVWTH ENST00000262608.8 Not Supported HLA-B*35:01 9 None 0 0 10761.970 30462.795 24.000 42.000 NA NA NA NA 0.071 Poor Pending -22-29886116-29886117-C-A 12.NEFH.ENST00000310624.6.missense.830P/T NEFH P830T 0 SPVKEEEKT ENST00000310624.6 Not Supported HLA-B*35:01 9 None 0 0 12628.540 17588.290 26.000 32.000 NA NA NA NA 0.038 Poor Pending -22-37966274-37966275-C-G 14.LGALS2.ENST00000215886.4.missense.132E/Q LGALS2 E132Q 0 FNMSSFKLKQ ENST00000215886.4 Not Supported HLA-A*02:01 10 None 0 0 16963.785 16973.740 33.000 39.000 NA NA NA NA 0.496 Poor Pending -22-50555769-50555770-G-A 21.MOV10L1.ENST00000262794.5.missense.482A/T MOV10L1 A482T 0 SAKTTVVVTT ENST00000262794.5 Not Supported HLA-A*02:01 10 None 0 0 27206.914 17665.800 40.000 26.000 NA NA NA NA 0.042 Poor Pending +22-20709231-20709232-G-C 8.FAM230A.ENST00000434783.3.missense.322E/Q 1 FAM230A E322Q 1 IANQDAAQG ENST00000434783.3 Not Supported HLA-B*35:01 4 None 1 0 5738.350 5541.375 10.499 7.674 NA NA NA NA 0.500 Poor Pending +22-50869713-50869714-C-A 24.PPP6R2.ENST00000395741.3.missense.414S/Y 1 PPP6R2 S414Y 1 YESRVEPPH ENST00000395741.3 Not Supported HLA-B*35:01 1 None 1 0 6159.300 18030.513 14.000 33.000 NA NA NA NA 0.043 Poor Pending +22-22550449-22550450-C-G 9.IGLV6-57.ENST00000390285.3.missense.43R/G 1 IGLV6-57 R43G 1 ISCTGSSGSI ENST00000390285.3 Not Supported HLA-A*02:01 5 None 1 0 9672.631 20663.370 30.000 34.000 NA NA NA NA 1.000 Poor Pending +22-18020271-18020272-G-A 5.CECR2.ENST00000262608.8.missense.535R/H 1 CECR2 R535H 1 SGGSHVWTH ENST00000262608.8 Not Supported HLA-B*35:01 9 None 1 0 10761.970 30462.795 24.000 42.000 NA NA NA NA 0.071 Poor Pending +22-29886116-29886117-C-A 12.NEFH.ENST00000310624.6.missense.830P/T 1 NEFH P830T 1 SPVKEEEKT ENST00000310624.6 Not Supported HLA-B*35:01 9 None 1 0 12628.540 17588.290 26.000 32.000 NA NA NA NA 0.038 Poor Pending +22-37966274-37966275-C-G 14.LGALS2.ENST00000215886.4.missense.132E/Q 1 LGALS2 E132Q 1 FNMSSFKLKQ ENST00000215886.4 Not Supported HLA-A*02:01 10 None 1 0 16963.785 16973.740 33.000 39.000 NA NA NA NA 0.496 Poor Pending +22-50555769-50555770-G-A 21.MOV10L1.ENST00000262794.5.missense.482A/T 1 MOV10L1 A482T 1 SAKTTVVVTT ENST00000262794.5 Not Supported HLA-A*02:01 10 None 1 0 27206.914 17665.800 40.000 26.000 NA NA NA NA 0.042 Poor Pending diff --git a/tests/test_data/aggregate_all_epitopes/output.lowest_top_score_metric.metrics.json b/tests/test_data/aggregate_all_epitopes/output.lowest_top_score_metric.metrics.json index d44973ea..c5e5fc40 100644 --- a/tests/test_data/aggregate_all_epitopes/output.lowest_top_score_metric.metrics.json +++ b/tests/test_data/aggregate_all_epitopes/output.lowest_top_score_metric.metrics.json @@ -11204,11 +11204,194 @@ "best_hla_allele": "HLA-A*02:01" }, "22-37966274-37966275-C-G": { - "good_binders": {}, - "sets": [], - "transcript_counts": [], - "peptide_counts": [], - "set_expr": [], + "good_binders": { + "Transcript Set 1": { + "peptides": { + "NMSSFKLKQ": { + "ic50s_MT": [ + 5560.06005859375, + "X" + ], + "percentiles_MT": [ + 16.06100082397461, + "X" + ], + "ic50s_WT": [ + 4288.48, + "X" + ], + "percentiles_WT": [ + 16.061, + "X" + ], + "hla_types": [ + "HLA-A*02:01", + "HLA-B*35:01" + ], + "mutation_position": "9", + "problematic_positions": "None", + "anchor_fails": "None", + "individual_ic50_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "NetMHC", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC" + ], + "MT": { + "HLA-A*02:01": [ + 23159.70167587253, + 5796.07, + 26623.75, + 23957.42, + 24620.69, + 5560.06, + 53840.61, + 51573.9 + ] + }, + "WT": { + "HLA-A*02:01": [ + 23171.763315324777, + 5822.96, + 29451.39, + 28485.48, + 21363.54, + 4288.48, + 91224.19, + 72016.17 + ] + } + }, + "individual_ic50_percentile_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "NetMHC", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC" + ], + "MT": { + "HLA-A*02:01": [ + 16.061124801635742, + "NA", + 47.0, + 33.0, + 32.0, + 34.0, + 41.0, + 40.0 + ] + }, + "WT": { + "HLA-A*02:01": [ + 16.061125000000004, + "NA", + 54.0, + 44.0, + 27.0, + 30.0, + 47.0, + 44.0 + ] + } + }, + "individual_el_calls": { + "algorithms": [], + "MT": { + "HLA-A*02:01": [] + }, + "WT": { + "HLA-A*02:01": [] + } + }, + "individual_el_percentile_calls": { + "algorithms": [], + "MT": { + "HLA-A*02:01": [] + }, + "WT": { + "HLA-A*02:01": [] + } + }, + "individual_percentile_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "NetMHC", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC" + ], + "MT": { + "HLA-A*02:01": [ + 16.061124801635742, + "NA", + 47.0, + 33.0, + 32.0, + 34.0, + 41.0, + 40.0 + ] + }, + "WT": { + "HLA-A*02:01": [ + 16.061125000000004, + "NA", + 54.0, + 44.0, + 27.0, + 30.0, + 47.0, + 44.0 + ] + } + }, + "wt_peptide": "NMSSFKLKE" + } + }, + "transcripts": [ + "ENST00000215886.4-LGALS2-E/Q-132" + ], + "transcript_expr": [ + "NA" + ], + "tsl": [ + "Not Supported" + ], + "biotype": [ + "protein_coding" + ], + "transcript_length": [ + 132 + ], + "transcript_count": 1, + "peptide_count": 1, + "total_expr": 0 + } + }, + "sets": [ + "Transcript Set 1" + ], + "transcript_counts": [ + 1 + ], + "peptide_counts": [ + 1 + ], + "set_expr": [ + 0 + ], "DNA VAF": 0.496, "RNA VAF": "NA", "gene_expr": "NA", @@ -18857,11 +19040,194 @@ "best_hla_allele": "HLA-A*02:01" }, "22-50555769-50555770-G-A": { - "good_binders": {}, - "sets": [], - "transcript_counts": [], - "peptide_counts": [], - "set_expr": [], + "good_binders": { + "Transcript Set 1": { + "peptides": { + "TTVVVTTQKR": { + "ic50s_MT": [ + 5574.97021484375, + "X" + ], + "percentiles_MT": [ + 19.725000381469727, + "X" + ], + "ic50s_WT": [ + 5581.59, + "X" + ], + "percentiles_WT": [ + 18.527, + "X" + ], + "hla_types": [ + "HLA-A*02:01", + "HLA-B*35:01" + ], + "mutation_position": "7", + "problematic_positions": "None", + "anchor_fails": "None", + "individual_ic50_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "NetMHC", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC" + ], + "MT": { + "HLA-A*02:01": [ + 24841.35422970731, + 5574.97, + 35483.9, + 37132.0, + 37574.55, + 50000.0, + 144371.01, + 176937.55 + ] + }, + "WT": { + "HLA-A*02:01": [ + 24463.09556790621, + 5581.59, + 33212.18, + 37333.42, + 34773.18, + 50000.0, + 184280.76, + 206928.35 + ] + } + }, + "individual_ic50_percentile_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "NetMHC", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC" + ], + "MT": { + "HLA-A*02:01": [ + 19.72512435913086, + "NA", + 72.0, + 73.0, + 64.0, + 54.0, + 73.0, + 76.0 + ] + }, + "WT": { + "HLA-A*02:01": [ + 18.52725, + "NA", + 65.0, + 74.0, + 54.0, + 54.0, + 77.0, + 78.0 + ] + } + }, + "individual_el_calls": { + "algorithms": [], + "MT": { + "HLA-A*02:01": [] + }, + "WT": { + "HLA-A*02:01": [] + } + }, + "individual_el_percentile_calls": { + "algorithms": [], + "MT": { + "HLA-A*02:01": [] + }, + "WT": { + "HLA-A*02:01": [] + } + }, + "individual_percentile_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "NetMHC", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC" + ], + "MT": { + "HLA-A*02:01": [ + 19.72512435913086, + "NA", + 72.0, + 73.0, + 64.0, + 54.0, + 73.0, + 76.0 + ] + }, + "WT": { + "HLA-A*02:01": [ + 18.52725, + "NA", + 65.0, + 74.0, + 54.0, + 54.0, + 77.0, + 78.0 + ] + } + }, + "wt_peptide": "TTVVVTAQKR" + } + }, + "transcripts": [ + "ENST00000262794.5-MOV10L1-A/T-482" + ], + "transcript_expr": [ + "NA" + ], + "tsl": [ + "Not Supported" + ], + "biotype": [ + "protein_coding" + ], + "transcript_length": [ + 1211 + ], + "transcript_count": 1, + "peptide_count": 1, + "total_expr": 0 + } + }, + "sets": [ + "Transcript Set 1" + ], + "transcript_counts": [ + 1 + ], + "peptide_counts": [ + 1 + ], + "set_expr": [ + 0 + ], "DNA VAF": 0.042, "RNA VAF": "NA", "gene_expr": "NA", diff --git a/tests/test_data/aggregate_all_epitopes/output.lowest_top_score_metric.tsv b/tests/test_data/aggregate_all_epitopes/output.lowest_top_score_metric.tsv index e5d73420..dfe05000 100644 --- a/tests/test_data/aggregate_all_epitopes/output.lowest_top_score_metric.tsv +++ b/tests/test_data/aggregate_all_epitopes/output.lowest_top_score_metric.tsv @@ -20,5 +20,5 @@ ID Index A*02:01 B*35:01 Gene AA Change Num Passing Transcripts Best Peptide Bes 22-29886116-29886117-C-A 12.NEFH.ENST00000310624.6.missense.830P/T 1 NEFH P830T 1 KEEEKTQEV ENST00000310624.6 Not Supported HLA-A*02:01 6 None 1 0 2406.560 2521.061 2.474 2.533 NA NA NA NA 0.038 Poor Pending 22-50869713-50869714-C-A 24.PPP6R2.ENST00000395741.3.missense.414S/Y 1 2 PPP6R2 S414Y 1 YESRVEPPH ENST00000395741.3 Not Supported HLA-B*35:01 1 None 3 0 2538.870 15799.380 4.000 15.000 NA NA NA NA 0.043 Poor Pending 22-18020271-18020272-G-A 5.CECR2.ENST00000262608.8.missense.535R/H 1 2 CECR2 R535H 1 HVWTHSRDP ENST00000262608.8 Not Supported HLA-B*35:01 5 None 2 0 4098.080 11132.170 8.500 19.000 NA NA NA NA 0.071 Poor Pending -22-37966274-37966275-C-G 14.LGALS2.ENST00000215886.4.missense.132E/Q LGALS2 E132Q 0 NMSSFKLKQ ENST00000215886.4 Not Supported HLA-A*02:01 9 None 0 0 5560.060 4288.480 16.061 16.061 NA NA NA NA 0.496 Poor Pending -22-50555769-50555770-G-A 21.MOV10L1.ENST00000262794.5.missense.482A/T MOV10L1 A482T 0 TTVVVTTQKR ENST00000262794.5 Not Supported HLA-A*02:01 7 None 0 0 5574.970 5581.590 19.725 18.527 NA NA NA NA 0.042 Poor Pending +22-37966274-37966275-C-G 14.LGALS2.ENST00000215886.4.missense.132E/Q 1 LGALS2 E132Q 1 NMSSFKLKQ ENST00000215886.4 Not Supported HLA-A*02:01 9 None 1 0 5560.060 4288.480 16.061 16.061 NA NA NA NA 0.496 Poor Pending +22-50555769-50555770-G-A 21.MOV10L1.ENST00000262794.5.missense.482A/T 1 MOV10L1 A482T 1 TTVVVTTQKR ENST00000262794.5 Not Supported HLA-A*02:01 7 None 1 0 5574.970 5581.590 19.725 18.527 NA NA NA NA 0.042 Poor Pending diff --git a/tests/test_data/aggregate_all_epitopes/output.metrics.json b/tests/test_data/aggregate_all_epitopes/output.metrics.json index 5e02006a..1600d58c 100644 --- a/tests/test_data/aggregate_all_epitopes/output.metrics.json +++ b/tests/test_data/aggregate_all_epitopes/output.metrics.json @@ -1960,11 +1960,194 @@ "best_hla_allele": "HLA-A*02:01" }, "22-18020271-18020272-G-A": { - "good_binders": {}, - "sets": [], - "transcript_counts": [], - "peptide_counts": [], - "set_expr": [], + "good_binders": { + "Transcript Set 1": { + "peptides": { + "SGGSHVWTH": { + "ic50s_MT": [ + "X", + 10761.9697265625 + ], + "percentiles_MT": [ + "X", + 24.0 + ], + "ic50s_WT": [ + "X", + 30462.795 + ], + "percentiles_WT": [ + "X", + 42.0 + ], + "hla_types": [ + "HLA-A*02:01", + "HLA-B*35:01" + ], + "mutation_position": "9", + "problematic_positions": "None", + "anchor_fails": "None", + "individual_ic50_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "NetMHC", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC" + ], + "MT": { + "HLA-B*35:01": [ + 12573.719007242402, + 6627.91, + 13543.0, + 16946.23, + 21020.53, + 8950.22, + 8195.59, + 8387.64 + ] + }, + "WT": { + "HLA-B*35:01": [ + 14851.530349766888, + 6509.93, + 29526.7, + 31398.89, + 35960.47, + 19088.05, + 42714.96, + 41175.61 + ] + } + }, + "individual_ic50_percentile_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "NetMHC", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC" + ], + "MT": { + "HLA-B*35:01": [ + 5.171750068664551, + "NA", + 9.699999809265137, + 24.0, + 12.0, + 27.0, + 26.0, + 26.0 + ] + }, + "WT": { + "HLA-B*35:01": [ + 6.084125000000004, + "NA", + 33.0, + 53.0, + 35.0, + 42.0, + 50.0, + 49.0 + ] + } + }, + "individual_el_calls": { + "algorithms": [], + "MT": { + "HLA-B*35:01": [] + }, + "WT": { + "HLA-B*35:01": [] + } + }, + "individual_el_percentile_calls": { + "algorithms": [], + "MT": { + "HLA-B*35:01": [] + }, + "WT": { + "HLA-B*35:01": [] + } + }, + "individual_percentile_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "NetMHC", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC" + ], + "MT": { + "HLA-B*35:01": [ + 5.171750068664551, + "NA", + 9.699999809265137, + 24.0, + 12.0, + 27.0, + 26.0, + 26.0 + ] + }, + "WT": { + "HLA-B*35:01": [ + 6.084125000000004, + "NA", + 33.0, + 53.0, + 35.0, + 42.0, + 50.0, + 49.0 + ] + } + }, + "wt_peptide": "SGGSHVWTR" + } + }, + "transcripts": [ + "ENST00000262608.8-CECR2-R/H-535" + ], + "transcript_expr": [ + "NA" + ], + "tsl": [ + "Not Supported" + ], + "biotype": [ + "protein_coding" + ], + "transcript_length": [ + 1443 + ], + "transcript_count": 1, + "peptide_count": 1, + "total_expr": 0 + } + }, + "sets": [ + "Transcript Set 1" + ], + "transcript_counts": [ + 1 + ], + "peptide_counts": [ + 1 + ], + "set_expr": [ + 0 + ], "DNA VAF": 0.071, "RNA VAF": "NA", "gene_expr": "NA", @@ -3125,57 +3308,31 @@ "best_hla_allele": "HLA-A*02:01" }, "22-20709231-20709232-G-C": { - "good_binders": {}, - "sets": [], - "transcript_counts": [], - "peptide_counts": [], - "set_expr": [], - "DNA VAF": 0.5, - "RNA VAF": "NA", - "gene_expr": "NA", - "best_peptide_mt": "IANQDAAQG", - "best_peptide_wt": "IANEDAAQG", - "best_hla_allele": "HLA-B*35:01" - }, - "22-22550449-22550450-C-G": { - "good_binders": {}, - "sets": [], - "transcript_counts": [], - "peptide_counts": [], - "set_expr": [], - "DNA VAF": 1.0, - "RNA VAF": "NA", - "gene_expr": "NA", - "best_peptide_mt": "ISCTGSSGSI", - "best_peptide_wt": "ISCTRSSGSI", - "best_hla_allele": "HLA-A*02:01" - }, - "22-22550509-22550510-T-G": { "good_binders": { "Transcript Set 1": { "peptides": { - "GSAPTTVIY": { + "IANQDAAQG": { "ic50s_MT": [ "X", - 567.0800170898438 + 5738.35009765625 ], "percentiles_MT": [ "X", - 3.4000000953674316 + 10.49899959564209 ], "ic50s_WT": [ "X", - 901.875 + 5541.375 ], "percentiles_WT": [ "X", - 4.1 + 7.674 ], "hla_types": [ "HLA-A*02:01", "HLA-B*35:01" ], - "mutation_position": "3", + "mutation_position": "4", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -3191,26 +3348,26 @@ ], "MT": { "HLA-B*35:01": [ - 107.29542054898047, - 4753.83, - 441.74, - 688.93, - 932.48, - 3000.81, - 445.23, - 358.62 + 21319.565474518397, + 5347.98, + 3830.88, + 9602.34, + 23286.3, + 6128.72, + 1407.93, + 952.01 ] }, "WT": { "HLA-B*35:01": [ - 129.3374595606424, - 4665.8, - 824.5, - 979.25, - 1008.87, - 3272.12, - 735.5, - 592.43 + 17720.666141659938, + 5213.62, + 2854.77, + 7326.61, + 19945.03, + 5869.13, + 989.87, + 670.87 ] } }, @@ -3227,26 +3384,26 @@ ], "MT": { "HLA-B*35:01": [ - 0.3167499899864197, + 10.498749732971191, "NA", - 0.6700000166893005, - 3.4000000953674316, - 0.7200000286102295, - 12.0, - 4.3, - 3.8 + 3.200000047683716, + 16.0, + 14.0, + 21.0, + 9.4, + 7.0 ] }, "WT": { "HLA-B*35:01": [ - 0.37775, + 7.674250000000002, "NA", - 1.2, - 4.1, - 0.76, - 12.0, - 6.0, - 5.2 + 2.6, + 13.0, + 9.5, + 20.0, + 7.2, + 5.7 ] } }, @@ -3281,41 +3438,433 @@ ], "MT": { "HLA-B*35:01": [ - 0.3167499899864197, + 10.498749732971191, "NA", - 0.6700000166893005, - 3.4000000953674316, - 0.7200000286102295, - 12.0, - 4.3, - 3.8 + 3.200000047683716, + 16.0, + 14.0, + 21.0, + 9.4, + 7.0 ] }, "WT": { "HLA-B*35:01": [ - 0.37775, + 7.674250000000002, "NA", - 1.2, - 4.1, - 0.76, - 12.0, - 6.0, - 5.2 + 2.6, + 13.0, + 9.5, + 20.0, + 7.2, + 5.7 ] } }, - "wt_peptide": "GSSPTTVIY" - }, - "RPGSAPTTV": { - "ic50s_MT": [ - "X", - 4313.1201171875 - ], - "percentiles_MT": [ - "X", - 6.199999809265137 - ], - "ic50s_WT": [ + "wt_peptide": "IANEDAAQG" + } + }, + "transcripts": [ + "ENST00000434783.3-FAM230A-E/Q-322" + ], + "transcript_expr": [ + "NA" + ], + "tsl": [ + "Not Supported" + ], + "biotype": [ + "protein_coding" + ], + "transcript_length": [ + 905 + ], + "transcript_count": 1, + "peptide_count": 1, + "total_expr": 0 + } + }, + "sets": [ + "Transcript Set 1" + ], + "transcript_counts": [ + 1 + ], + "peptide_counts": [ + 1 + ], + "set_expr": [ + 0 + ], + "DNA VAF": 0.5, + "RNA VAF": "NA", + "gene_expr": "NA", + "best_peptide_mt": "IANQDAAQG", + "best_peptide_wt": "IANEDAAQG", + "best_hla_allele": "HLA-B*35:01" + }, + "22-22550449-22550450-C-G": { + "good_binders": { + "Transcript Set 1": { + "peptides": { + "ISCTGSSGSI": { + "ic50s_MT": [ + 9672.630859375, + "X" + ], + "percentiles_MT": [ + 30.0, + "X" + ], + "ic50s_WT": [ + 20663.37, + "X" + ], + "percentiles_WT": [ + 34.0, + "X" + ], + "hla_types": [ + "HLA-A*02:01", + "HLA-B*35:01" + ], + "mutation_position": "5", + "problematic_positions": "None", + "anchor_fails": "None", + "individual_ic50_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "NetMHC", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC" + ], + "MT": { + "HLA-A*02:01": [ + 9894.212296142823, + 5592.52, + 29287.42, + 21852.38, + 19194.09, + 6399.79, + 9451.05, + 9393.34 + ] + }, + "WT": { + "HLA-A*02:01": [ + 18433.068441828786, + 5595.33, + 31830.58, + 24747.82, + 23533.77, + 7860.43, + 20346.04, + 20980.7 + ] + } + }, + "individual_ic50_percentile_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "NetMHC", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC" + ], + "MT": { + "HLA-A*02:01": [ + 5.401750087738037, + "NA", + 53.0, + 30.0, + 24.0, + 25.0, + 30.0, + 30.0 + ] + }, + "WT": { + "HLA-A*02:01": [ + 10.374125, + "NA", + 61.0, + 34.0, + 30.0, + 28.0, + 41.0, + 42.0 + ] + } + }, + "individual_el_calls": { + "algorithms": [], + "MT": { + "HLA-A*02:01": [] + }, + "WT": { + "HLA-A*02:01": [] + } + }, + "individual_el_percentile_calls": { + "algorithms": [], + "MT": { + "HLA-A*02:01": [] + }, + "WT": { + "HLA-A*02:01": [] + } + }, + "individual_percentile_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "NetMHC", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC" + ], + "MT": { + "HLA-A*02:01": [ + 5.401750087738037, + "NA", + 53.0, + 30.0, + 24.0, + 25.0, + 30.0, + 30.0 + ] + }, + "WT": { + "HLA-A*02:01": [ + 10.374125, + "NA", + 61.0, + 34.0, + 30.0, + 28.0, + 41.0, + 42.0 + ] + } + }, + "wt_peptide": "ISCTRSSGSI" + } + }, + "transcripts": [ + "ENST00000390285.3-IGLV6-57-R/G-43" + ], + "transcript_expr": [ + "NA" + ], + "tsl": [ + "Not Supported" + ], + "biotype": [ + "IG_V_gene" + ], + "transcript_length": [ + 148 + ], + "transcript_count": 1, + "peptide_count": 1, + "total_expr": 0 + } + }, + "sets": [ + "Transcript Set 1" + ], + "transcript_counts": [ + 1 + ], + "peptide_counts": [ + 1 + ], + "set_expr": [ + 0 + ], + "DNA VAF": 1.0, + "RNA VAF": "NA", + "gene_expr": "NA", + "best_peptide_mt": "ISCTGSSGSI", + "best_peptide_wt": "ISCTRSSGSI", + "best_hla_allele": "HLA-A*02:01" + }, + "22-22550509-22550510-T-G": { + "good_binders": { + "Transcript Set 1": { + "peptides": { + "GSAPTTVIY": { + "ic50s_MT": [ + "X", + 567.0800170898438 + ], + "percentiles_MT": [ + "X", + 3.4000000953674316 + ], + "ic50s_WT": [ + "X", + 901.875 + ], + "percentiles_WT": [ + "X", + 4.1 + ], + "hla_types": [ + "HLA-A*02:01", + "HLA-B*35:01" + ], + "mutation_position": "3", + "problematic_positions": "None", + "anchor_fails": "None", + "individual_ic50_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "NetMHC", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC" + ], + "MT": { + "HLA-B*35:01": [ + 107.29542054898047, + 4753.83, + 441.74, + 688.93, + 932.48, + 3000.81, + 445.23, + 358.62 + ] + }, + "WT": { + "HLA-B*35:01": [ + 129.3374595606424, + 4665.8, + 824.5, + 979.25, + 1008.87, + 3272.12, + 735.5, + 592.43 + ] + } + }, + "individual_ic50_percentile_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "NetMHC", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC" + ], + "MT": { + "HLA-B*35:01": [ + 0.3167499899864197, + "NA", + 0.6700000166893005, + 3.4000000953674316, + 0.7200000286102295, + 12.0, + 4.3, + 3.8 + ] + }, + "WT": { + "HLA-B*35:01": [ + 0.37775, + "NA", + 1.2, + 4.1, + 0.76, + 12.0, + 6.0, + 5.2 + ] + } + }, + "individual_el_calls": { + "algorithms": [], + "MT": { + "HLA-B*35:01": [] + }, + "WT": { + "HLA-B*35:01": [] + } + }, + "individual_el_percentile_calls": { + "algorithms": [], + "MT": { + "HLA-B*35:01": [] + }, + "WT": { + "HLA-B*35:01": [] + } + }, + "individual_percentile_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "NetMHC", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC" + ], + "MT": { + "HLA-B*35:01": [ + 0.3167499899864197, + "NA", + 0.6700000166893005, + 3.4000000953674316, + 0.7200000286102295, + 12.0, + 4.3, + 3.8 + ] + }, + "WT": { + "HLA-B*35:01": [ + 0.37775, + "NA", + 1.2, + 4.1, + 0.76, + 12.0, + 6.0, + 5.2 + ] + } + }, + "wt_peptide": "GSSPTTVIY" + }, + "RPGSAPTTV": { + "ic50s_MT": [ + "X", + 4313.1201171875 + ], + "percentiles_MT": [ + "X", + 6.199999809265137 + ], + "ic50s_WT": [ "X", 4734.31 ], @@ -3550,15 +4099,211 @@ ] }, "WT": { - "HLA-A*02:01": [ - 1235.1985060957002, - 5570.78, - 9997.36, - 11294.36, - 10831.91, - 202.86, - 1079.22, - 1102.63 + "HLA-A*02:01": [ + 1235.1985060957002, + 5570.78, + 9997.36, + 11294.36, + 10831.91, + 202.86, + 1079.22, + 1102.63 + ] + } + }, + "individual_ic50_percentile_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "NetMHC", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC" + ], + "MT": { + "HLA-A*02:01": [ + 2.625, + "NA", + 26.0, + 19.0, + 15.0, + 4.699999809265137, + 12.0, + 13.0 + ] + }, + "WT": { + "HLA-A*02:01": [ + 1.8984999999999992, + "NA", + 19.0, + 17.0, + 15.0, + 5.1, + 7.6, + 7.7 + ] + } + }, + "individual_el_calls": { + "algorithms": [], + "MT": { + "HLA-A*02:01": [] + }, + "WT": { + "HLA-A*02:01": [] + } + }, + "individual_el_percentile_calls": { + "algorithms": [], + "MT": { + "HLA-A*02:01": [] + }, + "WT": { + "HLA-A*02:01": [] + } + }, + "individual_percentile_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "NetMHC", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC" + ], + "MT": { + "HLA-A*02:01": [ + 2.625, + "NA", + 26.0, + 19.0, + 15.0, + 4.699999809265137, + 12.0, + 13.0 + ] + }, + "WT": { + "HLA-A*02:01": [ + 1.8984999999999992, + "NA", + 19.0, + 17.0, + 15.0, + 5.1, + 7.6, + 7.7 + ] + } + }, + "wt_peptide": "DLIGKPGGV" + } + }, + "transcripts": [ + "ENST00000338754.4-TPST2-P/H-274" + ], + 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"HLA-A*02:01": [] + "HLA-B*35:01": [] }, "WT": { - "HLA-A*02:01": [] + "HLA-B*35:01": [] } }, "individual_percentile_calls": { @@ -3628,35 +4373,35 @@ "SMMPMBEC" ], "MT": { - "HLA-A*02:01": [ - 2.625, + "HLA-B*35:01": [ + 2.828000068664551, "NA", + 11.0, 26.0, - 19.0, - 15.0, - 4.699999809265137, 12.0, - 13.0 + 29.0, + 31.0, + 32.0 ] }, "WT": { - "HLA-A*02:01": [ - 1.8984999999999992, + "HLA-B*35:01": [ + 3.8806250000000015, "NA", - 19.0, - 17.0, - 15.0, - 5.1, - 7.6, - 7.7 + 14.0, + 50.0, + 18.0, + 41.0, + 32.0, + 46.0 ] } }, - "wt_peptide": "DLIGKPGGV" + "wt_peptide": "SPVKEEEKP" } }, "transcripts": [ - "ENST00000338754.4-TPST2-P/H-274" + "ENST00000310624.6-NEFH-P/T-830" ], "transcript_expr": [ "NA" @@ -3668,7 +4413,7 @@ "protein_coding" ], "transcript_length": [ - 377 + 1020 ], "transcript_count": 1, "peptide_count": 1, @@ -3687,19 +4432,6 @@ "set_expr": [ 0 ], - "DNA VAF": 0.179, - "RNA VAF": "NA", - "gene_expr": "NA", - "best_peptide_mt": "DLIGKHGGV", - "best_peptide_wt": 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[ - 0.420625, + "HLA-A*02:01": [ + 43.934125, "NA", - 0.54, - 0.37, - 0.35, - 0.7, - 0.3, - 0.2 + 39.0, + 49.0, + 15.0, + 48.0, + 18.0, + 20.0 ] } }, - "wt_peptide": "MVCELAGNPF" + "wt_peptide": "FNMSSFKLKE" } }, "transcripts": [ - "ENST00000402918.2-ELFN2-P/L-186" + "ENST00000215886.4-LGALS2-E/Q-132" ], "transcript_expr": [ "NA" @@ -4853,10 +5781,10 @@ "protein_coding" ], "transcript_length": [ - 820 + 132 ], "transcript_count": 1, - "peptide_count": 7, + "peptide_count": 1, "total_expr": 0 } }, @@ -4867,24 +5795,11 @@ 1 ], "peptide_counts": [ - 7 + 1 ], "set_expr": [ 0 ], - "DNA VAF": 0.135, - "RNA VAF": "NA", - "gene_expr": "NA", - "best_peptide_mt": "NLFNCECDL", - "best_peptide_wt": "NPFNCECDL", - "best_hla_allele": "HLA-A*02:01" - }, - "22-37966274-37966275-C-G": { - "good_binders": {}, - "sets": [], - "transcript_counts": [], - "peptide_counts": [], - "set_expr": [], "DNA VAF": 0.496, "RNA VAF": "NA", "gene_expr": "NA", @@ -7660,15 +8575,211 @@ ] }, "WT": { - "HLA-B*35:01": [ - 31.13186469159585, - 4664.77, - 14.39, - 17.78, - 10.26, - 828.06, - 48.71, - 72.72 + "HLA-B*35:01": [ + 31.13186469159585, + 4664.77, + 14.39, + 17.78, + 10.26, + 828.06, + 48.71, + 72.72 + ] + } + }, + "individual_ic50_percentile_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "NetMHC", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC" + ], + "MT": { + "HLA-B*35:01": [ + 0.10249999910593033, + "NA", + 0.10000000149011612, + 0.8899999856948853, + 0.05999999865889549, + 3.299999952316284, + 1.3, + 1.7 + ] + }, + "WT": { + "HLA-B*35:01": [ + 0.02875, + "NA", + 0.04, + 0.43, + 0.03, + 2.4, + 0.8, + 1.1 + ] + } + }, + "individual_el_calls": { + "algorithms": [], + "MT": { + "HLA-B*35:01": [] + }, + "WT": { + "HLA-B*35:01": [] + } + }, + "individual_el_percentile_calls": { + "algorithms": [], + "MT": { + "HLA-B*35:01": [] + }, + "WT": { + "HLA-B*35:01": [] + } + }, + "individual_percentile_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + 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+ "HLA-A*02:01": [ + 13.856625000000005, "NA", - 0.04, - 0.43, - 0.03, - 2.4, - 0.8, - 1.1 + 25.0, + 26.0, + 18.0, + 44.0, + 41.0, + 38.0 ] } }, - "wt_peptide": "YSYGLLHTY" + "wt_peptide": "SAKTTVVVTA" } }, "transcripts": [ - "ENST00000253255.5-PKDREJ-T/I-1875" + "ENST00000262794.5-MOV10L1-A/T-482" ], "transcript_expr": [ "NA" @@ -7778,10 +8889,10 @@ "protein_coding" ], "transcript_length": [ - 2253 + 1211 ], "transcript_count": 1, - "peptide_count": 6, + "peptide_count": 1, "total_expr": 0 } }, @@ -7792,24 +8903,11 @@ 1 ], "peptide_counts": [ - 6 + 1 ], "set_expr": [ 0 ], - "DNA VAF": 0.233, - "RNA VAF": "NA", - "gene_expr": "NA", - "best_peptide_mt": "HIYGSGGYAL", - "best_peptide_wt": "HTYGSGGYAL", - "best_hla_allele": "HLA-A*02:01" - }, - "22-50555769-50555770-G-A": { - "good_binders": {}, - "sets": [], - "transcript_counts": [], - "peptide_counts": [], - "set_expr": [], "DNA VAF": 0.042, "RNA VAF": "NA", "gene_expr": "NA", @@ -9858,11 +10956,194 @@ "best_hla_allele": "HLA-B*35:01" }, "22-50869713-50869714-C-A": { - "good_binders": {}, - "sets": [], - "transcript_counts": [], - "peptide_counts": [], - "set_expr": [], + "good_binders": { + "Transcript Set 1": { + "peptides": { + "YESRVEPPH": { + "ic50s_MT": [ + "X", + 6159.2998046875 + ], + "percentiles_MT": [ + "X", + 14.0 + ], + "ic50s_WT": [ + "X", + 18030.513 + ], + "percentiles_WT": [ + "X", + 33.0 + ], + "hla_types": [ + "HLA-A*02:01", + "HLA-B*35:01" + ], + "mutation_position": "1", + "problematic_positions": "None", + "anchor_fails": "None", + "individual_ic50_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "NetMHC", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC" + ], + "MT": { + "HLA-B*35:01": [ + 17558.295646686685, + 5987.68, + 5243.65, + 10699.58, + 13202.43, + 6330.92, + 4135.99, + 2538.87 + ] + }, + "WT": { + "HLA-B*35:01": [ + 18379.255660686867, + 6063.92, + 17681.77, + 23318.07, + 25776.49, + 12382.34, + 24466.96, + 15799.38 + ] + } + }, + "individual_ic50_percentile_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "NetMHC", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC" + ], + "MT": { + "HLA-B*35:01": [ + 7.555500030517578, + "NA", + 4.0, + 17.0, + 5.699999809265137, + 21.0, + 18.0, + 14.0 + ] + }, + "WT": { + "HLA-B*35:01": [ + 8.065000000000005, + "NA", + 15.0, + 33.0, + 16.0, + 33.0, + 40.0, + 34.0 + ] + } + }, + "individual_el_calls": { + "algorithms": [], + "MT": { + "HLA-B*35:01": [] + }, + "WT": { + "HLA-B*35:01": [] + } + }, + "individual_el_percentile_calls": { + "algorithms": [], + "MT": { + "HLA-B*35:01": [] + }, + "WT": { + "HLA-B*35:01": [] + } + }, + "individual_percentile_calls": { + "algorithms": [ + "MHCflurry", + "MHCnuggetsI", + "NetMHC", + "NetMHCcons", + "NetMHCpan", + "PickPocket", + "SMM", + "SMMPMBEC" + ], + "MT": { + "HLA-B*35:01": [ + 7.555500030517578, + "NA", + 4.0, + 17.0, + 5.699999809265137, + 21.0, + 18.0, + 14.0 + ] + }, + "WT": { + "HLA-B*35:01": [ + 8.065000000000005, + "NA", + 15.0, + 33.0, + 16.0, + 33.0, + 40.0, + 34.0 + ] + } + }, + "wt_peptide": "SESRVEPPH" + } + }, + "transcripts": [ + "ENST00000395741.3-PPP6R2-S/Y-414" + ], + "transcript_expr": [ + "NA" + ], + "tsl": [ + "Not Supported" + ], + "biotype": [ + "protein_coding" + ], + "transcript_length": [ + 933 + ], + "transcript_count": 1, + "peptide_count": 1, + "total_expr": 0 + } + }, + "sets": [ + "Transcript Set 1" + ], + "transcript_counts": [ + 1 + ], + "peptide_counts": [ + 1 + ], + "set_expr": [ + 0 + ], "DNA VAF": 0.043, "RNA VAF": "NA", "gene_expr": "NA", diff --git a/tests/test_data/aggregate_all_epitopes/output.pvacbind.lowest_top_score_metric.tsv b/tests/test_data/aggregate_all_epitopes/output.pvacbind.lowest_top_score_metric.tsv index 0443d905..c89ea9f4 100644 --- a/tests/test_data/aggregate_all_epitopes/output.pvacbind.lowest_top_score_metric.tsv +++ b/tests/test_data/aggregate_all_epitopes/output.pvacbind.lowest_top_score_metric.tsv @@ -41,9 +41,9 @@ ID DRB1*11:01 E*01:01 G*01:09 Best Peptide Prob Pos Num Included Peptides Num Pa 24 1 1 MVCELAGNL None 2 0 3454.020 4.100 Poor Pending 23 1 FNCECDLFG None 1 0 4778.520 6.200 Poor Pending 12 1 SVNEALNNL None 1 0 4989.870 7.300 Poor Pending -14 VQGIANQDAAQGIAK None 0 0 5209.800 69.230 Poor Pending -45 RTEASGSES None 0 0 5267.250 7.900 Poor Pending -46 GYESRVEPP None 0 0 5620.540 8.700 Poor Pending -13 AVQGIANED None 0 0 5743.490 9.000 Poor Pending -3 VIPTVSTPPP None 0 0 8664.370 1.800 Poor Pending -4 VIPTVSTPPP None 0 0 8664.370 1.800 Poor Pending +14 1 VQGIANQDAAQGIAK None 1 0 5209.800 69.230 Poor Pending +45 1 RTEASGSES None 1 0 5267.250 7.900 Poor Pending +46 1 GYESRVEPP None 1 0 5620.540 8.700 Poor Pending +13 1 AVQGIANED None 1 0 5743.490 9.000 Poor Pending +3 1 VIPTVSTPPP None 1 0 8664.370 1.800 Poor Pending +4 1 VIPTVSTPPP None 1 0 8664.370 1.800 Poor Pending diff --git a/tests/test_data/aggregate_all_epitopes/output.pvacbind.tsv b/tests/test_data/aggregate_all_epitopes/output.pvacbind.tsv index e9f127d8..93071450 100644 --- a/tests/test_data/aggregate_all_epitopes/output.pvacbind.tsv +++ b/tests/test_data/aggregate_all_epitopes/output.pvacbind.tsv @@ -38,12 +38,12 @@ ID DRB1*11:01 E*01:01 G*01:09 Best Peptide Prob Pos Num Included Peptides Num Pa 1 1 1 PLLPLLLLLLGASGG None 2 0 4650.000 67.090 Poor Pending 1_duplicate 1 1 PLLPLLLLLLGASGG None 2 0 4650.000 67.090 Poor Pending 12 1 SVNEALNNL None 1 0 4989.870 7.300 Poor Pending -14 VQGIANQDAAQGIAK None 0 0 5209.800 69.230 Poor Pending -45 RTEASGSES None 0 0 5267.250 7.900 Poor Pending -46 GYESRVEPP None 0 0 5620.540 8.700 Poor Pending -13 AVQGIANED None 0 0 5743.490 9.000 Poor Pending -22 KTQEVKVKE None 0 0 7366.350 14.000 Poor Pending -23 SLMVCELAGNPFNCE None 0 0 7387.300 75.990 Poor Pending -21 KSPVKEEEK None 0 0 10081.440 21.000 Poor Pending -3 VIPTVSTPP None 0 0 10992.950 23.000 Poor Pending -4 VIPTVSTPP None 0 0 10992.950 23.000 Poor Pending +14 1 VQGIANQDAAQGIAK None 1 0 5209.800 69.230 Poor Pending +45 1 RTEASGSES None 1 0 5267.250 7.900 Poor Pending +46 1 GYESRVEPP None 1 0 5620.540 8.700 Poor Pending +13 1 AVQGIANED None 1 0 5743.490 9.000 Poor Pending +22 1 KTQEVKVKE None 1 0 7366.350 14.000 Poor Pending +23 1 SLMVCELAGNPFNCE None 1 0 7387.300 75.990 Poor Pending +21 1 KSPVKEEEK None 1 0 10081.440 21.000 Poor Pending +3 1 VIPTVSTPP None 1 0 10992.950 23.000 Poor Pending +4 1 VIPTVSTPP None 1 0 10992.950 23.000 Poor Pending diff --git a/tests/test_data/aggregate_all_epitopes/output.pvacfuse.tsv b/tests/test_data/aggregate_all_epitopes/output.pvacfuse.tsv index 40829a44..81c6cd99 100644 --- a/tests/test_data/aggregate_all_epitopes/output.pvacfuse.tsv +++ b/tests/test_data/aggregate_all_epitopes/output.pvacfuse.tsv @@ -1,31 +1,31 @@ ID A*29:02 Gene Best Peptide Best Transcript Allele Prob Pos Num Included Peptides Num Passing Peptides IC50 MT %ile MT Expr Read Support Tier Evaluation 7.EIF3K_CYP39A1.ENST00000588934_ENST00000275016.frameshift_fusion.118 4 EIF3K_CYP39A1 HFQAFWHQF ENST00000588934_ENST00000275016 HLA-A*29:02 None 4 2 257.230 0.730 0.573 2103 Pass Pending -1.EIF3K_CYP39A1.ENST00000593149_ENST00000275016.inframe_fusion.79 EIF3K_CYP39A1 MLGDLSASI ENST00000593149_ENST00000275016 HLA-A*29:02 None 0 0 6540.210 5.200 0.573 2103 Poor Pending -11.EIF3K_CYP39A1.ENST00000614624_ENST00000275016.inframe_fusion.133 EIF3K_CYP39A1 MLGDLSASI ENST00000614624_ENST00000275016 HLA-A*29:02 None 0 0 6540.210 5.200 0.573 2103 Poor Pending -3.EIF3K_CYP39A1.ENST00000248342_ENST00000275016.inframe_fusion.166 EIF3K_CYP39A1 MLGDLSASI ENST00000248342_ENST00000275016 HLA-A*29:02 None 0 0 6540.210 5.200 0.573 2103 Poor Pending -5.EIF3K_CYP39A1.ENST00000538434_ENST00000275016.inframe_fusion.79 EIF3K_CYP39A1 MLGDLSASI ENST00000538434_ENST00000275016 HLA-A*29:02 None 0 0 6540.210 5.200 0.573 2103 Poor Pending -8.EIF3K_CYP39A1.ENST00000545173_ENST00000275016.inframe_fusion.166 EIF3K_CYP39A1 MLGDLSASI ENST00000545173_ENST00000275016 HLA-A*29:02 None 0 0 6540.210 5.200 0.573 2103 Poor Pending -12.EIF3K_CYP39A1.ENST00000614624_ENST00000619708.frameshift_fusion.133 EIF3K_CYP39A1 MLGDLSDAL ENST00000614624_ENST00000619708 HLA-A*29:02 None 0 0 12112.160 8.900 0.573 2103 Poor Pending -2.EIF3K_CYP39A1.ENST00000593149_ENST00000619708.frameshift_fusion.79 EIF3K_CYP39A1 MLGDLSDAL ENST00000593149_ENST00000619708 HLA-A*29:02 None 0 0 12112.160 8.900 0.573 2103 Poor Pending -4.EIF3K_CYP39A1.ENST00000248342_ENST00000619708.frameshift_fusion.166 EIF3K_CYP39A1 MLGDLSDAL ENST00000248342_ENST00000619708 HLA-A*29:02 None 0 0 12112.160 8.900 0.573 2103 Poor Pending -6.EIF3K_CYP39A1.ENST00000538434_ENST00000619708.frameshift_fusion.79 EIF3K_CYP39A1 MLGDLSDAL ENST00000538434_ENST00000619708 HLA-A*29:02 None 0 0 12112.160 8.900 0.573 2103 Poor Pending -9.EIF3K_CYP39A1.ENST00000545173_ENST00000619708.frameshift_fusion.166 EIF3K_CYP39A1 MLGDLSDAL ENST00000545173_ENST00000619708 HLA-A*29:02 None 0 0 12112.160 8.900 0.573 2103 Poor Pending -23.TMEM104_RAB37.ENST00000417024_ENST00000340415.inframe_fusion.225 TMEM104_RAB37 YRIYLTILV ENST00000417024_ENST00000340415 HLA-A*29:02 None 0 0 6204.380 5.000 0.110 401 Poor Pending -24.TMEM104_RAB37.ENST00000417024_ENST00000402449.inframe_fusion.225 TMEM104_RAB37 YRIYLTILV ENST00000417024_ENST00000402449 HLA-A*29:02 None 0 0 6204.380 5.000 0.110 401 Poor Pending -25.TMEM104_RAB37.ENST00000582773_ENST00000340415.inframe_fusion.212 TMEM104_RAB37 YRIYLTILV ENST00000582773_ENST00000340415 HLA-A*29:02 None 0 0 6204.380 5.000 0.110 401 Poor Pending -26.TMEM104_RAB37.ENST00000582773_ENST00000402449.inframe_fusion.212 TMEM104_RAB37 YRIYLTILV ENST00000582773_ENST00000402449 HLA-A*29:02 None 0 0 6204.380 5.000 0.110 401 Poor Pending -27.TMEM104_RAB37.ENST00000582330_ENST00000340415.inframe_fusion.212 TMEM104_RAB37 YRIYLTILV ENST00000582330_ENST00000340415 HLA-A*29:02 None 0 0 6204.380 5.000 0.110 401 Poor Pending -28.TMEM104_RAB37.ENST00000582330_ENST00000402449.inframe_fusion.212 TMEM104_RAB37 YRIYLTILV ENST00000582330_ENST00000402449 HLA-A*29:02 None 0 0 6204.380 5.000 0.110 401 Poor Pending -29.TMEM104_RAB37.ENST00000335464_ENST00000340415.inframe_fusion.212 TMEM104_RAB37 YRIYLTILV ENST00000335464_ENST00000340415 HLA-A*29:02 None 0 0 6204.380 5.000 0.110 401 Poor Pending -30.TMEM104_RAB37.ENST00000335464_ENST00000402449.inframe_fusion.212 TMEM104_RAB37 YRIYLTILV ENST00000335464_ENST00000402449 HLA-A*29:02 None 0 0 6204.380 5.000 0.110 401 Poor Pending -10.EIF3K_CYP39A1.ENST00000592558_ENST00000275016.inframe_fusion.140 EIF3K_CYP39A1 KSSIPKNVF ENST00000592558_ENST00000275016 HLA-A*29:02 None 0 0 22972.240 22.000 0.573 2103 Poor Pending -15.PLA2R1_RBMS1.ENST00000283243_ENST00000348849.inframe_fusion.865 PLA2R1_RBMS1 FIHSKIKAQ ENST00000283243_ENST00000348849 HLA-A*29:02 None 0 0 26500.160 28.000 0.331 1230 Poor Pending -16.PLA2R1_RBMS1.ENST00000283243_ENST00000409075.inframe_fusion.865 PLA2R1_RBMS1 FIHSKIKAQ ENST00000283243_ENST00000409075 HLA-A*29:02 None 0 0 26500.160 28.000 0.331 1230 Poor Pending -17.PLA2R1_RBMS1.ENST00000283243_ENST00000409289.inframe_fusion.865 PLA2R1_RBMS1 FIHSKIKAQ ENST00000283243_ENST00000409289 HLA-A*29:02 None 0 0 26500.160 28.000 0.331 1230 Poor Pending -18.PLA2R1_RBMS1.ENST00000283243_ENST00000409972.inframe_fusion.865 PLA2R1_RBMS1 FIHSKIKAQ ENST00000283243_ENST00000409972 HLA-A*29:02 None 0 0 26500.160 28.000 0.331 1230 Poor Pending -19.PLA2R1_RBMS1.ENST00000392771_ENST00000348849.inframe_fusion.865 PLA2R1_RBMS1 FIHSKIKAQ ENST00000392771_ENST00000348849 HLA-A*29:02 None 0 0 26500.160 28.000 0.331 1230 Poor Pending -20.PLA2R1_RBMS1.ENST00000392771_ENST00000409075.inframe_fusion.865 PLA2R1_RBMS1 FIHSKIKAQ ENST00000392771_ENST00000409075 HLA-A*29:02 None 0 0 26500.160 28.000 0.331 1230 Poor Pending -21.PLA2R1_RBMS1.ENST00000392771_ENST00000409289.inframe_fusion.865 PLA2R1_RBMS1 FIHSKIKAQ ENST00000392771_ENST00000409289 HLA-A*29:02 None 0 0 26500.160 28.000 0.331 1230 Poor Pending -22.PLA2R1_RBMS1.ENST00000392771_ENST00000409972.inframe_fusion.865 PLA2R1_RBMS1 FIHSKIKAQ ENST00000392771_ENST00000409972 HLA-A*29:02 None 0 0 26500.160 28.000 0.331 1230 Poor Pending -13.HNRNPUL2_AHNAK.ENST00000301785_ENST00000257247.frameshift_fusion.660 HNRNPUL2_AHNAK GYDGEGGDN ENST00000301785_ENST00000257247 HLA-A*29:02 None 0 0 28325.960 32.000 0.153 570 Poor Pending -14.HNRNPUL2_AHNAK.ENST00000301785_ENST00000378024.frameshift_fusion.660 HNRNPUL2_AHNAK GYDGEGGDN ENST00000301785_ENST00000378024 HLA-A*29:02 None 0 0 28325.960 32.000 0.153 570 Poor Pending +1.EIF3K_CYP39A1.ENST00000593149_ENST00000275016.inframe_fusion.79 1 EIF3K_CYP39A1 MLGDLSASI ENST00000593149_ENST00000275016 HLA-A*29:02 None 1 0 6540.210 5.200 0.573 2103 Poor Pending +11.EIF3K_CYP39A1.ENST00000614624_ENST00000275016.inframe_fusion.133 1 EIF3K_CYP39A1 MLGDLSASI ENST00000614624_ENST00000275016 HLA-A*29:02 None 1 0 6540.210 5.200 0.573 2103 Poor Pending +3.EIF3K_CYP39A1.ENST00000248342_ENST00000275016.inframe_fusion.166 1 EIF3K_CYP39A1 MLGDLSASI ENST00000248342_ENST00000275016 HLA-A*29:02 None 1 0 6540.210 5.200 0.573 2103 Poor Pending +5.EIF3K_CYP39A1.ENST00000538434_ENST00000275016.inframe_fusion.79 1 EIF3K_CYP39A1 MLGDLSASI ENST00000538434_ENST00000275016 HLA-A*29:02 None 1 0 6540.210 5.200 0.573 2103 Poor Pending +8.EIF3K_CYP39A1.ENST00000545173_ENST00000275016.inframe_fusion.166 1 EIF3K_CYP39A1 MLGDLSASI ENST00000545173_ENST00000275016 HLA-A*29:02 None 1 0 6540.210 5.200 0.573 2103 Poor Pending +12.EIF3K_CYP39A1.ENST00000614624_ENST00000619708.frameshift_fusion.133 1 EIF3K_CYP39A1 MLGDLSDAL ENST00000614624_ENST00000619708 HLA-A*29:02 None 1 0 12112.160 8.900 0.573 2103 Poor Pending +2.EIF3K_CYP39A1.ENST00000593149_ENST00000619708.frameshift_fusion.79 1 EIF3K_CYP39A1 MLGDLSDAL ENST00000593149_ENST00000619708 HLA-A*29:02 None 1 0 12112.160 8.900 0.573 2103 Poor Pending +4.EIF3K_CYP39A1.ENST00000248342_ENST00000619708.frameshift_fusion.166 1 EIF3K_CYP39A1 MLGDLSDAL ENST00000248342_ENST00000619708 HLA-A*29:02 None 1 0 12112.160 8.900 0.573 2103 Poor Pending +6.EIF3K_CYP39A1.ENST00000538434_ENST00000619708.frameshift_fusion.79 1 EIF3K_CYP39A1 MLGDLSDAL ENST00000538434_ENST00000619708 HLA-A*29:02 None 1 0 12112.160 8.900 0.573 2103 Poor Pending +9.EIF3K_CYP39A1.ENST00000545173_ENST00000619708.frameshift_fusion.166 1 EIF3K_CYP39A1 MLGDLSDAL ENST00000545173_ENST00000619708 HLA-A*29:02 None 1 0 12112.160 8.900 0.573 2103 Poor Pending +23.TMEM104_RAB37.ENST00000417024_ENST00000340415.inframe_fusion.225 1 TMEM104_RAB37 YRIYLTILV ENST00000417024_ENST00000340415 HLA-A*29:02 None 1 0 6204.380 5.000 0.110 401 Poor Pending +24.TMEM104_RAB37.ENST00000417024_ENST00000402449.inframe_fusion.225 1 TMEM104_RAB37 YRIYLTILV ENST00000417024_ENST00000402449 HLA-A*29:02 None 1 0 6204.380 5.000 0.110 401 Poor Pending +25.TMEM104_RAB37.ENST00000582773_ENST00000340415.inframe_fusion.212 1 TMEM104_RAB37 YRIYLTILV ENST00000582773_ENST00000340415 HLA-A*29:02 None 1 0 6204.380 5.000 0.110 401 Poor Pending +26.TMEM104_RAB37.ENST00000582773_ENST00000402449.inframe_fusion.212 1 TMEM104_RAB37 YRIYLTILV ENST00000582773_ENST00000402449 HLA-A*29:02 None 1 0 6204.380 5.000 0.110 401 Poor Pending +27.TMEM104_RAB37.ENST00000582330_ENST00000340415.inframe_fusion.212 1 TMEM104_RAB37 YRIYLTILV ENST00000582330_ENST00000340415 HLA-A*29:02 None 1 0 6204.380 5.000 0.110 401 Poor Pending +28.TMEM104_RAB37.ENST00000582330_ENST00000402449.inframe_fusion.212 1 TMEM104_RAB37 YRIYLTILV ENST00000582330_ENST00000402449 HLA-A*29:02 None 1 0 6204.380 5.000 0.110 401 Poor Pending +29.TMEM104_RAB37.ENST00000335464_ENST00000340415.inframe_fusion.212 1 TMEM104_RAB37 YRIYLTILV ENST00000335464_ENST00000340415 HLA-A*29:02 None 1 0 6204.380 5.000 0.110 401 Poor Pending +30.TMEM104_RAB37.ENST00000335464_ENST00000402449.inframe_fusion.212 1 TMEM104_RAB37 YRIYLTILV ENST00000335464_ENST00000402449 HLA-A*29:02 None 1 0 6204.380 5.000 0.110 401 Poor Pending +10.EIF3K_CYP39A1.ENST00000592558_ENST00000275016.inframe_fusion.140 1 EIF3K_CYP39A1 KSSIPKNVF ENST00000592558_ENST00000275016 HLA-A*29:02 None 1 0 22972.240 22.000 0.573 2103 Poor Pending +15.PLA2R1_RBMS1.ENST00000283243_ENST00000348849.inframe_fusion.865 1 PLA2R1_RBMS1 FIHSKIKAQ ENST00000283243_ENST00000348849 HLA-A*29:02 None 1 0 26500.160 28.000 0.331 1230 Poor Pending +16.PLA2R1_RBMS1.ENST00000283243_ENST00000409075.inframe_fusion.865 1 PLA2R1_RBMS1 FIHSKIKAQ ENST00000283243_ENST00000409075 HLA-A*29:02 None 1 0 26500.160 28.000 0.331 1230 Poor Pending +17.PLA2R1_RBMS1.ENST00000283243_ENST00000409289.inframe_fusion.865 1 PLA2R1_RBMS1 FIHSKIKAQ ENST00000283243_ENST00000409289 HLA-A*29:02 None 1 0 26500.160 28.000 0.331 1230 Poor Pending +18.PLA2R1_RBMS1.ENST00000283243_ENST00000409972.inframe_fusion.865 1 PLA2R1_RBMS1 FIHSKIKAQ ENST00000283243_ENST00000409972 HLA-A*29:02 None 1 0 26500.160 28.000 0.331 1230 Poor Pending +19.PLA2R1_RBMS1.ENST00000392771_ENST00000348849.inframe_fusion.865 1 PLA2R1_RBMS1 FIHSKIKAQ ENST00000392771_ENST00000348849 HLA-A*29:02 None 1 0 26500.160 28.000 0.331 1230 Poor Pending +20.PLA2R1_RBMS1.ENST00000392771_ENST00000409075.inframe_fusion.865 1 PLA2R1_RBMS1 FIHSKIKAQ ENST00000392771_ENST00000409075 HLA-A*29:02 None 1 0 26500.160 28.000 0.331 1230 Poor Pending +21.PLA2R1_RBMS1.ENST00000392771_ENST00000409289.inframe_fusion.865 1 PLA2R1_RBMS1 FIHSKIKAQ ENST00000392771_ENST00000409289 HLA-A*29:02 None 1 0 26500.160 28.000 0.331 1230 Poor Pending +22.PLA2R1_RBMS1.ENST00000392771_ENST00000409972.inframe_fusion.865 1 PLA2R1_RBMS1 FIHSKIKAQ ENST00000392771_ENST00000409972 HLA-A*29:02 None 1 0 26500.160 28.000 0.331 1230 Poor Pending +13.HNRNPUL2_AHNAK.ENST00000301785_ENST00000257247.frameshift_fusion.660 1 HNRNPUL2_AHNAK GYDGEGGDN ENST00000301785_ENST00000257247 HLA-A*29:02 None 1 0 28325.960 32.000 0.153 570 Poor Pending +14.HNRNPUL2_AHNAK.ENST00000301785_ENST00000378024.frameshift_fusion.660 1 HNRNPUL2_AHNAK GYDGEGGDN ENST00000301785_ENST00000378024 HLA-A*29:02 None 1 0 28325.960 32.000 0.153 570 Poor Pending diff --git a/tests/test_data/aggregate_all_epitopes/output.tsv b/tests/test_data/aggregate_all_epitopes/output.tsv index 41145ad6..52d36186 100644 --- a/tests/test_data/aggregate_all_epitopes/output.tsv +++ b/tests/test_data/aggregate_all_epitopes/output.tsv @@ -15,10 +15,10 @@ ID Index A*02:01 B*35:01 Gene AA Change Num Passing Transcripts Best Peptide Bes 22-41920894-41920895-G-C 19.ACO2.ENST00000216254.4.missense.510E/Q 1 ACO2 E510Q 1 NPQTDYLTG ENST00000216254.4 Not Supported HLA-B*35:01 3 None 1 0 3121.315 3595.485 6.600 6.500 NA NA NA NA 0.250 Poor Pending 22-41895790-41895791-C-A 18.ACO2.ENST00000216254.4.missense.33A/E 1 ACO2 A33E 1 EMSHFEPNEY ENST00000216254.4 Not Supported HLA-B*35:01 1 None 1 0 3903.700 4456.030 2.600 3.700 NA NA NA NA 0.044 Poor Pending 22-26936775-26936776-G-T 11.TPST2.ENST00000338754.4.missense.274P/H 1 TPST2 P274H 1 DLIGKHGGV ENST00000338754.4 Not Supported HLA-A*02:01 6 None 1 0 4145.685 3402.989 13.000 7.700 NA NA NA NA 0.179 Poor Pending -22-20709231-20709232-G-C 8.FAM230A.ENST00000434783.3.missense.322E/Q FAM230A E322Q 0 IANQDAAQG ENST00000434783.3 Not Supported HLA-B*35:01 4 None 0 0 5738.350 5541.375 10.499 7.674 NA NA NA NA 0.500 Poor Pending -22-50869713-50869714-C-A 24.PPP6R2.ENST00000395741.3.missense.414S/Y PPP6R2 S414Y 0 YESRVEPPH ENST00000395741.3 Not Supported HLA-B*35:01 1 None 0 0 6159.300 18030.513 14.000 33.000 NA NA NA NA 0.043 Poor Pending -22-22550449-22550450-C-G 9.IGLV6-57.ENST00000390285.3.missense.43R/G IGLV6-57 R43G 0 ISCTGSSGSI ENST00000390285.3 Not Supported HLA-A*02:01 5 None 0 0 9672.631 20663.370 30.000 34.000 NA NA NA NA 1.000 Poor Pending -22-18020271-18020272-G-A 5.CECR2.ENST00000262608.8.missense.535R/H CECR2 R535H 0 SGGSHVWTH ENST00000262608.8 Not Supported HLA-B*35:01 9 None 0 0 10761.970 30462.795 24.000 42.000 NA NA NA NA 0.071 Poor Pending -22-29886116-29886117-C-A 12.NEFH.ENST00000310624.6.missense.830P/T NEFH P830T 0 SPVKEEEKT ENST00000310624.6 Not Supported HLA-B*35:01 9 None 0 0 12628.540 17588.290 26.000 32.000 NA NA NA NA 0.038 Poor Pending -22-37966274-37966275-C-G 14.LGALS2.ENST00000215886.4.missense.132E/Q LGALS2 E132Q 0 FNMSSFKLKQ ENST00000215886.4 Not Supported HLA-A*02:01 10 None 0 0 16963.785 16973.740 33.000 39.000 NA NA NA NA 0.496 Poor Pending -22-50555769-50555770-G-A 21.MOV10L1.ENST00000262794.5.missense.482A/T MOV10L1 A482T 0 SAKTTVVVTT ENST00000262794.5 Not Supported HLA-A*02:01 10 None 0 0 27206.914 17665.800 40.000 26.000 NA NA NA NA 0.042 Poor Pending +22-20709231-20709232-G-C 8.FAM230A.ENST00000434783.3.missense.322E/Q 1 FAM230A E322Q 1 IANQDAAQG ENST00000434783.3 Not Supported HLA-B*35:01 4 None 1 0 5738.350 5541.375 10.499 7.674 NA NA NA NA 0.500 Poor Pending +22-50869713-50869714-C-A 24.PPP6R2.ENST00000395741.3.missense.414S/Y 1 PPP6R2 S414Y 1 YESRVEPPH ENST00000395741.3 Not Supported HLA-B*35:01 1 None 1 0 6159.300 18030.513 14.000 33.000 NA NA NA NA 0.043 Poor Pending +22-22550449-22550450-C-G 9.IGLV6-57.ENST00000390285.3.missense.43R/G 1 IGLV6-57 R43G 1 ISCTGSSGSI ENST00000390285.3 Not Supported HLA-A*02:01 5 None 1 0 9672.631 20663.370 30.000 34.000 NA NA NA NA 1.000 Poor Pending +22-18020271-18020272-G-A 5.CECR2.ENST00000262608.8.missense.535R/H 1 CECR2 R535H 1 SGGSHVWTH ENST00000262608.8 Not Supported HLA-B*35:01 9 None 1 0 10761.970 30462.795 24.000 42.000 NA NA NA NA 0.071 Poor Pending +22-29886116-29886117-C-A 12.NEFH.ENST00000310624.6.missense.830P/T 1 NEFH P830T 1 SPVKEEEKT ENST00000310624.6 Not Supported HLA-B*35:01 9 None 1 0 12628.540 17588.290 26.000 32.000 NA NA NA NA 0.038 Poor Pending +22-37966274-37966275-C-G 14.LGALS2.ENST00000215886.4.missense.132E/Q 1 LGALS2 E132Q 1 FNMSSFKLKQ ENST00000215886.4 Not Supported HLA-A*02:01 10 None 1 0 16963.785 16973.740 33.000 39.000 NA NA NA NA 0.496 Poor Pending +22-50555769-50555770-G-A 21.MOV10L1.ENST00000262794.5.missense.482A/T 1 MOV10L1 A482T 1 SAKTTVVVTT ENST00000262794.5 Not Supported HLA-A*02:01 10 None 1 0 27206.914 17665.800 40.000 26.000 NA NA NA NA 0.042 Poor Pending diff --git a/tests/test_data/pvacbind/MHC_Class_I/Test.all_epitopes.aggregated.tsv b/tests/test_data/pvacbind/MHC_Class_I/Test.all_epitopes.aggregated.tsv index 7c120ca6..a09d68be 100644 --- a/tests/test_data/pvacbind/MHC_Class_I/Test.all_epitopes.aggregated.tsv +++ b/tests/test_data/pvacbind/MHC_Class_I/Test.all_epitopes.aggregated.tsv @@ -34,16 +34,16 @@ ID E*01:01 G*01:09 Best Peptide Prob Pos Num Included Peptides Num Passing Pepti 23 1 FNCECDLFG None 1 0 4778.520 6.200 Poor True Pending 12 1 SVNEALNNL None 1 0 4989.870 7.300 Poor True Pending 29 1 GQHWARLRG None 1 0 4989.870 6.700 Poor True Pending -45 RTEASGSES None 0 0 5267.250 7.900 Poor True Pending -11 KSVNEALNH None 0 0 5441.030 8.100 Poor True Pending -46 GYESRVEPP None 0 0 5620.540 8.700 Poor True Pending -14 ANQDAAQGI None 0 0 5681.680 8.800 Poor False Pending -13 AVQGIANED None 0 0 5743.490 9.000 Poor False Pending -20 KHGGVSLSK None 0 0 6539.790 13.000 Poor True Pending -39 KRNSRRQLP None 0 0 7860.430 18.000 Poor True Pending -40 KRNSRRQLP None 0 0 7860.430 18.000 Poor True Pending -19 IGKPGGVSL None 0 0 7945.940 1.400 Poor True Pending -15 TRSSGSIAS None 0 0 8571.130 20.000 Poor True Pending -3 VIPTVSTPPP None 0 0 8664.370 1.800 Poor True Pending -4 VIPTVSTPPP None 0 0 8664.370 1.800 Poor True Pending -16 KTVTISCTG None 0 0 9447.760 19.000 Poor True Pending +45 1 RTEASGSES None 1 0 5267.250 7.900 Poor True Pending +11 1 KSVNEALNH None 1 0 5441.030 8.100 Poor True Pending +46 1 GYESRVEPP None 1 0 5620.540 8.700 Poor True Pending +14 1 ANQDAAQGI None 1 0 5681.680 8.800 Poor False Pending +13 1 AVQGIANED None 1 0 5743.490 9.000 Poor False Pending +20 1 KHGGVSLSK None 1 0 6539.790 13.000 Poor True Pending +39 1 KRNSRRQLP None 1 0 7860.430 18.000 Poor True Pending +40 1 KRNSRRQLP None 1 0 7860.430 18.000 Poor True Pending +19 1 IGKPGGVSL None 1 0 7945.940 1.400 Poor True Pending +15 1 TRSSGSIAS None 1 0 8571.130 20.000 Poor True Pending +3 1 VIPTVSTPPP None 1 0 8664.370 1.800 Poor True Pending +4 1 VIPTVSTPPP None 1 0 8664.370 1.800 Poor True Pending +16 1 KTVTISCTG None 1 0 9447.760 19.000 Poor True Pending diff --git a/tests/test_data/pvacbind/MHC_Class_II/Test.all_epitopes.aggregated.tsv b/tests/test_data/pvacbind/MHC_Class_II/Test.all_epitopes.aggregated.tsv index b025708e..bd56bec0 100644 --- a/tests/test_data/pvacbind/MHC_Class_II/Test.all_epitopes.aggregated.tsv +++ b/tests/test_data/pvacbind/MHC_Class_II/Test.all_epitopes.aggregated.tsv @@ -33,17 +33,17 @@ ID DRB1*11:01 Best Peptide Prob Pos Num Included Peptides Num Passing Peptides I 19 1 LIGKPGGVSLSKIER None 1 0 3993.400 62.000 Poor True Pending 28 1 SLLHTVSPEPARPPQ None 1 0 4019.300 63.000 Poor True Pending 31 1 DDMDCLSDRCKILQV None 1 0 4408.600 65.000 Poor True Pending -11 KSVNEALNHLLTEEE None 0 0 5425.500 69.000 Poor True Pending -24 SLMVCELAGNLFNCE None 0 0 5515.200 70.000 Poor True Pending -8 GGSHVWTHSRDPEGS None 0 0 6419.700 73.000 Poor True Pending -14 VQGIANQDAAQGIAK None 0 0 6577.200 73.000 Poor False Pending -23 SLMVCELAGNPFNCE None 0 0 6648.100 74.000 Poor True Pending -27 SLLHTVSPEPPRPPQ None 0 0 8706.600 79.000 Poor True Pending -13 VQGIANEDAAQGIAK None 0 0 9312.400 81.000 Poor False Pending -3 AAAAAVIPTVSTPPP None 0 0 9996.200 82.000 Poor True Pending -4 AAAAAVIPTVSTPPP None 0 0 9996.200 82.000 Poor True Pending -12 KSVNEALNNLLTEEE None 0 0 11571.600 85.000 Poor True Pending -22 EEEKTQEVKVKEPPK None 0 0 13934.400 88.000 Poor True Pending -21 EEEKPQEVKVKEPPK None 0 0 16895.300 92.000 Poor True Pending -46 EASGYESRVEPPHEN None 0 0 19617.200 94.000 Poor True Pending -45 AREERTEASGSESRV None 0 0 29389.600 99.000 Poor True Pending +11 1 KSVNEALNHLLTEEE None 1 0 5425.500 69.000 Poor True Pending +24 1 SLMVCELAGNLFNCE None 1 0 5515.200 70.000 Poor True Pending +8 1 GGSHVWTHSRDPEGS None 1 0 6419.700 73.000 Poor True Pending +14 1 VQGIANQDAAQGIAK None 1 0 6577.200 73.000 Poor False Pending +23 1 SLMVCELAGNPFNCE None 1 0 6648.100 74.000 Poor True Pending +27 1 SLLHTVSPEPPRPPQ None 1 0 8706.600 79.000 Poor True Pending +13 1 VQGIANEDAAQGIAK None 1 0 9312.400 81.000 Poor False Pending +3 1 AAAAAVIPTVSTPPP None 1 0 9996.200 82.000 Poor True Pending +4 1 AAAAAVIPTVSTPPP None 1 0 9996.200 82.000 Poor True Pending +12 1 KSVNEALNNLLTEEE None 1 0 11571.600 85.000 Poor True Pending +22 1 EEEKTQEVKVKEPPK None 1 0 13934.400 88.000 Poor True Pending +21 1 EEEKPQEVKVKEPPK None 1 0 16895.300 92.000 Poor True Pending +46 1 EASGYESRVEPPHEN None 1 0 19617.200 94.000 Poor True Pending +45 1 AREERTEASGSESRV None 1 0 29389.600 99.000 Poor True Pending diff --git a/tests/test_data/pvacbind/combine_and_condense/combined/Test.all_epitopes.aggregated.tsv b/tests/test_data/pvacbind/combine_and_condense/combined/Test.all_epitopes.aggregated.tsv index 0443d905..c89ea9f4 100644 --- a/tests/test_data/pvacbind/combine_and_condense/combined/Test.all_epitopes.aggregated.tsv +++ b/tests/test_data/pvacbind/combine_and_condense/combined/Test.all_epitopes.aggregated.tsv @@ -41,9 +41,9 @@ ID DRB1*11:01 E*01:01 G*01:09 Best Peptide Prob Pos Num Included Peptides Num Pa 24 1 1 MVCELAGNL None 2 0 3454.020 4.100 Poor Pending 23 1 FNCECDLFG None 1 0 4778.520 6.200 Poor Pending 12 1 SVNEALNNL None 1 0 4989.870 7.300 Poor Pending -14 VQGIANQDAAQGIAK None 0 0 5209.800 69.230 Poor Pending -45 RTEASGSES None 0 0 5267.250 7.900 Poor Pending -46 GYESRVEPP None 0 0 5620.540 8.700 Poor Pending -13 AVQGIANED None 0 0 5743.490 9.000 Poor Pending -3 VIPTVSTPPP None 0 0 8664.370 1.800 Poor Pending -4 VIPTVSTPPP None 0 0 8664.370 1.800 Poor Pending +14 1 VQGIANQDAAQGIAK None 1 0 5209.800 69.230 Poor Pending +45 1 RTEASGSES None 1 0 5267.250 7.900 Poor Pending +46 1 GYESRVEPP None 1 0 5620.540 8.700 Poor Pending +13 1 AVQGIANED None 1 0 5743.490 9.000 Poor Pending +3 1 VIPTVSTPPP None 1 0 8664.370 1.800 Poor Pending +4 1 VIPTVSTPPP None 1 0 8664.370 1.800 Poor Pending diff --git a/tests/test_data/pvacfuse/arriba_fusions/MHC_Class_I/Test.all_epitopes.aggregated.tsv b/tests/test_data/pvacfuse/arriba_fusions/MHC_Class_I/Test.all_epitopes.aggregated.tsv index 9138ba82..4ab49744 100644 --- a/tests/test_data/pvacfuse/arriba_fusions/MHC_Class_I/Test.all_epitopes.aggregated.tsv +++ b/tests/test_data/pvacfuse/arriba_fusions/MHC_Class_I/Test.all_epitopes.aggregated.tsv @@ -9,6 +9,10 @@ ID A*29:02 Gene Best Peptide Best Transcript Allele Prob Pos Num Included Peptid 55.SERINC3-RNU6-317P(1181),BCAT2(623).ENST00000255175-..frameshift_fusion.82 1 SERINC3-RNU6-317P(1181),BCAT2(623) WNCRWESPY ENST00000255175-. HLA-A*29:02 None 1 1 389.270 0.950 NA 11 Pass Pending 10.UNC5C-ENSG00000254044.ENST00000453304-ENST00000521680.frameshift_fusion.61 6 UNC5C-ENSG00000254044 SYIQNCPLM ENST00000453304-ENST00000521680 HLA-A*29:02 None 6 1 443.400 1.000 NA 35 Pass Pending 23.MALT1-PRTG.ENST00000649217-..frameshift_fusion.50 3 MALT1-PRTG GVYAPSRFF ENST00000649217-. HLA-A*29:02 None 3 1 466.670 1.200 NA 11 Pass Pending +69.B4GALT1-ENSG00000271677(54939),ENOX2(20912).ENST00000535206-..frameshift_fusion.22 5 B4GALT1-ENSG00000271677(54939),ENOX2(20912) CLSMGHFLY ENST00000535206-. HLA-A*29:02 None 5 1 4.710 0.020 NA 3 LowReadSupport Pending +87.CRTC3-SNRPC.ENST00000268184-ENST00000244520.frameshift_fusion.48 2 CRTC3-SNRPC PWYDASTPY ENST00000268184-ENST00000244520 HLA-A*29:02 None 2 1 19.720 0.130 NA 2 LowReadSupport Pending +66.DEAF1-ENSG00000269915.ENST00000683307-..frameshift_fusion.43 1 DEAF1-ENSG00000269915 AAGGCHRLY ENST00000683307-. HLA-A*29:02 None 1 1 195.850 0.610 NA 4 LowReadSupport Pending +88.RAPGEF1-NUB1.ENST00000372195-ENST00000468404.frameshift_fusion.39 2 RAPGEF1-NUB1 VNSDPYVSY ENST00000372195-ENST00000468404 HLA-A*29:02 None 2 1 353.490 0.890 NA 2 LowReadSupport Pending 61.FOSL2-BABAM2.ENST00000264716-ENST00000344773.inframe_fusion.34 2 FOSL2-BABAM2 QVQYVIQGY ENST00000264716-ENST00000344773 HLA-A*29:02 None 2 0 537.280 1.200 NA 1 Poor Pending 40.BRINP2-ASTN1.ENST00000361539-..frameshift_fusion.50 4 BRINP2-ASTN1 RRWTCLFGY ENST00000361539-. HLA-A*29:02 None 4 0 611.990 1.300 NA 3 Poor Pending 18.PDIA5-ENSG00000280441.ENST00000316218-ENST00000623860.frameshift_fusion.45 2 PDIA5-ENSG00000280441 MTRVGTTEF ENST00000316218-ENST00000623860 HLA-A*29:02 None 2 0 670.310 1.400 NA 15 Poor Pending @@ -33,57 +37,53 @@ ID A*29:02 Gene Best Peptide Best Transcript Allele Prob Pos Num Included Peptid 67.PGAP1-PAX8.ENST00000354764-ENST00000681162.frameshift_fusion.11 1 PGAP1-PAX8 SFSQILGQI ENST00000354764-ENST00000681162 HLA-A*29:02 None 1 0 4431.220 4.000 NA 3 Poor Pending 38.TASP1-MACROD2.ENST00000337743-..frameshift_fusion.48 1 TASP1-MACROD2 VHADDAWRM ENST00000337743-. HLA-A*29:02 None 1 0 4749.090 4.200 NA 4 Poor Pending 37.MLLT10-AMD1P1.ENST00000631589-ENST00000457220.frameshift_fusion.49 1 MLLT10-AMD1P1 SVLISNMKM ENST00000631589-ENST00000457220 HLA-A*29:02 None 1 0 4988.200 4.300 NA 4 Poor Pending -7.DTNB-Y_RNA(12184),ASXL2(24381).ENST00000288642-..frameshift_fusion.22 DTNB-Y_RNA(12184),ASXL2(24381) QLFIEMLIH ENST00000288642-. HLA-A*29:02 None 0 0 5135.570 4.400 NA 53 Poor Pending -78.PCGF3-CPLX1.ENST00000362003-..frameshift_fusion.43 PCGF3-CPLX1 WLCRSSLAH ENST00000362003-. HLA-A*29:02 None 0 0 5314.310 4.500 NA 8 Poor Pending -11.TMEM104-RAB37.ENST00000335464-ENST00000340415.inframe_fusion.48 TMEM104-RAB37 YRIYLTILV ENST00000335464-ENST00000340415 HLA-A*29:02 None 0 0 6204.380 5.000 NA 32 Poor Pending -79.CT83-AGTR2(218431),RNU6-154P(7443).ENST00000371894-..frameshift_fusion.25 CT83-AGTR2(218431),RNU6-154P(7443) RFQSLTLLP ENST00000371894-. HLA-A*29:02 None 0 0 6291.790 5.100 NA 6 Poor Pending -48.WARS1-DEGS2.ENST00000355338-ENST00000305631.frameshift_fusion.50 WARS1-DEGS2 GIFFSHSQV ENST00000355338-ENST00000305631 HLA-A*29:02 None 0 0 6385.960 5.100 NA 16 Poor Pending -13.MDH1-LINC01278.ENST00000544381-ENST00000654880.frameshift_fusion.67 MDH1-LINC01278 MMSEVGSKV ENST00000544381-ENST00000654880 HLA-A*29:02 None 0 0 6491.430 5.200 NA 26 Poor Pending -75.REV1-REV1.ENST00000258428-ENST00000258428.frameshift_fusion.57 REV1-REV1 QWNLSWHLW ENST00000258428-ENST00000258428 HLA-A*29:02 None 0 0 6536.670 5.200 NA 16 Poor Pending -2.EIF3K-CYP39A1.ENST00000614624-ENST00000275016.inframe_fusion.58 EIF3K-CYP39A1 MLGDLSASI ENST00000614624-ENST00000275016 HLA-A*29:02 None 0 0 6540.210 5.200 NA 168 Poor Pending -56.ERO1A-FERMT2.ENST00000395686-ENST00000341590.inframe_fusion.42 ERO1A-FERMT2 FCEADGSIY ENST00000395686-ENST00000341590 HLA-A*29:02 None 0 0 6942.580 5.500 NA 9 Poor Pending -31.TBC1D16-ENSG00000225156.ENST00000310924-ENST00000425325.frameshift_fusion.45 TBC1D16-ENSG00000225156 SLQRWAPLL ENST00000310924-ENST00000425325 HLA-A*29:02 None 0 0 7337.630 5.700 NA 8 Poor Pending -34.EFTUD2-KIF18B.ENST00000426333-ENST00000593135.frameshift_fusion.44 EFTUD2-KIF18B KFFGEFTGW ENST00000426333-ENST00000593135 HLA-A*29:02 None 0 0 8064.860 6.200 NA 8 Poor Pending -85.SSBP4-ELL.ENST00000348495-..frameshift_fusion.36 SSBP4-ELL AFQDYRQGL ENST00000348495-. HLA-A*29:02 None 0 0 9254.420 7.000 NA 3 Poor Pending -14.ATG2B-ENSG00000285883(75498),CRAT37(26889).ENST00000359933-..frameshift_fusion.59 ATG2B-ENSG00000285883(75498),CRAT37(26889) QVQAILLPQ ENST00000359933-. HLA-A*29:02 None 0 0 9312.470 7.000 NA 24 Poor Pending -49.BGN-ATP2B3.ENST00000331595-ENST00000263519.frameshift_fusion.46 BGN-ATP2B3 QVSTLSSFL ENST00000331595-ENST00000263519 HLA-A*29:02 None 0 0 9507.950 7.200 NA 16 Poor Pending -30.MFSD3-MROH1.ENST00000301327-ENST00000326134.inframe_fusion.48 MFSD3-MROH1 QLAPRALQI ENST00000301327-ENST00000326134 HLA-A*29:02 None 0 0 9918.060 7.400 NA 9 Poor Pending -50.BGN-ATP2B3.ENST00000331595-ENST00000263519.frameshift_fusion.27 BGN-ATP2B3 AFSPPPNLA ENST00000331595-ENST00000263519 HLA-A*29:02 None 0 0 10308.770 7.700 NA 1 Poor Pending -74.IL13RA1-IL13RA1.ENST00000652600-ENST00000652600.frameshift_fusion.49 IL13RA1-IL13RA1 VFYAQKPGK ENST00000652600-ENST00000652600 HLA-A*29:02 None 0 0 10916.500 8.100 NA 17 Poor Pending -71.TMEM129-GUCY1B1.ENST00000303277-ENST00000264424.frameshift_fusion.44 TMEM129-GUCY1B1 WIRILSLES ENST00000303277-ENST00000264424 HLA-A*29:02 None 0 0 11227.110 8.300 NA 2 Poor Pending -64.SERINC3-BCAT2.ENST00000255175-..frameshift_fusion.36 SERINC3-BCAT2 ISIHPKIQM ENST00000255175-. HLA-A*29:02 None 0 0 12737.130 9.400 NA 5 Poor Pending -36.SLMAP-B3GNT7(30544),ZBTB8OSP2(2215).ENST00000659705-..frameshift_fusion.66 SLMAP-B3GNT7(30544),ZBTB8OSP2(2215) WFDHKTGKA ENST00000659705-. HLA-A*29:02 None 0 0 13736.780 12.000 NA 5 Poor Pending -73.FRMD3-FRMD3.ENST00000376438-ENST00000376438.inframe_fusion.40 FRMD3-FRMD3 LLLESGVPL ENST00000376438-ENST00000376438 HLA-A*29:02 None 0 0 15217.110 13.000 NA 30 Poor Pending -9.KMT2E-LHFPL3-AS2(2768),ENSG00000237513(11530).ENST00000311117-..frameshift_fusion.56 KMT2E-LHFPL3-AS2(2768),ENSG00000237513(11530) WLTPKIPAL ENST00000311117-. HLA-A*29:02 None 0 0 15445.690 13.000 NA 46 Poor Pending -24.LTBP1-BIRC6.ENST00000404816-ENST00000421745.inframe_fusion.60 LTBP1-BIRC6 IHSHDDLLE ENST00000404816-ENST00000421745 HLA-A*29:02 None 0 0 15544.280 13.000 NA 11 Poor Pending -54.PCK2-LINC00596(469),DHRS4-AS1(3182).ENST00000559250-..frameshift_fusion.40 PCK2-LINC00596(469),DHRS4-AS1(3182) VYEAFNWRS ENST00000559250-. HLA-A*29:02 None 0 0 15551.510 13.000 NA 12 Poor Pending -80.FBXW10-FBXW10.ENST00000308799-ENST00000308799.frameshift_fusion.26 FBXW10-FBXW10 SRHHRCVFF ENST00000308799-ENST00000308799 HLA-A*29:02 None 0 0 15866.960 13.000 NA 4 Poor Pending -32.KPNA1-EEFSEC.ENST00000344337-ENST00000254730.frameshift_fusion.33 KPNA1-EEFSEC VELLMGPDH ENST00000344337-ENST00000254730 HLA-A*29:02 None 0 0 16179.890 14.000 NA 8 Poor Pending -59.ATAD1-ENSG00000224745.ENST00000680388-..frameshift_fusion.34 ATAD1-ENSG00000224745 DHSCQVLIM ENST00000680388-. HLA-A*29:02 None 0 0 16720.560 14.000 NA 7 Poor Pending -25.WDR1-ENSG00000271544(16068),RAF1P1(623).ENST00000382452-..frameshift_fusion.35 WDR1-ENSG00000271544(16068),RAF1P1(623) FKFTVGGEL ENST00000382452-. HLA-A*29:02 None 0 0 17395.990 15.000 NA 11 Poor Pending -52.PDLIM5-ENSG00000287552.ENST00000615540-ENST00000667612.frameshift_fusion.47 PDLIM5-ENSG00000287552 ANLNCRLLK ENST00000615540-ENST00000667612 HLA-A*29:02 None 0 0 17720.270 15.000 NA 14 Poor Pending -58.AGPAT5-MCPH1-AS1.ENST00000285518-..frameshift_fusion.68 AGPAT5-MCPH1-AS1 FENYTGVQV ENST00000285518-. HLA-A*29:02 None 0 0 19576.230 17.000 NA 8 Poor Pending -68.SHQ1-HNRNPA3P8(24281),ENSG00000242586(200566).ENST00000325599-..frameshift_fusion.64 SHQ1-HNRNPA3P8(24281),ENSG00000242586(200566) VWIQKVNQV ENST00000325599-. HLA-A*29:02 None 0 0 20048.460 18.000 NA 3 Poor Pending -92.CLTC-LAMC1.ENST00000621829-ENST00000258341.inframe_fusion.55 CLTC-LAMC1 TWKDSQAAQ ENST00000621829-ENST00000258341 HLA-A*29:02 None 0 0 20222.090 18.000 NA 2 Poor Pending -84.ST3GAL4-KIRREL3.ENST00000444328-..frameshift_fusion.20 ST3GAL4-KIRREL3 GDSKVAGGF ENST00000444328-. HLA-A*29:02 None 0 0 21608.330 20.000 NA 3 Poor Pending -3.EIF3K-CYP39A1.ENST00000614624-ENST00000275016.inframe_fusion.13 EIF3K-CYP39A1 KSSIPKNVF ENST00000614624-ENST00000275016 HLA-A*29:02 None 0 0 22972.240 22.000 NA 1 Poor Pending -42.HNRNPUL2-BSCL2-AHNAK.ENST00000403734-ENST00000257247.inframe_fusion.30 HNRNPUL2-BSCL2-AHNAK GYGDQIVGA ENST00000403734-ENST00000257247 HLA-A*29:02 None 0 0 23093.850 22.000 NA 0 Poor Pending -45.HNRNPUL2-AHNAK.ENST00000301785-ENST00000257247.inframe_fusion.30 HNRNPUL2-AHNAK GYGDQIVGA ENST00000301785-ENST00000257247 HLA-A*29:02 None 0 0 23093.850 22.000 NA 0 Poor Pending -70.GRIK2-GRIK2.ENST00000421544-..frameshift_fusion.34 GRIK2-GRIK2 VSSASRANI ENST00000421544-. HLA-A*29:02 None 0 0 23249.290 22.000 NA 2 Poor Pending -86.RALGPS2-TTC32.ENST00000367634-ENST00000333610.frameshift_fusion.69 RALGPS2-TTC32 CQSNKQQQM ENST00000367634-ENST00000333610 HLA-A*29:02 None 0 0 23876.680 23.000 NA 2 Poor Pending -4.PLA2R1-RBMS1.ENST00000283243-ENST00000348849.inframe_fusion.72 PLA2R1-RBMS1 FIHSKIKAQ ENST00000283243-ENST00000348849 HLA-A*29:02 None 0 0 26500.160 28.000 NA 87 Poor Pending -41.HNRNPUL2-BSCL2-AHNAK.ENST00000403734-ENST00000257247.frameshift_fusion.51 HNRNPUL2-BSCL2-AHNAK GYGCDRDSR ENST00000403734-ENST00000257247 HLA-A*29:02 None 0 0 27023.080 29.000 NA 40 Poor Pending -44.HNRNPUL2-AHNAK.ENST00000301785-ENST00000257247.frameshift_fusion.51 HNRNPUL2-AHNAK GYGCDRDSR ENST00000301785-ENST00000257247 HLA-A*29:02 None 0 0 27023.080 29.000 NA 40 Poor Pending -89.CAMK2D-LUC7L2.ENST00000683023-ENST00000541170.inframe_fusion.34 CAMK2D-LUC7L2 LSARGDTTR ENST00000683023-ENST00000541170 HLA-A*29:02 None 0 0 29338.800 35.000 NA 2 Poor Pending -93.CAMK2D-FMC1-LUC7L2.ENST00000683023-ENST00000541515.inframe_fusion.34 CAMK2D-FMC1-LUC7L2 LSARGDTTR ENST00000683023-ENST00000541515 HLA-A*29:02 None 0 0 29338.800 35.000 NA 2 Poor Pending -81.ODF2-SPTAN1.ENST00000604420-ENST00000372731.frameshift_fusion.11 ODF2-SPTAN1 SSGGSPRPV ENST00000604420-ENST00000372731 HLA-A*29:02 None 0 0 29811.750 36.000 NA 3 Poor Pending -72.SOX6-SOX6.ENST00000396356-ENST00000396356.inframe_fusion.56 SOX6-SOX6 KDSSCMEKL ENST00000396356-ENST00000396356 HLA-A*29:02 None 0 0 31278.870 40.000 NA 49 Poor Pending -6.UNC5C-STPG2-AS1.ENST00000453304-..frameshift_fusion.53 UNC5C-STPG2-AS1 PEGIPVAEI ENST00000453304-. HLA-A*29:02 None 0 0 31407.380 41.000 NA 59 Poor Pending -43.HNRNPUL2-BSCL2-AHNAK.ENST00000403734-ENST00000257247.frameshift_fusion.50 HNRNPUL2-BSCL2-AHNAK RSRGQGYDG ENST00000403734-ENST00000257247 HLA-A*29:02 None 0 0 32059.380 43.000 NA 0 Poor Pending -46.HNRNPUL2-AHNAK.ENST00000301785-ENST00000257247.frameshift_fusion.50 HNRNPUL2-AHNAK RSRGQGYDG ENST00000301785-ENST00000257247 HLA-A*29:02 None 0 0 32059.380 43.000 NA 0 Poor Pending -17.ATAD1-PTEN.ENST00000680388-..frameshift_fusion.57 ATAD1-PTEN TDHSCQATR ENST00000680388-. HLA-A*29:02 None 0 0 33708.870 49.000 NA 16 Poor Pending -82.ODF2-SPTAN1.ENST00000393533-ENST00000372731.frameshift_fusion.9 ODF2-SPTAN1 QQGPHQNRP ENST00000393533-ENST00000372731 HLA-A*29:02 None 0 0 37840.150 67.000 NA 1 Poor Pending -69.B4GALT1-ENSG00000271677(54939),ENOX2(20912).ENST00000535206-..frameshift_fusion.22 5 B4GALT1-ENSG00000271677(54939),ENOX2(20912) CLSMGHFLY ENST00000535206-. HLA-A*29:02 None 5 1 4.710 0.020 NA 3 LowReadSupport Pending -87.CRTC3-SNRPC.ENST00000268184-ENST00000244520.frameshift_fusion.48 2 CRTC3-SNRPC PWYDASTPY ENST00000268184-ENST00000244520 HLA-A*29:02 None 2 1 19.720 0.130 NA 2 LowReadSupport Pending -66.DEAF1-ENSG00000269915.ENST00000683307-..frameshift_fusion.43 1 DEAF1-ENSG00000269915 AAGGCHRLY ENST00000683307-. HLA-A*29:02 None 1 1 195.850 0.610 NA 4 LowReadSupport Pending -88.RAPGEF1-NUB1.ENST00000372195-ENST00000468404.frameshift_fusion.39 2 RAPGEF1-NUB1 VNSDPYVSY ENST00000372195-ENST00000468404 HLA-A*29:02 None 2 1 353.490 0.890 NA 2 LowReadSupport Pending +7.DTNB-Y_RNA(12184),ASXL2(24381).ENST00000288642-..frameshift_fusion.22 1 DTNB-Y_RNA(12184),ASXL2(24381) QLFIEMLIH ENST00000288642-. HLA-A*29:02 None 1 0 5135.570 4.400 NA 53 Poor Pending +78.PCGF3-CPLX1.ENST00000362003-..frameshift_fusion.43 1 PCGF3-CPLX1 WLCRSSLAH ENST00000362003-. HLA-A*29:02 None 1 0 5314.310 4.500 NA 8 Poor Pending +11.TMEM104-RAB37.ENST00000335464-ENST00000340415.inframe_fusion.48 1 TMEM104-RAB37 YRIYLTILV ENST00000335464-ENST00000340415 HLA-A*29:02 None 1 0 6204.380 5.000 NA 32 Poor Pending +79.CT83-AGTR2(218431),RNU6-154P(7443).ENST00000371894-..frameshift_fusion.25 1 CT83-AGTR2(218431),RNU6-154P(7443) RFQSLTLLP ENST00000371894-. HLA-A*29:02 None 1 0 6291.790 5.100 NA 6 Poor Pending +48.WARS1-DEGS2.ENST00000355338-ENST00000305631.frameshift_fusion.50 1 WARS1-DEGS2 GIFFSHSQV ENST00000355338-ENST00000305631 HLA-A*29:02 None 1 0 6385.960 5.100 NA 16 Poor Pending +13.MDH1-LINC01278.ENST00000544381-ENST00000654880.frameshift_fusion.67 1 MDH1-LINC01278 MMSEVGSKV ENST00000544381-ENST00000654880 HLA-A*29:02 None 1 0 6491.430 5.200 NA 26 Poor Pending +75.REV1-REV1.ENST00000258428-ENST00000258428.frameshift_fusion.57 1 REV1-REV1 QWNLSWHLW ENST00000258428-ENST00000258428 HLA-A*29:02 None 1 0 6536.670 5.200 NA 16 Poor Pending +2.EIF3K-CYP39A1.ENST00000614624-ENST00000275016.inframe_fusion.58 1 EIF3K-CYP39A1 MLGDLSASI ENST00000614624-ENST00000275016 HLA-A*29:02 None 1 0 6540.210 5.200 NA 168 Poor Pending +56.ERO1A-FERMT2.ENST00000395686-ENST00000341590.inframe_fusion.42 1 ERO1A-FERMT2 FCEADGSIY ENST00000395686-ENST00000341590 HLA-A*29:02 None 1 0 6942.580 5.500 NA 9 Poor Pending +31.TBC1D16-ENSG00000225156.ENST00000310924-ENST00000425325.frameshift_fusion.45 1 TBC1D16-ENSG00000225156 SLQRWAPLL ENST00000310924-ENST00000425325 HLA-A*29:02 None 1 0 7337.630 5.700 NA 8 Poor Pending +34.EFTUD2-KIF18B.ENST00000426333-ENST00000593135.frameshift_fusion.44 1 EFTUD2-KIF18B KFFGEFTGW ENST00000426333-ENST00000593135 HLA-A*29:02 None 1 0 8064.860 6.200 NA 8 Poor Pending +85.SSBP4-ELL.ENST00000348495-..frameshift_fusion.36 1 SSBP4-ELL AFQDYRQGL ENST00000348495-. HLA-A*29:02 None 1 0 9254.420 7.000 NA 3 Poor Pending +14.ATG2B-ENSG00000285883(75498),CRAT37(26889).ENST00000359933-..frameshift_fusion.59 1 ATG2B-ENSG00000285883(75498),CRAT37(26889) QVQAILLPQ ENST00000359933-. HLA-A*29:02 None 1 0 9312.470 7.000 NA 24 Poor Pending +49.BGN-ATP2B3.ENST00000331595-ENST00000263519.frameshift_fusion.46 1 BGN-ATP2B3 QVSTLSSFL ENST00000331595-ENST00000263519 HLA-A*29:02 None 1 0 9507.950 7.200 NA 16 Poor Pending +30.MFSD3-MROH1.ENST00000301327-ENST00000326134.inframe_fusion.48 1 MFSD3-MROH1 QLAPRALQI ENST00000301327-ENST00000326134 HLA-A*29:02 None 1 0 9918.060 7.400 NA 9 Poor Pending +50.BGN-ATP2B3.ENST00000331595-ENST00000263519.frameshift_fusion.27 1 BGN-ATP2B3 AFSPPPNLA ENST00000331595-ENST00000263519 HLA-A*29:02 None 1 0 10308.770 7.700 NA 1 Poor Pending +74.IL13RA1-IL13RA1.ENST00000652600-ENST00000652600.frameshift_fusion.49 1 IL13RA1-IL13RA1 VFYAQKPGK ENST00000652600-ENST00000652600 HLA-A*29:02 None 1 0 10916.500 8.100 NA 17 Poor Pending +71.TMEM129-GUCY1B1.ENST00000303277-ENST00000264424.frameshift_fusion.44 1 TMEM129-GUCY1B1 WIRILSLES ENST00000303277-ENST00000264424 HLA-A*29:02 None 1 0 11227.110 8.300 NA 2 Poor Pending +64.SERINC3-BCAT2.ENST00000255175-..frameshift_fusion.36 1 SERINC3-BCAT2 ISIHPKIQM ENST00000255175-. HLA-A*29:02 None 1 0 12737.130 9.400 NA 5 Poor Pending +36.SLMAP-B3GNT7(30544),ZBTB8OSP2(2215).ENST00000659705-..frameshift_fusion.66 1 SLMAP-B3GNT7(30544),ZBTB8OSP2(2215) WFDHKTGKA ENST00000659705-. HLA-A*29:02 None 1 0 13736.780 12.000 NA 5 Poor Pending +73.FRMD3-FRMD3.ENST00000376438-ENST00000376438.inframe_fusion.40 1 FRMD3-FRMD3 LLLESGVPL ENST00000376438-ENST00000376438 HLA-A*29:02 None 1 0 15217.110 13.000 NA 30 Poor Pending +9.KMT2E-LHFPL3-AS2(2768),ENSG00000237513(11530).ENST00000311117-..frameshift_fusion.56 1 KMT2E-LHFPL3-AS2(2768),ENSG00000237513(11530) WLTPKIPAL ENST00000311117-. HLA-A*29:02 None 1 0 15445.690 13.000 NA 46 Poor Pending +24.LTBP1-BIRC6.ENST00000404816-ENST00000421745.inframe_fusion.60 1 LTBP1-BIRC6 IHSHDDLLE ENST00000404816-ENST00000421745 HLA-A*29:02 None 1 0 15544.280 13.000 NA 11 Poor Pending +54.PCK2-LINC00596(469),DHRS4-AS1(3182).ENST00000559250-..frameshift_fusion.40 1 PCK2-LINC00596(469),DHRS4-AS1(3182) VYEAFNWRS ENST00000559250-. HLA-A*29:02 None 1 0 15551.510 13.000 NA 12 Poor Pending +80.FBXW10-FBXW10.ENST00000308799-ENST00000308799.frameshift_fusion.26 1 FBXW10-FBXW10 SRHHRCVFF ENST00000308799-ENST00000308799 HLA-A*29:02 None 1 0 15866.960 13.000 NA 4 Poor Pending +32.KPNA1-EEFSEC.ENST00000344337-ENST00000254730.frameshift_fusion.33 1 KPNA1-EEFSEC VELLMGPDH ENST00000344337-ENST00000254730 HLA-A*29:02 None 1 0 16179.890 14.000 NA 8 Poor Pending +59.ATAD1-ENSG00000224745.ENST00000680388-..frameshift_fusion.34 1 ATAD1-ENSG00000224745 DHSCQVLIM ENST00000680388-. HLA-A*29:02 None 1 0 16720.560 14.000 NA 7 Poor Pending +25.WDR1-ENSG00000271544(16068),RAF1P1(623).ENST00000382452-..frameshift_fusion.35 1 WDR1-ENSG00000271544(16068),RAF1P1(623) FKFTVGGEL ENST00000382452-. HLA-A*29:02 None 1 0 17395.990 15.000 NA 11 Poor Pending +52.PDLIM5-ENSG00000287552.ENST00000615540-ENST00000667612.frameshift_fusion.47 1 PDLIM5-ENSG00000287552 ANLNCRLLK ENST00000615540-ENST00000667612 HLA-A*29:02 None 1 0 17720.270 15.000 NA 14 Poor Pending +58.AGPAT5-MCPH1-AS1.ENST00000285518-..frameshift_fusion.68 1 AGPAT5-MCPH1-AS1 FENYTGVQV ENST00000285518-. HLA-A*29:02 None 1 0 19576.230 17.000 NA 8 Poor Pending +68.SHQ1-HNRNPA3P8(24281),ENSG00000242586(200566).ENST00000325599-..frameshift_fusion.64 1 SHQ1-HNRNPA3P8(24281),ENSG00000242586(200566) VWIQKVNQV ENST00000325599-. HLA-A*29:02 None 1 0 20048.460 18.000 NA 3 Poor Pending +92.CLTC-LAMC1.ENST00000621829-ENST00000258341.inframe_fusion.55 1 CLTC-LAMC1 TWKDSQAAQ ENST00000621829-ENST00000258341 HLA-A*29:02 None 1 0 20222.090 18.000 NA 2 Poor Pending +84.ST3GAL4-KIRREL3.ENST00000444328-..frameshift_fusion.20 1 ST3GAL4-KIRREL3 GDSKVAGGF ENST00000444328-. HLA-A*29:02 None 1 0 21608.330 20.000 NA 3 Poor Pending +3.EIF3K-CYP39A1.ENST00000614624-ENST00000275016.inframe_fusion.13 1 EIF3K-CYP39A1 KSSIPKNVF ENST00000614624-ENST00000275016 HLA-A*29:02 None 1 0 22972.240 22.000 NA 1 Poor Pending +42.HNRNPUL2-BSCL2-AHNAK.ENST00000403734-ENST00000257247.inframe_fusion.30 1 HNRNPUL2-BSCL2-AHNAK GYGDQIVGA ENST00000403734-ENST00000257247 HLA-A*29:02 None 1 0 23093.850 22.000 NA 0 Poor Pending +45.HNRNPUL2-AHNAK.ENST00000301785-ENST00000257247.inframe_fusion.30 1 HNRNPUL2-AHNAK GYGDQIVGA ENST00000301785-ENST00000257247 HLA-A*29:02 None 1 0 23093.850 22.000 NA 0 Poor Pending +70.GRIK2-GRIK2.ENST00000421544-..frameshift_fusion.34 1 GRIK2-GRIK2 VSSASRANI ENST00000421544-. HLA-A*29:02 None 1 0 23249.290 22.000 NA 2 Poor Pending +86.RALGPS2-TTC32.ENST00000367634-ENST00000333610.frameshift_fusion.69 1 RALGPS2-TTC32 CQSNKQQQM ENST00000367634-ENST00000333610 HLA-A*29:02 None 1 0 23876.680 23.000 NA 2 Poor Pending +4.PLA2R1-RBMS1.ENST00000283243-ENST00000348849.inframe_fusion.72 1 PLA2R1-RBMS1 FIHSKIKAQ ENST00000283243-ENST00000348849 HLA-A*29:02 None 1 0 26500.160 28.000 NA 87 Poor Pending +41.HNRNPUL2-BSCL2-AHNAK.ENST00000403734-ENST00000257247.frameshift_fusion.51 1 HNRNPUL2-BSCL2-AHNAK GYGCDRDSR ENST00000403734-ENST00000257247 HLA-A*29:02 None 1 0 27023.080 29.000 NA 40 Poor Pending +44.HNRNPUL2-AHNAK.ENST00000301785-ENST00000257247.frameshift_fusion.51 1 HNRNPUL2-AHNAK GYGCDRDSR ENST00000301785-ENST00000257247 HLA-A*29:02 None 1 0 27023.080 29.000 NA 40 Poor Pending +89.CAMK2D-LUC7L2.ENST00000683023-ENST00000541170.inframe_fusion.34 1 CAMK2D-LUC7L2 LSARGDTTR ENST00000683023-ENST00000541170 HLA-A*29:02 None 1 0 29338.800 35.000 NA 2 Poor Pending +93.CAMK2D-FMC1-LUC7L2.ENST00000683023-ENST00000541515.inframe_fusion.34 1 CAMK2D-FMC1-LUC7L2 LSARGDTTR ENST00000683023-ENST00000541515 HLA-A*29:02 None 1 0 29338.800 35.000 NA 2 Poor Pending +81.ODF2-SPTAN1.ENST00000604420-ENST00000372731.frameshift_fusion.11 1 ODF2-SPTAN1 SSGGSPRPV ENST00000604420-ENST00000372731 HLA-A*29:02 None 1 0 29811.750 36.000 NA 3 Poor Pending +72.SOX6-SOX6.ENST00000396356-ENST00000396356.inframe_fusion.56 1 SOX6-SOX6 KDSSCMEKL ENST00000396356-ENST00000396356 HLA-A*29:02 None 1 0 31278.870 40.000 NA 49 Poor Pending +6.UNC5C-STPG2-AS1.ENST00000453304-..frameshift_fusion.53 1 UNC5C-STPG2-AS1 PEGIPVAEI ENST00000453304-. HLA-A*29:02 None 1 0 31407.380 41.000 NA 59 Poor Pending +43.HNRNPUL2-BSCL2-AHNAK.ENST00000403734-ENST00000257247.frameshift_fusion.50 1 HNRNPUL2-BSCL2-AHNAK RSRGQGYDG ENST00000403734-ENST00000257247 HLA-A*29:02 None 1 0 32059.380 43.000 NA 0 Poor Pending +46.HNRNPUL2-AHNAK.ENST00000301785-ENST00000257247.frameshift_fusion.50 1 HNRNPUL2-AHNAK RSRGQGYDG ENST00000301785-ENST00000257247 HLA-A*29:02 None 1 0 32059.380 43.000 NA 0 Poor Pending +17.ATAD1-PTEN.ENST00000680388-..frameshift_fusion.57 1 ATAD1-PTEN TDHSCQATR ENST00000680388-. HLA-A*29:02 None 1 0 33708.870 49.000 NA 16 Poor Pending +82.ODF2-SPTAN1.ENST00000393533-ENST00000372731.frameshift_fusion.9 1 ODF2-SPTAN1 QQGPHQNRP ENST00000393533-ENST00000372731 HLA-A*29:02 None 1 0 37840.150 67.000 NA 1 Poor Pending diff --git a/tests/test_data/pvacfuse/combined/Test.all_epitopes.aggregated.tsv b/tests/test_data/pvacfuse/combined/Test.all_epitopes.aggregated.tsv index e6590405..916b61c7 100644 --- a/tests/test_data/pvacfuse/combined/Test.all_epitopes.aggregated.tsv +++ b/tests/test_data/pvacfuse/combined/Test.all_epitopes.aggregated.tsv @@ -26,11 +26,11 @@ ID A*29:02 DRB1*11:01 Gene Best Peptide Best Transcript Allele Prob Pos Num Incl 31.TIMP3-TMEM35B.ENST00000266085-ENST00000373337.frameshift_fusion.167 9 TIMP3-TMEM35B KNECLWTDRGVGQAL ENST00000266085-ENST00000373337 HLA-DRB1*11:01 None 9 0 967.800 34.000 NA NA Poor Pending 27.SMG1-PHF20.ENST00000446231-ENST00000374012.frameshift_fusion.3540 2 SMG1-PHF20 ATYQPSFAADDKAST ENST00000446231-ENST00000374012 HLA-DRB1*11:01 None 2 0 3365.800 58.000 NA NA Poor Pending 29.TAOK3-MARCH1.ENST00000392533-ENST00000503008.frameshift_fusion.214 2 TAOK3-MARCH1 KVDIWSLGITCIELV ENST00000392533-ENST00000503008 HLA-DRB1*11:01 None 2 0 3702.500 61.000 NA NA Poor Pending -28.SNRPB2-METTL18.ENST00000246071-ENST00000310392.frameshift_fusion.215 SNRPB2-METTL18 AARDALQGFKITPSQ ENST00000246071-ENST00000310392 HLA-DRB1*11:01 None 0 0 5520.300 70.000 NA NA Poor Pending -38.TUB-RIC3.ENST00000305253-ENST00000309737.frameshift_fusion.165 TUB-RIC3 TRPTAPASAKRTKAA ENST00000305253-ENST00000309737 HLA-DRB1*11:01 None 0 0 6022.200 72.000 NA NA Poor Pending -17.MAX-TMEM260.ENST00000358664-ENST00000261556.frameshift_fusion.57 MAX-TMEM260 HSLRDSVPSLQGEKG ENST00000358664-ENST00000261556 HLA-DRB1*11:01 None 0 0 6591.000 73.000 NA NA Poor Pending -3.BTBD8-ELAVL4.ENST00000342818-ENST00000357083.frameshift_fusion.181 BTBD8-ELAVL4 FISNGSPQL ENST00000342818-ENST00000357083 HLA-A*29:02 None 0 0 7438.830 5.800 NA NA Poor Pending -5.CEP192-TMEM260.ENST00000506447-ENST00000261556.inframe_fusion.1724 CEP192-TMEM260 IVSFTPKDPEACEES ENST00000506447-ENST00000261556 HLA-DRB1*11:01 None 0 0 8015.600 77.000 NA NA Poor Pending -6.CLEC16A-RMI2.ENST00000409790-ENST00000312499.frameshift_fusion.242 CLEC16A-RMI2 SHVIELDDCVQTDEE ENST00000409790-ENST00000312499 HLA-DRB1*11:01 None 0 0 15376.500 90.000 NA NA Poor Pending -32.TIMP3-COL3A1.ENST00000266085-ENST00000304636.frameshift_fusion.211 TIMP3-COL3A1 PDKSIINATDPGPEA ENST00000266085-ENST00000304636 HLA-DRB1*11:01 None 0 0 15900.100 91.000 NA NA Poor Pending -19.MIPOL1-PGAP1.ENST00000327441-ENST00000354764.frameshift_fusion.6 MIPOL1-PGAP1 NWSKVCCRL ENST00000327441-ENST00000354764 HLA-A*29:02 None 0 0 19941.140 18.000 NA NA Poor Pending +28.SNRPB2-METTL18.ENST00000246071-ENST00000310392.frameshift_fusion.215 1 SNRPB2-METTL18 AARDALQGFKITPSQ ENST00000246071-ENST00000310392 HLA-DRB1*11:01 None 1 0 5520.300 70.000 NA NA Poor Pending +38.TUB-RIC3.ENST00000305253-ENST00000309737.frameshift_fusion.165 1 TUB-RIC3 TRPTAPASAKRTKAA ENST00000305253-ENST00000309737 HLA-DRB1*11:01 None 1 0 6022.200 72.000 NA NA Poor Pending +17.MAX-TMEM260.ENST00000358664-ENST00000261556.frameshift_fusion.57 1 MAX-TMEM260 HSLRDSVPSLQGEKG ENST00000358664-ENST00000261556 HLA-DRB1*11:01 None 1 0 6591.000 73.000 NA NA Poor Pending +3.BTBD8-ELAVL4.ENST00000342818-ENST00000357083.frameshift_fusion.181 1 BTBD8-ELAVL4 FISNGSPQL ENST00000342818-ENST00000357083 HLA-A*29:02 None 1 0 7438.830 5.800 NA NA Poor Pending +5.CEP192-TMEM260.ENST00000506447-ENST00000261556.inframe_fusion.1724 1 CEP192-TMEM260 IVSFTPKDPEACEES ENST00000506447-ENST00000261556 HLA-DRB1*11:01 None 1 0 8015.600 77.000 NA NA Poor Pending +6.CLEC16A-RMI2.ENST00000409790-ENST00000312499.frameshift_fusion.242 1 CLEC16A-RMI2 SHVIELDDCVQTDEE ENST00000409790-ENST00000312499 HLA-DRB1*11:01 None 1 0 15376.500 90.000 NA NA Poor Pending +32.TIMP3-COL3A1.ENST00000266085-ENST00000304636.frameshift_fusion.211 1 TIMP3-COL3A1 PDKSIINATDPGPEA ENST00000266085-ENST00000304636 HLA-DRB1*11:01 None 1 0 15900.100 91.000 NA NA Poor Pending +19.MIPOL1-PGAP1.ENST00000327441-ENST00000354764.frameshift_fusion.6 1 MIPOL1-PGAP1 NWSKVCCRL ENST00000327441-ENST00000354764 HLA-A*29:02 None 1 0 19941.140 18.000 NA NA Poor Pending diff --git a/tests/test_data/pvacfuse/fusions/MHC_Class_I/Test.all_epitopes.aggregated.tsv b/tests/test_data/pvacfuse/fusions/MHC_Class_I/Test.all_epitopes.aggregated.tsv index 105d1cc3..5738d01f 100644 --- a/tests/test_data/pvacfuse/fusions/MHC_Class_I/Test.all_epitopes.aggregated.tsv +++ b/tests/test_data/pvacfuse/fusions/MHC_Class_I/Test.all_epitopes.aggregated.tsv @@ -12,25 +12,25 @@ ID A*29:02 Gene Best Peptide Best Transcript Allele Prob Pos Num Included Peptid 37.TTC39B-C6orf62.ENST00000512701-ENST00000378119.inframe_fusion.465 1 TTC39B-C6orf62 KWSKAKFEF ENST00000512701-ENST00000378119 HLA-A*29:02 None 1 0 4132.470 3.800 NA NA Poor True Pending 11.DNAJC7-CDK17.ENST00000457167-ENST00000261211.frameshift_fusion.25 1 DNAJC7-CDK17 IKGFKTCKY ENST00000457167-ENST00000261211 HLA-A*29:02 None 1 0 4464.320 4.000 NA NA Poor True Pending 12.DNAJC7-CDK17.ENST00000457167-ENST00000261211.frameshift_fusion.25 1 DNAJC7-CDK17 IKGFKTCKY ENST00000457167-ENST00000261211 HLA-A*29:02 None 1 0 4464.320 4.000 NA NA Poor True Pending -3.BTBD8-ELAVL4.ENST00000342818-ENST00000357083.frameshift_fusion.181 BTBD8-ELAVL4 FISNGSPQL ENST00000342818-ENST00000357083 HLA-A*29:02 None 0 0 7438.830 5.800 NA NA Poor True Pending -18.MED31-RFC1.ENST00000225728-ENST00000381897.frameshift_fusion.131 MED31-RFC1 SMIQIQSQR ENST00000225728-ENST00000381897 HLA-A*29:02 None 0 0 7538.090 5.900 NA NA Poor True Pending -14.HBS1L-BCAS3.ENST00000367837-ENST00000390652.inframe_fusion.435 HBS1L-BCAS3 FLKQAGFKV ENST00000367837-ENST00000390652 HLA-A*29:02 None 0 0 10032.580 7.500 NA NA Poor True Pending -31.TIMP3-TMEM35B.ENST00000266085-ENST00000373337.frameshift_fusion.167 TIMP3-TMEM35B SFGADECPV ENST00000266085-ENST00000373337 HLA-A*29:02 None 0 0 12379.260 9.100 NA NA Poor True Pending -1.ABCA12-EXTL2.ENST00000272895-ENST00000370114.frameshift_fusion.1659 ABCA12-EXTL2 VMEVLKCKH ENST00000272895-ENST00000370114 HLA-A*29:02 None 0 0 14503.370 12.000 NA NA Poor True Pending -29.TAOK3-MARCH1.ENST00000392533-ENST00000503008.frameshift_fusion.214 TAOK3-MARCH1 LVGETTDDH ENST00000392533-ENST00000503008 HLA-A*29:02 None 0 0 16432.350 14.000 NA NA Poor True Pending -27.SMG1-PHF20.ENST00000446231-ENST00000374012.frameshift_fusion.3540 SMG1-PHF20 SFAADDKAS ENST00000446231-ENST00000374012 HLA-A*29:02 None 0 0 17955.930 15.000 NA NA Poor True Pending -24.SAAL1-HNRNPC.ENST00000524803-ENST00000554455.frameshift_fusion.346 SAAL1-HNRNPC YLKIEKWPA ENST00000524803-ENST00000554455 HLA-A*29:02 None 0 0 19752.610 17.000 NA NA Poor True Pending -19.MIPOL1-PGAP1.ENST00000327441-ENST00000354764.frameshift_fusion.6 MIPOL1-PGAP1 NWSKVCCRL ENST00000327441-ENST00000354764 HLA-A*29:02 None 0 0 19941.140 18.000 NA NA Poor False Pending -41.ZC3H11A-KLHL12.ENST00000545588-ENST00000367261.frameshift_fusion.291 ZC3H11A-KLHL12 KRKFSAGGF ENST00000545588-ENST00000367261 HLA-A*29:02 None 0 0 20599.710 19.000 NA NA Poor True Pending -21.PHTF1-YARS.ENST00000369604-ENST00000373477.inframe_fusion.15 PHTF1-YARS WYQKKESKI ENST00000369604-ENST00000373477 HLA-A*29:02 None 0 0 21517.340 20.000 NA NA Poor True Pending -36.TTC26-NDUFV2.ENST00000464848-ENST00000318388.inframe_fusion.239 TTC26-NDUFV2 LYNGRAAEG ENST00000464848-ENST00000318388 HLA-A*29:02 None 0 0 24401.630 24.000 NA NA Poor True Pending -34.TPM3-GATAD2B.ENST00000368530-ENST00000368655.inframe_fusion.81 TPM3-GATAD2B DMDRMTEDA ENST00000368530-ENST00000368655 HLA-A*29:02 None 0 0 24709.020 25.000 NA NA Poor True Pending -28.SNRPB2-METTL18.ENST00000246071-ENST00000310392.frameshift_fusion.215 SNRPB2-METTL18 QGFKITPSQ ENST00000246071-ENST00000310392 HLA-A*29:02 None 0 0 27021.620 29.000 NA NA Poor True Pending -2.AMD1-REV3L.ENST00000368885-ENST00000358835.inframe_fusion.36 AMD1-REV3L IPREIGGRL ENST00000368885-ENST00000358835 HLA-A*29:02 None 0 0 28400.540 32.000 NA NA Poor True Pending -32.TIMP3-COL3A1.ENST00000266085-ENST00000304636.frameshift_fusion.211 TIMP3-COL3A1 INATDPGPE ENST00000266085-ENST00000304636 HLA-A*29:02 None 0 0 28451.910 33.000 NA NA Poor True Pending -4.CDC37L1-BTG3.ENST00000381854-ENST00000339775.frameshift_fusion.169 CDC37L1-BTG3 YEQKIRHFD ENST00000381854-ENST00000339775 HLA-A*29:02 None 0 0 28661.390 33.000 NA NA Poor True Pending -15.LCORL-GNAS.ENST00000382226-ENST00000371100.inframe_fusion.143 LCORL-GNAS LFRKKGAGE ENST00000382226-ENST00000371100 HLA-A*29:02 None 0 0 29148.000 34.000 NA NA Poor True Pending -6.CLEC16A-RMI2.ENST00000409790-ENST00000312499.frameshift_fusion.242 CLEC16A-RMI2 GDGSGSGLQ ENST00000409790-ENST00000312499 HLA-A*29:02 None 0 0 29331.180 35.000 NA NA Poor True Pending -38.TUB-RIC3.ENST00000305253-ENST00000309737.frameshift_fusion.165 TUB-RIC3 ASAKRTKAA ENST00000305253-ENST00000309737 HLA-A*29:02 None 0 0 34397.110 51.000 NA NA Poor True Pending -5.CEP192-TMEM260.ENST00000506447-ENST00000261556.inframe_fusion.1724 CEP192-TMEM260 ESVCDQRTN ENST00000506447-ENST00000261556 HLA-A*29:02 None 0 0 37430.500 64.000 NA NA Poor True Pending -17.MAX-TMEM260.ENST00000358664-ENST00000261556.frameshift_fusion.57 MAX-TMEM260 PSLQGEKGN ENST00000358664-ENST00000261556 HLA-A*29:02 None 0 0 39260.220 74.000 NA NA Poor True Pending +3.BTBD8-ELAVL4.ENST00000342818-ENST00000357083.frameshift_fusion.181 1 BTBD8-ELAVL4 FISNGSPQL ENST00000342818-ENST00000357083 HLA-A*29:02 None 1 0 7438.830 5.800 NA NA Poor True Pending +18.MED31-RFC1.ENST00000225728-ENST00000381897.frameshift_fusion.131 1 MED31-RFC1 SMIQIQSQR ENST00000225728-ENST00000381897 HLA-A*29:02 None 1 0 7538.090 5.900 NA NA Poor True Pending +14.HBS1L-BCAS3.ENST00000367837-ENST00000390652.inframe_fusion.435 1 HBS1L-BCAS3 FLKQAGFKV ENST00000367837-ENST00000390652 HLA-A*29:02 None 1 0 10032.580 7.500 NA NA Poor True Pending +31.TIMP3-TMEM35B.ENST00000266085-ENST00000373337.frameshift_fusion.167 1 TIMP3-TMEM35B SFGADECPV ENST00000266085-ENST00000373337 HLA-A*29:02 None 1 0 12379.260 9.100 NA NA Poor True Pending +1.ABCA12-EXTL2.ENST00000272895-ENST00000370114.frameshift_fusion.1659 1 ABCA12-EXTL2 VMEVLKCKH ENST00000272895-ENST00000370114 HLA-A*29:02 None 1 0 14503.370 12.000 NA NA Poor True Pending +29.TAOK3-MARCH1.ENST00000392533-ENST00000503008.frameshift_fusion.214 1 TAOK3-MARCH1 LVGETTDDH ENST00000392533-ENST00000503008 HLA-A*29:02 None 1 0 16432.350 14.000 NA NA Poor True Pending +27.SMG1-PHF20.ENST00000446231-ENST00000374012.frameshift_fusion.3540 1 SMG1-PHF20 SFAADDKAS ENST00000446231-ENST00000374012 HLA-A*29:02 None 1 0 17955.930 15.000 NA NA Poor True Pending +24.SAAL1-HNRNPC.ENST00000524803-ENST00000554455.frameshift_fusion.346 1 SAAL1-HNRNPC YLKIEKWPA ENST00000524803-ENST00000554455 HLA-A*29:02 None 1 0 19752.610 17.000 NA NA Poor True Pending +19.MIPOL1-PGAP1.ENST00000327441-ENST00000354764.frameshift_fusion.6 1 MIPOL1-PGAP1 NWSKVCCRL ENST00000327441-ENST00000354764 HLA-A*29:02 None 1 0 19941.140 18.000 NA NA Poor False Pending +41.ZC3H11A-KLHL12.ENST00000545588-ENST00000367261.frameshift_fusion.291 1 ZC3H11A-KLHL12 KRKFSAGGF ENST00000545588-ENST00000367261 HLA-A*29:02 None 1 0 20599.710 19.000 NA NA Poor True Pending +21.PHTF1-YARS.ENST00000369604-ENST00000373477.inframe_fusion.15 1 PHTF1-YARS WYQKKESKI ENST00000369604-ENST00000373477 HLA-A*29:02 None 1 0 21517.340 20.000 NA NA Poor True Pending +36.TTC26-NDUFV2.ENST00000464848-ENST00000318388.inframe_fusion.239 1 TTC26-NDUFV2 LYNGRAAEG ENST00000464848-ENST00000318388 HLA-A*29:02 None 1 0 24401.630 24.000 NA NA Poor True Pending +34.TPM3-GATAD2B.ENST00000368530-ENST00000368655.inframe_fusion.81 1 TPM3-GATAD2B DMDRMTEDA ENST00000368530-ENST00000368655 HLA-A*29:02 None 1 0 24709.020 25.000 NA NA Poor True Pending +28.SNRPB2-METTL18.ENST00000246071-ENST00000310392.frameshift_fusion.215 1 SNRPB2-METTL18 QGFKITPSQ ENST00000246071-ENST00000310392 HLA-A*29:02 None 1 0 27021.620 29.000 NA NA Poor True Pending +2.AMD1-REV3L.ENST00000368885-ENST00000358835.inframe_fusion.36 1 AMD1-REV3L IPREIGGRL ENST00000368885-ENST00000358835 HLA-A*29:02 None 1 0 28400.540 32.000 NA NA Poor True Pending +32.TIMP3-COL3A1.ENST00000266085-ENST00000304636.frameshift_fusion.211 1 TIMP3-COL3A1 INATDPGPE ENST00000266085-ENST00000304636 HLA-A*29:02 None 1 0 28451.910 33.000 NA NA Poor True Pending +4.CDC37L1-BTG3.ENST00000381854-ENST00000339775.frameshift_fusion.169 1 CDC37L1-BTG3 YEQKIRHFD ENST00000381854-ENST00000339775 HLA-A*29:02 None 1 0 28661.390 33.000 NA NA Poor True Pending +15.LCORL-GNAS.ENST00000382226-ENST00000371100.inframe_fusion.143 1 LCORL-GNAS LFRKKGAGE ENST00000382226-ENST00000371100 HLA-A*29:02 None 1 0 29148.000 34.000 NA NA Poor True Pending +6.CLEC16A-RMI2.ENST00000409790-ENST00000312499.frameshift_fusion.242 1 CLEC16A-RMI2 GDGSGSGLQ ENST00000409790-ENST00000312499 HLA-A*29:02 None 1 0 29331.180 35.000 NA NA Poor True Pending +38.TUB-RIC3.ENST00000305253-ENST00000309737.frameshift_fusion.165 1 TUB-RIC3 ASAKRTKAA ENST00000305253-ENST00000309737 HLA-A*29:02 None 1 0 34397.110 51.000 NA NA Poor True Pending +5.CEP192-TMEM260.ENST00000506447-ENST00000261556.inframe_fusion.1724 1 CEP192-TMEM260 ESVCDQRTN ENST00000506447-ENST00000261556 HLA-A*29:02 None 1 0 37430.500 64.000 NA NA Poor True Pending +17.MAX-TMEM260.ENST00000358664-ENST00000261556.frameshift_fusion.57 1 MAX-TMEM260 PSLQGEKGN ENST00000358664-ENST00000261556 HLA-A*29:02 None 1 0 39260.220 74.000 NA NA Poor True Pending diff --git a/tests/test_data/pvacfuse/fusions_agfusion_starfusion/MHC_Class_I/Test.all_epitopes.aggregated.tsv b/tests/test_data/pvacfuse/fusions_agfusion_starfusion/MHC_Class_I/Test.all_epitopes.aggregated.tsv index 2feb06ff..eab1b009 100644 --- a/tests/test_data/pvacfuse/fusions_agfusion_starfusion/MHC_Class_I/Test.all_epitopes.aggregated.tsv +++ b/tests/test_data/pvacfuse/fusions_agfusion_starfusion/MHC_Class_I/Test.all_epitopes.aggregated.tsv @@ -1,31 +1,31 @@ ID A*29:02 Gene Best Peptide Best Transcript Allele Prob Pos Num Included Peptides Num Passing Peptides IC50 MT %ile MT Expr Read Support Tier Evaluation 7.EIF3K_CYP39A1.ENST00000588934_ENST00000275016.frameshift_fusion.118 4 EIF3K_CYP39A1 HFQAFWHQF ENST00000588934-ENST00000275016 HLA-A*29:02 None 4 2 257.230 0.730 NA NA Pass Pending -23.TMEM104_RAB37.ENST00000417024_ENST00000340415.inframe_fusion.225 TMEM104_RAB37 YRIYLTILV ENST00000417024-ENST00000340415 HLA-A*29:02 None 0 0 6204.380 5.000 0.110 401.000 Poor Pending -24.TMEM104_RAB37.ENST00000417024_ENST00000402449.inframe_fusion.225 TMEM104_RAB37 YRIYLTILV ENST00000417024-ENST00000402449 HLA-A*29:02 None 0 0 6204.380 5.000 0.110 401.000 Poor Pending -25.TMEM104_RAB37.ENST00000582773_ENST00000340415.inframe_fusion.212 TMEM104_RAB37 YRIYLTILV ENST00000582773-ENST00000340415 HLA-A*29:02 None 0 0 6204.380 5.000 0.110 401.000 Poor Pending -26.TMEM104_RAB37.ENST00000582773_ENST00000402449.inframe_fusion.212 TMEM104_RAB37 YRIYLTILV ENST00000582773-ENST00000402449 HLA-A*29:02 None 0 0 6204.380 5.000 0.110 401.000 Poor Pending -27.TMEM104_RAB37.ENST00000582330_ENST00000340415.inframe_fusion.212 TMEM104_RAB37 YRIYLTILV ENST00000582330-ENST00000340415 HLA-A*29:02 None 0 0 6204.380 5.000 0.110 401.000 Poor Pending -28.TMEM104_RAB37.ENST00000582330_ENST00000402449.inframe_fusion.212 TMEM104_RAB37 YRIYLTILV ENST00000582330-ENST00000402449 HLA-A*29:02 None 0 0 6204.380 5.000 0.110 401.000 Poor Pending -29.TMEM104_RAB37.ENST00000335464_ENST00000340415.inframe_fusion.212 TMEM104_RAB37 YRIYLTILV ENST00000335464-ENST00000340415 HLA-A*29:02 None 0 0 6204.380 5.000 0.110 401.000 Poor Pending -30.TMEM104_RAB37.ENST00000335464_ENST00000402449.inframe_fusion.212 TMEM104_RAB37 YRIYLTILV ENST00000335464-ENST00000402449 HLA-A*29:02 None 0 0 6204.380 5.000 0.110 401.000 Poor Pending -1.EIF3K_CYP39A1.ENST00000593149_ENST00000275016.inframe_fusion.79 EIF3K_CYP39A1 MLGDLSASI ENST00000593149-ENST00000275016 HLA-A*29:02 None 0 0 6540.210 5.200 0.573 2103.000 Poor Pending -11.EIF3K_CYP39A1.ENST00000614624_ENST00000275016.inframe_fusion.133 EIF3K_CYP39A1 MLGDLSASI ENST00000614624-ENST00000275016 HLA-A*29:02 None 0 0 6540.210 5.200 0.573 2103.000 Poor Pending -3.EIF3K_CYP39A1.ENST00000248342_ENST00000275016.inframe_fusion.166 EIF3K_CYP39A1 MLGDLSASI ENST00000248342-ENST00000275016 HLA-A*29:02 None 0 0 6540.210 5.200 0.573 2103.000 Poor Pending -5.EIF3K_CYP39A1.ENST00000538434_ENST00000275016.inframe_fusion.79 EIF3K_CYP39A1 MLGDLSASI ENST00000538434-ENST00000275016 HLA-A*29:02 None 0 0 6540.210 5.200 0.573 2103.000 Poor Pending -8.EIF3K_CYP39A1.ENST00000545173_ENST00000275016.inframe_fusion.166 EIF3K_CYP39A1 MLGDLSASI ENST00000545173-ENST00000275016 HLA-A*29:02 None 0 0 6540.210 5.200 0.573 2103.000 Poor Pending -12.EIF3K_CYP39A1.ENST00000614624_ENST00000619708.frameshift_fusion.133 EIF3K_CYP39A1 MLGDLSDAL ENST00000614624-ENST00000619708 HLA-A*29:02 None 0 0 12112.160 8.900 NA NA Poor Pending -2.EIF3K_CYP39A1.ENST00000593149_ENST00000619708.frameshift_fusion.79 EIF3K_CYP39A1 MLGDLSDAL ENST00000593149-ENST00000619708 HLA-A*29:02 None 0 0 12112.160 8.900 NA NA Poor Pending -4.EIF3K_CYP39A1.ENST00000248342_ENST00000619708.frameshift_fusion.166 EIF3K_CYP39A1 MLGDLSDAL ENST00000248342-ENST00000619708 HLA-A*29:02 None 0 0 12112.160 8.900 NA NA Poor Pending -6.EIF3K_CYP39A1.ENST00000538434_ENST00000619708.frameshift_fusion.79 EIF3K_CYP39A1 MLGDLSDAL ENST00000538434-ENST00000619708 HLA-A*29:02 None 0 0 12112.160 8.900 NA NA Poor Pending -9.EIF3K_CYP39A1.ENST00000545173_ENST00000619708.frameshift_fusion.166 EIF3K_CYP39A1 MLGDLSDAL ENST00000545173-ENST00000619708 HLA-A*29:02 None 0 0 12112.160 8.900 NA NA Poor Pending -10.EIF3K_CYP39A1.ENST00000592558_ENST00000275016.inframe_fusion.140 EIF3K_CYP39A1 KSSIPKNVF ENST00000592558-ENST00000275016 HLA-A*29:02 None 0 0 22972.240 22.000 NA NA Poor Pending -15.PLA2R1_RBMS1.ENST00000283243_ENST00000348849.inframe_fusion.865 PLA2R1_RBMS1 FIHSKIKAQ ENST00000283243-ENST00000348849 HLA-A*29:02 None 0 0 26500.160 28.000 0.331 1230.000 Poor Pending -16.PLA2R1_RBMS1.ENST00000283243_ENST00000409075.inframe_fusion.865 PLA2R1_RBMS1 FIHSKIKAQ ENST00000283243-ENST00000409075 HLA-A*29:02 None 0 0 26500.160 28.000 0.331 1230.000 Poor Pending -17.PLA2R1_RBMS1.ENST00000283243_ENST00000409289.inframe_fusion.865 PLA2R1_RBMS1 FIHSKIKAQ ENST00000283243-ENST00000409289 HLA-A*29:02 None 0 0 26500.160 28.000 0.331 1230.000 Poor Pending -18.PLA2R1_RBMS1.ENST00000283243_ENST00000409972.inframe_fusion.865 PLA2R1_RBMS1 FIHSKIKAQ ENST00000283243-ENST00000409972 HLA-A*29:02 None 0 0 26500.160 28.000 0.331 1230.000 Poor Pending -19.PLA2R1_RBMS1.ENST00000392771_ENST00000348849.inframe_fusion.865 PLA2R1_RBMS1 FIHSKIKAQ ENST00000392771-ENST00000348849 HLA-A*29:02 None 0 0 26500.160 28.000 0.331 1230.000 Poor Pending -20.PLA2R1_RBMS1.ENST00000392771_ENST00000409075.inframe_fusion.865 PLA2R1_RBMS1 FIHSKIKAQ ENST00000392771-ENST00000409075 HLA-A*29:02 None 0 0 26500.160 28.000 0.331 1230.000 Poor Pending -21.PLA2R1_RBMS1.ENST00000392771_ENST00000409289.inframe_fusion.865 PLA2R1_RBMS1 FIHSKIKAQ ENST00000392771-ENST00000409289 HLA-A*29:02 None 0 0 26500.160 28.000 0.331 1230.000 Poor Pending -22.PLA2R1_RBMS1.ENST00000392771_ENST00000409972.inframe_fusion.865 PLA2R1_RBMS1 FIHSKIKAQ ENST00000392771-ENST00000409972 HLA-A*29:02 None 0 0 26500.160 28.000 0.331 1230.000 Poor Pending -13.HNRNPUL2_AHNAK.ENST00000301785_ENST00000257247.frameshift_fusion.660 HNRNPUL2_AHNAK GYDGEGGDN ENST00000301785-ENST00000257247 HLA-A*29:02 None 0 0 28325.960 32.000 0.153 570.000 Poor Pending -14.HNRNPUL2_AHNAK.ENST00000301785_ENST00000378024.frameshift_fusion.660 HNRNPUL2_AHNAK GYDGEGGDN ENST00000301785-ENST00000378024 HLA-A*29:02 None 0 0 28325.960 32.000 0.153 570.000 Poor Pending +1.EIF3K_CYP39A1.ENST00000593149_ENST00000275016.inframe_fusion.79 1 EIF3K_CYP39A1 MLGDLSASI ENST00000593149-ENST00000275016 HLA-A*29:02 None 1 0 6540.210 5.200 0.573 2103.000 Poor Pending +11.EIF3K_CYP39A1.ENST00000614624_ENST00000275016.inframe_fusion.133 1 EIF3K_CYP39A1 MLGDLSASI ENST00000614624-ENST00000275016 HLA-A*29:02 None 1 0 6540.210 5.200 0.573 2103.000 Poor Pending +3.EIF3K_CYP39A1.ENST00000248342_ENST00000275016.inframe_fusion.166 1 EIF3K_CYP39A1 MLGDLSASI ENST00000248342-ENST00000275016 HLA-A*29:02 None 1 0 6540.210 5.200 0.573 2103.000 Poor Pending +5.EIF3K_CYP39A1.ENST00000538434_ENST00000275016.inframe_fusion.79 1 EIF3K_CYP39A1 MLGDLSASI ENST00000538434-ENST00000275016 HLA-A*29:02 None 1 0 6540.210 5.200 0.573 2103.000 Poor Pending +8.EIF3K_CYP39A1.ENST00000545173_ENST00000275016.inframe_fusion.166 1 EIF3K_CYP39A1 MLGDLSASI ENST00000545173-ENST00000275016 HLA-A*29:02 None 1 0 6540.210 5.200 0.573 2103.000 Poor Pending +23.TMEM104_RAB37.ENST00000417024_ENST00000340415.inframe_fusion.225 1 TMEM104_RAB37 YRIYLTILV ENST00000417024-ENST00000340415 HLA-A*29:02 None 1 0 6204.380 5.000 0.110 401.000 Poor Pending +24.TMEM104_RAB37.ENST00000417024_ENST00000402449.inframe_fusion.225 1 TMEM104_RAB37 YRIYLTILV ENST00000417024-ENST00000402449 HLA-A*29:02 None 1 0 6204.380 5.000 0.110 401.000 Poor Pending +25.TMEM104_RAB37.ENST00000582773_ENST00000340415.inframe_fusion.212 1 TMEM104_RAB37 YRIYLTILV ENST00000582773-ENST00000340415 HLA-A*29:02 None 1 0 6204.380 5.000 0.110 401.000 Poor Pending +26.TMEM104_RAB37.ENST00000582773_ENST00000402449.inframe_fusion.212 1 TMEM104_RAB37 YRIYLTILV ENST00000582773-ENST00000402449 HLA-A*29:02 None 1 0 6204.380 5.000 0.110 401.000 Poor Pending +27.TMEM104_RAB37.ENST00000582330_ENST00000340415.inframe_fusion.212 1 TMEM104_RAB37 YRIYLTILV ENST00000582330-ENST00000340415 HLA-A*29:02 None 1 0 6204.380 5.000 0.110 401.000 Poor Pending +28.TMEM104_RAB37.ENST00000582330_ENST00000402449.inframe_fusion.212 1 TMEM104_RAB37 YRIYLTILV ENST00000582330-ENST00000402449 HLA-A*29:02 None 1 0 6204.380 5.000 0.110 401.000 Poor Pending +29.TMEM104_RAB37.ENST00000335464_ENST00000340415.inframe_fusion.212 1 TMEM104_RAB37 YRIYLTILV ENST00000335464-ENST00000340415 HLA-A*29:02 None 1 0 6204.380 5.000 0.110 401.000 Poor Pending +30.TMEM104_RAB37.ENST00000335464_ENST00000402449.inframe_fusion.212 1 TMEM104_RAB37 YRIYLTILV ENST00000335464-ENST00000402449 HLA-A*29:02 None 1 0 6204.380 5.000 0.110 401.000 Poor Pending +15.PLA2R1_RBMS1.ENST00000283243_ENST00000348849.inframe_fusion.865 1 PLA2R1_RBMS1 FIHSKIKAQ ENST00000283243-ENST00000348849 HLA-A*29:02 None 1 0 26500.160 28.000 0.331 1230.000 Poor Pending +16.PLA2R1_RBMS1.ENST00000283243_ENST00000409075.inframe_fusion.865 1 PLA2R1_RBMS1 FIHSKIKAQ ENST00000283243-ENST00000409075 HLA-A*29:02 None 1 0 26500.160 28.000 0.331 1230.000 Poor Pending +17.PLA2R1_RBMS1.ENST00000283243_ENST00000409289.inframe_fusion.865 1 PLA2R1_RBMS1 FIHSKIKAQ ENST00000283243-ENST00000409289 HLA-A*29:02 None 1 0 26500.160 28.000 0.331 1230.000 Poor Pending +18.PLA2R1_RBMS1.ENST00000283243_ENST00000409972.inframe_fusion.865 1 PLA2R1_RBMS1 FIHSKIKAQ ENST00000283243-ENST00000409972 HLA-A*29:02 None 1 0 26500.160 28.000 0.331 1230.000 Poor Pending +19.PLA2R1_RBMS1.ENST00000392771_ENST00000348849.inframe_fusion.865 1 PLA2R1_RBMS1 FIHSKIKAQ ENST00000392771-ENST00000348849 HLA-A*29:02 None 1 0 26500.160 28.000 0.331 1230.000 Poor Pending +20.PLA2R1_RBMS1.ENST00000392771_ENST00000409075.inframe_fusion.865 1 PLA2R1_RBMS1 FIHSKIKAQ ENST00000392771-ENST00000409075 HLA-A*29:02 None 1 0 26500.160 28.000 0.331 1230.000 Poor Pending +21.PLA2R1_RBMS1.ENST00000392771_ENST00000409289.inframe_fusion.865 1 PLA2R1_RBMS1 FIHSKIKAQ ENST00000392771-ENST00000409289 HLA-A*29:02 None 1 0 26500.160 28.000 0.331 1230.000 Poor Pending +22.PLA2R1_RBMS1.ENST00000392771_ENST00000409972.inframe_fusion.865 1 PLA2R1_RBMS1 FIHSKIKAQ ENST00000392771-ENST00000409972 HLA-A*29:02 None 1 0 26500.160 28.000 0.331 1230.000 Poor Pending +12.EIF3K_CYP39A1.ENST00000614624_ENST00000619708.frameshift_fusion.133 1 EIF3K_CYP39A1 MLGDLSDAL ENST00000614624-ENST00000619708 HLA-A*29:02 None 1 0 12112.160 8.900 NA NA Poor Pending +2.EIF3K_CYP39A1.ENST00000593149_ENST00000619708.frameshift_fusion.79 1 EIF3K_CYP39A1 MLGDLSDAL ENST00000593149-ENST00000619708 HLA-A*29:02 None 1 0 12112.160 8.900 NA NA Poor Pending +4.EIF3K_CYP39A1.ENST00000248342_ENST00000619708.frameshift_fusion.166 1 EIF3K_CYP39A1 MLGDLSDAL ENST00000248342-ENST00000619708 HLA-A*29:02 None 1 0 12112.160 8.900 NA NA Poor Pending +6.EIF3K_CYP39A1.ENST00000538434_ENST00000619708.frameshift_fusion.79 1 EIF3K_CYP39A1 MLGDLSDAL ENST00000538434-ENST00000619708 HLA-A*29:02 None 1 0 12112.160 8.900 NA NA Poor Pending +9.EIF3K_CYP39A1.ENST00000545173_ENST00000619708.frameshift_fusion.166 1 EIF3K_CYP39A1 MLGDLSDAL ENST00000545173-ENST00000619708 HLA-A*29:02 None 1 0 12112.160 8.900 NA NA Poor Pending +10.EIF3K_CYP39A1.ENST00000592558_ENST00000275016.inframe_fusion.140 1 EIF3K_CYP39A1 KSSIPKNVF ENST00000592558-ENST00000275016 HLA-A*29:02 None 1 0 22972.240 22.000 NA NA Poor Pending +13.HNRNPUL2_AHNAK.ENST00000301785_ENST00000257247.frameshift_fusion.660 1 HNRNPUL2_AHNAK GYDGEGGDN ENST00000301785-ENST00000257247 HLA-A*29:02 None 1 0 28325.960 32.000 0.153 570.000 Poor Pending +14.HNRNPUL2_AHNAK.ENST00000301785_ENST00000378024.frameshift_fusion.660 1 HNRNPUL2_AHNAK GYDGEGGDN ENST00000301785-ENST00000378024 HLA-A*29:02 None 1 0 28325.960 32.000 0.153 570.000 Poor Pending diff --git a/tests/test_data/pvacseq/MHC_Class_I/Test.all_epitopes.aggregated.metrics.json b/tests/test_data/pvacseq/MHC_Class_I/Test.all_epitopes.aggregated.metrics.json index 50e7d25e..da507f59 100644 --- a/tests/test_data/pvacseq/MHC_Class_I/Test.all_epitopes.aggregated.metrics.json +++ b/tests/test_data/pvacseq/MHC_Class_I/Test.all_epitopes.aggregated.metrics.json @@ -1184,11 +1184,140 @@ } }, "22-20709231-20709232-G-C": { - "good_binders": {}, - "sets": [], - "transcript_counts": [], - "peptide_counts": [], - "set_expr": [], + "good_binders": { + "Transcript Set 1": { + "peptides": { + "ANQDAAQGI": { + "ic50s_MT": [ + "X", + 5681.68017578125 + ], + "percentiles_MT": [ + "X", + 8.800000190734863 + ], + "ic50s_WT": [ + "X", + 9654.43 + ], + "percentiles_WT": [ + "X", + 20.0 + ], + "hla_types": [ + "HLA-E*01:01", + "HLA-G*01:09" + ], + "mutation_position": "3", + "problematic_positions": "None", + "anchor_fails": "None", + "individual_ic50_calls": { + "algorithms": [ + "NetMHC", + "PickPocket" + ], + "MT": { + "HLA-G*01:09": [ + "NA", + 5681.68 + ] + }, + "WT": { + "HLA-G*01:09": [ + "NA", + 9654.43 + ] + } + }, + "individual_ic50_percentile_calls": { + "algorithms": [ + "NetMHC", + "PickPocket" + ], + "MT": { + "HLA-G*01:09": [ + "NA", + 8.800000190734863 + ] + }, + "WT": { + "HLA-G*01:09": [ + "NA", + 20.0 + ] + } + }, + "individual_el_calls": { + "algorithms": [], + "MT": { + "HLA-G*01:09": [] + }, + "WT": { + "HLA-G*01:09": [] + } + }, + "individual_el_percentile_calls": { + "algorithms": [], + "MT": { + "HLA-G*01:09": [] + }, + "WT": { + "HLA-G*01:09": [] + } + }, + "individual_percentile_calls": { + "algorithms": [ + "NetMHC", + "PickPocket" + ], + "MT": { + "HLA-G*01:09": [ + "NA", + 8.800000190734863 + ] + }, + "WT": { + "HLA-G*01:09": [ + "NA", + 20.0 + ] + } + }, + "wt_peptide": "ANEDAAQGI" + } + }, + "transcripts": [ + "ENST00000434783.3-FAM230A-E/Q-322" + ], + "transcript_expr": [ + "NA" + ], + "tsl": [ + "Not Supported" + ], + "biotype": [ + "protein_coding" + ], + "transcript_length": [ + 905 + ], + "transcript_count": 1, + "peptide_count": 1, + "total_expr": 0 + } + }, + "sets": [ + "Transcript Set 1" + ], + "transcript_counts": [ + 1 + ], + "peptide_counts": [ + 1 + ], + "set_expr": [ + 0 + ], "DNA VAF": 0.5, "RNA VAF": "NA", "gene_expr": "NA", @@ -1202,11 +1331,140 @@ } }, "22-22550449-22550450-C-G": { - "good_binders": {}, - "sets": [], - "transcript_counts": [], - "peptide_counts": [], - "set_expr": [], + "good_binders": { + "Transcript Set 1": { + "peptides": { + "KTVTISCTG": { + "ic50s_MT": [ + "X", + 9447.759765625 + ], + "percentiles_MT": [ + "X", + 19.0 + ], + "ic50s_WT": [ + "X", + 15208.39 + ], + "percentiles_WT": [ + "X", + 31.0 + ], + "hla_types": [ + "HLA-E*01:01", + "HLA-G*01:09" + ], + "mutation_position": "9", + "problematic_positions": "None", + "anchor_fails": "None", + "individual_ic50_calls": { + "algorithms": [ + "NetMHC", + "PickPocket" + ], + "MT": { + "HLA-G*01:09": [ + "NA", + 9447.76 + ] + }, + "WT": { + "HLA-G*01:09": [ + "NA", + 15208.39 + ] + } + }, + "individual_ic50_percentile_calls": { + "algorithms": [ + "NetMHC", + "PickPocket" + ], + "MT": { + "HLA-G*01:09": [ + "NA", + 19.0 + ] + }, + "WT": { + "HLA-G*01:09": [ + "NA", + 31.0 + ] + } + }, + "individual_el_calls": { + "algorithms": [], + "MT": { + "HLA-G*01:09": [] + }, + "WT": { + "HLA-G*01:09": [] + } + }, + "individual_el_percentile_calls": { + "algorithms": [], + "MT": { + "HLA-G*01:09": [] + }, + "WT": { + "HLA-G*01:09": [] + } + }, + "individual_percentile_calls": { + "algorithms": [ + "NetMHC", + "PickPocket" + ], + "MT": { + "HLA-G*01:09": [ + "NA", + 19.0 + ] + }, + "WT": { + "HLA-G*01:09": [ + "NA", + 31.0 + ] + } + }, + "wt_peptide": "KTVTISCTR" + } + }, + "transcripts": [ + "ENST00000390285.3-IGLV6-57-R/G-43" + ], + "transcript_expr": [ + "NA" + ], + "tsl": [ + "Not Supported" + ], + "biotype": [ + "IG_V_gene" + ], + "transcript_length": [ + 148 + ], + "transcript_count": 1, + "peptide_count": 1, + "total_expr": 0 + } + }, + "sets": [ + "Transcript Set 1" + ], + "transcript_counts": [ + 1 + ], + "peptide_counts": [ + 1 + ], + "set_expr": [ + 0 + ], "DNA VAF": 1.0, "RNA VAF": "NA", "gene_expr": "NA", @@ -1591,11 +1849,140 @@ } }, "22-26936775-26936776-G-T": { - "good_binders": {}, - "sets": [], - "transcript_counts": [], - "peptide_counts": [], - "set_expr": [], + "good_binders": { + "Transcript Set 1": { + "peptides": { + "KHGGVSLSK": { + "ic50s_MT": [ + 6539.7900390625, + "X" + ], + "percentiles_MT": [ + 13.0, + "X" + ], + "ic50s_WT": [ + 20149.14, + "X" + ], + "percentiles_WT": [ + 53.0, + "X" + ], + "hla_types": [ + "HLA-E*01:01", + "HLA-G*01:09" + ], + "mutation_position": "2", + "problematic_positions": "None", + "anchor_fails": "None", + "individual_ic50_calls": { + "algorithms": [ + "NetMHC", + "PickPocket" + ], + "MT": { + "HLA-E*01:01": [ + 42239.4, + 6539.79 + ] + }, + "WT": { + "HLA-E*01:01": [ + 43004.91, + 20149.14 + ] + } + }, + "individual_ic50_percentile_calls": { + "algorithms": [ + "NetMHC", + "PickPocket" + ], + "MT": { + "HLA-E*01:01": [ + 56.0, + 13.0 + ] + }, + "WT": { + "HLA-E*01:01": [ + 62.0, + 53.0 + ] + } + }, + "individual_el_calls": { + "algorithms": [], + "MT": { + "HLA-E*01:01": [] + }, + "WT": { + "HLA-E*01:01": [] + } + }, + "individual_el_percentile_calls": { + "algorithms": [], + "MT": { + "HLA-E*01:01": [] + }, + "WT": { + "HLA-E*01:01": [] + } + }, + "individual_percentile_calls": { + "algorithms": [ + "NetMHC", + "PickPocket" + ], + "MT": { + "HLA-E*01:01": [ + 56.0, + 13.0 + ] + }, + "WT": { + "HLA-E*01:01": [ + 62.0, + 53.0 + ] + } + }, + "wt_peptide": "KPGGVSLSK" + } + }, + "transcripts": [ + "ENST00000338754.4-TPST2-P/H-274" + ], + "transcript_expr": [ + "NA" + ], + "tsl": [ + "Not Supported" + ], + "biotype": [ + "protein_coding" + ], + "transcript_length": [ + 377 + ], + "transcript_count": 1, + "peptide_count": 1, + "total_expr": 0 + } + }, + "sets": [ + "Transcript Set 1" + ], + "transcript_counts": [ + 1 + ], + "peptide_counts": [ + 1 + ], + "set_expr": [ + 0 + ], "DNA VAF": 0.179, "RNA VAF": "NA", "gene_expr": "NA", @@ -1609,11 +1996,140 @@ } }, "22-29886116-29886117-C-A": { - "good_binders": {}, - "sets": [], - "transcript_counts": [], - "peptide_counts": [], - "set_expr": [], + "good_binders": { + "Transcript Set 1": { + "peptides": { + "KTQEVKVKE": { + "ic50s_MT": [ + "X", + 7366.35009765625 + ], + "percentiles_MT": [ + "X", + 14.0 + ], + "ic50s_WT": [ + "X", + 25842.4 + ], + "percentiles_WT": [ + "X", + 50.0 + ], + "hla_types": [ + "HLA-E*01:01", + "HLA-G*01:09" + ], + "mutation_position": "2", + "problematic_positions": "None", + "anchor_fails": "None", + "individual_ic50_calls": { + "algorithms": [ + "NetMHC", + "PickPocket" + ], + "MT": { + "HLA-G*01:09": [ + "NA", + 7366.35 + ] + }, + "WT": { + "HLA-G*01:09": [ + "NA", + 25842.4 + ] + } + }, + "individual_ic50_percentile_calls": { + "algorithms": [ + "NetMHC", + "PickPocket" + ], + "MT": { + "HLA-G*01:09": [ + "NA", + 14.0 + ] + }, + "WT": { + "HLA-G*01:09": [ + "NA", + 50.0 + ] + } + }, + "individual_el_calls": { + "algorithms": [], + "MT": { + "HLA-G*01:09": [] + }, + "WT": { + "HLA-G*01:09": [] + } + }, + "individual_el_percentile_calls": { + "algorithms": [], + "MT": { + "HLA-G*01:09": [] + }, + "WT": { + "HLA-G*01:09": [] + } + }, + "individual_percentile_calls": { + "algorithms": [ + "NetMHC", + "PickPocket" + ], + "MT": { + "HLA-G*01:09": [ + "NA", + 14.0 + ] + }, + "WT": { + "HLA-G*01:09": [ + "NA", + 50.0 + ] + } + }, + "wt_peptide": "KPQEVKVKE" + } + }, + "transcripts": [ + "ENST00000310624.6-NEFH-P/T-830" + ], + "transcript_expr": [ + "NA" + ], + "tsl": [ + "Not Supported" + ], + "biotype": [ + "protein_coding" + ], + "transcript_length": [ + 1020 + ], + "transcript_count": 1, + "peptide_count": 1, + "total_expr": 0 + } + }, + "sets": [ + "Transcript Set 1" + ], + "transcript_counts": [ + 1 + ], + "peptide_counts": [ + 1 + ], + "set_expr": [ + 0 + ], "DNA VAF": 0.038, "RNA VAF": "NA", "gene_expr": "NA", @@ -2166,11 +2682,140 @@ } }, "22-38119219-38119220-GA-G": { - "good_binders": {}, - "sets": [], - "transcript_counts": [], - "peptide_counts": [], - "set_expr": [], + "good_binders": { + "Transcript Set 1": { + "peptides": { + "GEKAGCPWS": { + "ic50s_MT": [ + 8119.759765625, + "X" + ], + "percentiles_MT": [ + 18.0, + "X" + ], + "ic50s_WT": [ + "NA", + "X" + ], + "percentiles_WT": [ + "NA", + "X" + ], + "hla_types": [ + "HLA-E*01:01", + "HLA-G*01:09" + ], + "mutation_position": "1-9", + "problematic_positions": "None", + "anchor_fails": "None", + "individual_ic50_calls": { + "algorithms": [ + "NetMHC", + "PickPocket" + ], + "MT": { + "HLA-E*01:01": [ + 38012.91, + 8119.76 + ] + }, + "WT": { + "HLA-E*01:01": [ + "NA", + "NA" + ] + } + }, + "individual_ic50_percentile_calls": { + "algorithms": [ + "NetMHC", + "PickPocket" + ], + "MT": { + "HLA-E*01:01": [ + 31.0, + 18.0 + ] + }, + "WT": { + "HLA-E*01:01": [ + "NA", + "NA" + ] + } + }, + "individual_el_calls": { + "algorithms": [], + "MT": { + "HLA-E*01:01": [] + }, + "WT": { + "HLA-E*01:01": [] + } + }, + "individual_el_percentile_calls": { + "algorithms": [], + "MT": { + "HLA-E*01:01": [] + }, + "WT": { + "HLA-E*01:01": [] + } + }, + "individual_percentile_calls": { + "algorithms": [ + "NetMHC", + "PickPocket" + ], + "MT": { + "HLA-E*01:01": [ + 31.0, + 18.0 + ] + }, + "WT": { + "HLA-E*01:01": [ + "NA", + "NA" + ] + } + }, + "wt_peptide": "FS-NA" + } + }, + "transcripts": [ + "ENST00000406386.3-TRIOBP-G/X-219" + ], + "transcript_expr": [ + "NA" + ], + "tsl": [ + "Not Supported" + ], + "biotype": [ + "protein_coding" + ], + "transcript_length": [ + 2365 + ], + "transcript_count": 1, + "peptide_count": 1, + "total_expr": 0 + } + }, + "sets": [ + "Transcript Set 1" + ], + "transcript_counts": [ + 1 + ], + "peptide_counts": [ + 1 + ], + "set_expr": [ + 0 + ], "DNA VAF": 0.768, "RNA VAF": "NA", "gene_expr": "NA", @@ -3704,11 +4349,158 @@ ] } }, - "wt_peptide": "YYSYGLLHT" + "wt_peptide": "YYSYGLLHT" + } + }, + "transcripts": [ + "ENST00000253255.5-PKDREJ-T/I-1875" + ], + "transcript_expr": [ + "NA" + ], + "tsl": [ + "Not Supported" + ], + "biotype": [ + "protein_coding" + ], + "transcript_length": [ + 2253 + ], + "transcript_count": 1, + "peptide_count": 6, + "total_expr": 0 + } + }, + "sets": [ + "Transcript Set 1" + ], + "transcript_counts": [ + 1 + ], + "peptide_counts": [ + 6 + ], + "set_expr": [ + 0 + ], + "DNA VAF": 0.233, + "RNA VAF": "NA", + "gene_expr": "NA", + "best_peptide_mt": "LYYSYGLLHI", + "best_peptide_wt": "LYYSYGLLHT", + "best_hla_allele": "HLA-G*01:09", + "reference_matches": { + "count": 0, + "query_peptide": "YSYGLLHIYGSGGYA", + "matches": [] + } + }, + "22-50555769-50555770-G-A": { + "good_binders": { + "Transcript Set 1": { + "peptides": { + "KTTVVVTTQ": { + "ic50s_MT": [ + "X", + 10874.650390625 + ], + "percentiles_MT": [ + "X", + 23.0 + ], + "ic50s_WT": [ + "X", + 16763.86 + ], + "percentiles_WT": [ + "X", + 34.0 + ], + "hla_types": [ + "HLA-E*01:01", + "HLA-G*01:09" + ], + "mutation_position": "8", + "problematic_positions": "None", + "anchor_fails": "None", + "individual_ic50_calls": { + "algorithms": [ + "NetMHC", + "PickPocket" + ], + "MT": { + "HLA-G*01:09": [ + "NA", + 10874.65 + ] + }, + "WT": { + "HLA-G*01:09": [ + "NA", + 16763.86 + ] + } + }, + "individual_ic50_percentile_calls": { + "algorithms": [ + "NetMHC", + "PickPocket" + ], + "MT": { + "HLA-G*01:09": [ + "NA", + 23.0 + ] + }, + "WT": { + "HLA-G*01:09": [ + "NA", + 34.0 + ] + } + }, + "individual_el_calls": { + "algorithms": [], + "MT": { + "HLA-G*01:09": [] + }, + "WT": { + "HLA-G*01:09": [] + } + }, + "individual_el_percentile_calls": { + "algorithms": [], + "MT": { + "HLA-G*01:09": [] + }, + "WT": { + "HLA-G*01:09": [] + } + }, + "individual_percentile_calls": { + "algorithms": [ + "NetMHC", + "PickPocket" + ], + "MT": { + "HLA-G*01:09": [ + "NA", + 23.0 + ] + }, + "WT": { + "HLA-G*01:09": [ + "NA", + 34.0 + ] + } + }, + "wt_peptide": "KTTVVVTAQ" } }, "transcripts": [ - "ENST00000253255.5-PKDREJ-T/I-1875" + "ENST00000262794.5-MOV10L1-A/T-482" ], "transcript_expr": [ "NA" @@ -3720,10 +4512,10 @@ "protein_coding" ], "transcript_length": [ - 2253 + 1211 ], "transcript_count": 1, - "peptide_count": 6, + "peptide_count": 1, "total_expr": 0 } }, @@ -3734,29 +4526,11 @@ 1 ], "peptide_counts": [ - 6 + 1 ], "set_expr": [ 0 ], - "DNA VAF": 0.233, - "RNA VAF": "NA", - "gene_expr": "NA", - "best_peptide_mt": "LYYSYGLLHI", - "best_peptide_wt": "LYYSYGLLHT", - "best_hla_allele": "HLA-G*01:09", - "reference_matches": { - "count": 0, - "query_peptide": "YSYGLLHIYGSGGYA", - "matches": [] - } - }, - "22-50555769-50555770-G-A": { - "good_binders": {}, - "sets": [], - "transcript_counts": [], - "peptide_counts": [], - "set_expr": [], "DNA VAF": 0.042, "RNA VAF": "NA", "gene_expr": "NA", @@ -4260,11 +5034,140 @@ } }, "22-50869713-50869714-C-A": { - "good_binders": {}, - "sets": [], - "transcript_counts": [], - "peptide_counts": [], - "set_expr": [], + "good_binders": { + "Transcript Set 1": { + "peptides": { + "GYESRVEPP": { + "ic50s_MT": [ + "X", + 5620.5400390625 + ], + "percentiles_MT": [ + "X", + 8.699999809265137 + ], + "ic50s_WT": [ + "X", + 22209.93 + ], + "percentiles_WT": [ + "X", + 44.0 + ], + "hla_types": [ + "HLA-E*01:01", + "HLA-G*01:09" + ], + "mutation_position": "2", + "problematic_positions": "None", + "anchor_fails": "None", + "individual_ic50_calls": { + "algorithms": [ + "NetMHC", + "PickPocket" + ], + "MT": { + "HLA-G*01:09": [ + "NA", + 5620.54 + ] + }, + "WT": { + "HLA-G*01:09": [ + "NA", + 22209.93 + ] + } + }, + "individual_ic50_percentile_calls": { + "algorithms": [ + "NetMHC", + "PickPocket" + ], + "MT": { + "HLA-G*01:09": [ + "NA", + 8.699999809265137 + ] + }, + "WT": { + "HLA-G*01:09": [ + "NA", + 44.0 + ] + } + }, + "individual_el_calls": { + "algorithms": [], + "MT": { + "HLA-G*01:09": [] + }, + "WT": { + "HLA-G*01:09": [] + } + }, + "individual_el_percentile_calls": { + "algorithms": [], + "MT": { + "HLA-G*01:09": [] + }, + "WT": { + "HLA-G*01:09": [] + } + }, + "individual_percentile_calls": { + "algorithms": [ + "NetMHC", + "PickPocket" + ], + "MT": { + "HLA-G*01:09": [ + "NA", + 8.699999809265137 + ] + }, + "WT": { + "HLA-G*01:09": [ + "NA", + 44.0 + ] + } + }, + "wt_peptide": "GSESRVEPP" + } + }, + "transcripts": [ + "ENST00000395741.3-PPP6R2-S/Y-414" + ], + "transcript_expr": [ + "NA" + ], + "tsl": [ + "Not Supported" + ], + "biotype": [ + "protein_coding" + ], + "transcript_length": [ + 933 + ], + "transcript_count": 1, + "peptide_count": 1, + "total_expr": 0 + } + }, + "sets": [ + "Transcript Set 1" + ], + "transcript_counts": [ + 1 + ], + "peptide_counts": [ + 1 + ], + "set_expr": [ + 0 + ], "DNA VAF": 0.043, "RNA VAF": "NA", "gene_expr": "NA", @@ -4278,11 +5181,140 @@ } }, "4-40434704-40434725-AGCGGCTGCGGCGGCTGCGGCC-A": { - "good_binders": {}, - "sets": [], - "transcript_counts": [], - "peptide_counts": [], - "set_expr": [], + "good_binders": { + "Transcript Set 1": { + "peptides": { + "SAAAAAAAV": { + "ic50s_MT": [ + 21040.3203125, + "X" + ], + "percentiles_MT": [ + 21.0, + "X" + ], + "ic50s_WT": [ + 21040.32, + "X" + ], + "percentiles_WT": [ + 30.0, + "X" + ], + "hla_types": [ + "HLA-E*01:01", + "HLA-G*01:09" + ], + "mutation_position": "8-9", + "problematic_positions": "None", + "anchor_fails": "None", + "individual_ic50_calls": { + "algorithms": [ + "NetMHC", + "PickPocket" + ], + "MT": { + "HLA-E*01:01": [ + 35210.08, + 21040.32 + ] + }, + "WT": { + "HLA-E*01:01": [ + 37973.02, + 21040.32 + ] + } + }, + "individual_ic50_percentile_calls": { + "algorithms": [ + "NetMHC", + "PickPocket" + ], + "MT": { + "HLA-E*01:01": [ + 21.0, + 55.0 + ] + }, + "WT": { + "HLA-E*01:01": [ + 30.0, + 55.0 + ] + } + }, + "individual_el_calls": { + "algorithms": [], + "MT": { + "HLA-E*01:01": [] + }, + "WT": { + "HLA-E*01:01": [] + } + }, + "individual_el_percentile_calls": { + "algorithms": [], + "MT": { + "HLA-E*01:01": [] + }, + "WT": { + "HLA-E*01:01": [] + } + }, + "individual_percentile_calls": { + "algorithms": [ + "NetMHC", + "PickPocket" + ], + "MT": { + "HLA-E*01:01": [ + 21.0, + 55.0 + ] + }, + "WT": { + "HLA-E*01:01": [ + 30.0, + 55.0 + ] + } + }, + "wt_peptide": "SAAAAAAAA" + } + }, + "transcripts": [ + "ENST00000381793.2-RBM47-AAAAAAAA/A-495-502" + ], + "transcript_expr": [ + "NA" + ], + "tsl": [ + "Not Supported" + ], + "biotype": [ + "protein_coding" + ], + "transcript_length": [ + 593 + ], + "transcript_count": 1, + "peptide_count": 1, + "total_expr": 0 + } + }, + "sets": [ + "Transcript Set 1" + ], + "transcript_counts": [ + 1 + ], + "peptide_counts": [ + 1 + ], + "set_expr": [ + 0 + ], "DNA VAF": 0.977, "RNA VAF": "NA", "gene_expr": "NA", diff --git a/tests/test_data/pvacseq/MHC_Class_I/Test.all_epitopes.aggregated.tsv b/tests/test_data/pvacseq/MHC_Class_I/Test.all_epitopes.aggregated.tsv index d563d4f3..57952150 100644 --- a/tests/test_data/pvacseq/MHC_Class_I/Test.all_epitopes.aggregated.tsv +++ b/tests/test_data/pvacseq/MHC_Class_I/Test.all_epitopes.aggregated.tsv @@ -14,11 +14,11 @@ ID Index E*01:01 G*01:09 Gene AA Change Num Passing Transcripts Best Peptide Bes 22-41895790-41895791-C-A 18.ACO2.ENST00000216254.4.missense.33A/E 2 ACO2 A33E 1 EMSHFEPNE ENST00000216254.4 Not Supported HLA-E*01:01 1 None 2 0 3932.890 2443.190 4.200 1.300 NA NA NA NA 0.044 Poor False Pending 22-50682229-50682230-T-C 23.TUBGCP6.ENST00000248846.5.missense.220H/R 1 1 TUBGCP6 H220R 1 RSRTYDMDV ENST00000248846.5 Not Supported HLA-G*01:09 1 None 2 0 4576.120 7609.380 6.300 15.000 NA NA NA NA 0.686 Poor False Pending 22-19175521-19175522-G-T 7.CLTCL1.ENST00000263200.10.missense.1469H/N 1 CLTCL1 H1469N 1 SVNEALNNL ENST00000263200.10 Not Supported HLA-G*01:09 8 None 1 0 4989.870 7775.840 7.300 15.000 NA NA NA NA 0.100 Poor False Pending -22-50869713-50869714-C-A 24.PPP6R2.ENST00000395741.3.missense.414S/Y PPP6R2 S414Y 0 GYESRVEPP ENST00000395741.3 Not Supported HLA-G*01:09 2 None 0 0 5620.540 22209.930 8.700 44.000 NA NA NA NA 0.043 Poor False Pending -22-20709231-20709232-G-C 8.FAM230A.ENST00000434783.3.missense.322E/Q FAM230A E322Q 0 ANQDAAQGI ENST00000434783.3 Not Supported HLA-G*01:09 3 None 0 0 5681.680 9654.430 8.800 20.000 NA NA NA NA 0.500 Poor False Pending -22-26936775-26936776-G-T 11.TPST2.ENST00000338754.4.missense.274P/H TPST2 P274H 0 KHGGVSLSK ENST00000338754.4 Not Supported HLA-E*01:01 2 None 0 0 6539.790 20149.140 13.000 53.000 NA NA NA NA 0.179 Poor False Pending -22-29886116-29886117-C-A 12.NEFH.ENST00000310624.6.missense.830P/T NEFH P830T 0 KTQEVKVKE ENST00000310624.6 Not Supported HLA-G*01:09 2 None 0 0 7366.350 25842.400 14.000 50.000 NA NA NA NA 0.038 Poor False Pending -22-38119219-38119220-GA-G 16.TRIOBP.ENST00000406386.3.FS.219GA/G TRIOBP FS219 0 GEKAGCPWS ENST00000406386.3 Not Supported HLA-E*01:01 1-9 None 0 0 8119.760 NA 18.000 NA NA NA NA NA 0.768 Poor False Pending -22-22550449-22550450-C-G 9.IGLV6-57.ENST00000390285.3.missense.43R/G IGLV6-57 R43G 0 KTVTISCTG ENST00000390285.3 Not Supported HLA-G*01:09 9 None 0 0 9447.760 15208.390 19.000 31.000 NA NA NA NA 1.000 Poor True Pending -22-50555769-50555770-G-A 21.MOV10L1.ENST00000262794.5.missense.482A/T MOV10L1 A482T 0 KTTVVVTTQ ENST00000262794.5 Not Supported HLA-G*01:09 8 None 0 0 10874.650 16763.860 23.000 34.000 NA NA NA NA 0.042 Poor False Pending -4-40434704-40434725-AGCGGCTGCGGCGGCTGCGGCC-A 2.RBM47.ENST00000381793.2.inframe_del.495-502AAAAAAAA/A RBM47 AAAAAAAA495-502A 0 SAAAAAAAV ENST00000381793.2 Not Supported HLA-E*01:01 8-9 None 0 0 21040.320 21040.320 21.000 30.000 NA NA NA NA 0.977 Poor True Pending +22-50869713-50869714-C-A 24.PPP6R2.ENST00000395741.3.missense.414S/Y 1 PPP6R2 S414Y 1 GYESRVEPP ENST00000395741.3 Not Supported HLA-G*01:09 2 None 1 0 5620.540 22209.930 8.700 44.000 NA NA NA NA 0.043 Poor False Pending +22-20709231-20709232-G-C 8.FAM230A.ENST00000434783.3.missense.322E/Q 1 FAM230A E322Q 1 ANQDAAQGI ENST00000434783.3 Not Supported HLA-G*01:09 3 None 1 0 5681.680 9654.430 8.800 20.000 NA NA NA NA 0.500 Poor False Pending +22-26936775-26936776-G-T 11.TPST2.ENST00000338754.4.missense.274P/H 1 TPST2 P274H 1 KHGGVSLSK ENST00000338754.4 Not Supported HLA-E*01:01 2 None 1 0 6539.790 20149.140 13.000 53.000 NA NA NA NA 0.179 Poor False Pending +22-29886116-29886117-C-A 12.NEFH.ENST00000310624.6.missense.830P/T 1 NEFH P830T 1 KTQEVKVKE ENST00000310624.6 Not Supported HLA-G*01:09 2 None 1 0 7366.350 25842.400 14.000 50.000 NA NA NA NA 0.038 Poor False Pending +22-38119219-38119220-GA-G 16.TRIOBP.ENST00000406386.3.FS.219GA/G 1 TRIOBP FS219 1 GEKAGCPWS ENST00000406386.3 Not Supported HLA-E*01:01 1-9 None 1 0 8119.760 NA 18.000 NA NA NA NA NA 0.768 Poor False Pending +22-22550449-22550450-C-G 9.IGLV6-57.ENST00000390285.3.missense.43R/G 1 IGLV6-57 R43G 1 KTVTISCTG ENST00000390285.3 Not Supported HLA-G*01:09 9 None 1 0 9447.760 15208.390 19.000 31.000 NA NA NA NA 1.000 Poor True Pending +22-50555769-50555770-G-A 21.MOV10L1.ENST00000262794.5.missense.482A/T 1 MOV10L1 A482T 1 KTTVVVTTQ ENST00000262794.5 Not Supported HLA-G*01:09 8 None 1 0 10874.650 16763.860 23.000 34.000 NA NA NA NA 0.042 Poor False Pending +4-40434704-40434725-AGCGGCTGCGGCGGCTGCGGCC-A 2.RBM47.ENST00000381793.2.inframe_del.495-502AAAAAAAA/A 1 RBM47 AAAAAAAA495-502A 1 SAAAAAAAV ENST00000381793.2 Not Supported HLA-E*01:01 8-9 None 1 0 21040.320 21040.320 21.000 30.000 NA NA NA NA 0.977 Poor True Pending diff --git a/tests/test_data/pvacseq/MHC_Class_II/Test.all_epitopes.aggregated.metrics.json b/tests/test_data/pvacseq/MHC_Class_II/Test.all_epitopes.aggregated.metrics.json index 0cd11d6b..7c42aa77 100644 --- a/tests/test_data/pvacseq/MHC_Class_II/Test.all_epitopes.aggregated.metrics.json +++ b/tests/test_data/pvacseq/MHC_Class_II/Test.all_epitopes.aggregated.metrics.json @@ -1441,11 +1441,126 @@ } }, "22-18020271-18020272-G-A": { - "good_binders": {}, - "sets": [], - "transcript_counts": [], - "peptide_counts": [], - "set_expr": [], + "good_binders": { + "Transcript Set 1": { + "peptides": { + "GGSHVWTHSRDPEGS": { + "ic50s_MT": [ + 6419.7001953125 + ], + "percentiles_MT": [ + 73.0 + ], + "ic50s_WT": [ + 1915.0 + ], + "percentiles_WT": [ + 47.0 + ], + "hla_types": [ + "HLA-DRB1*11:01" + ], + "mutation_position": "8", + "problematic_positions": "None", + "anchor_fails": "None", + "individual_ic50_calls": { + "algorithms": [ + "NNalign" + ], + "MT": { + "HLA-DRB1*11:01": [ + 6419.7 + ] + }, + "WT": { + "HLA-DRB1*11:01": [ + 1915.0 + ] + } + }, + "individual_ic50_percentile_calls": { + "algorithms": [ + "NNalign" + ], + "MT": { + "HLA-DRB1*11:01": [ + 73.0 + ] + }, + "WT": { + "HLA-DRB1*11:01": [ + 47.0 + ] + } + }, + "individual_el_calls": { + "algorithms": [], + "MT": { + "HLA-DRB1*11:01": [] + }, + "WT": { + "HLA-DRB1*11:01": [] + } + }, + "individual_el_percentile_calls": { + "algorithms": [], + "MT": { + "HLA-DRB1*11:01": [] + }, + "WT": { + "HLA-DRB1*11:01": [] + } + }, + "individual_percentile_calls": { + "algorithms": [ + "NNalign" + ], + "MT": { + "HLA-DRB1*11:01": [ + 73.0 + ] + }, + "WT": { + "HLA-DRB1*11:01": [ + 47.0 + ] + } + }, + "wt_peptide": "GGSHVWTRSRDPEGS" + } + }, + "transcripts": [ + "ENST00000262608.8-CECR2-R/H-535" + ], + "transcript_expr": [ + "NA" + ], + "tsl": [ + "Not Supported" + ], + "biotype": [ + "protein_coding" + ], + "transcript_length": [ + 1443 + ], + "transcript_count": 1, + "peptide_count": 1, + "total_expr": 0 + } + }, + "sets": [ + "Transcript Set 1" + ], + "transcript_counts": [ + 1 + ], + "peptide_counts": [ + 1 + ], + "set_expr": [ + 0 + ], "DNA VAF": 0.071, "RNA VAF": "NA", "gene_expr": "NA", @@ -2600,11 +2715,126 @@ } }, "22-19175521-19175522-G-T": { - "good_binders": {}, - "sets": [], - "transcript_counts": [], - "peptide_counts": [], - "set_expr": [], + "good_binders": { + "Transcript Set 1": { + "peptides": { + "KSVNEALNNLLTEEE": { + "ic50s_MT": [ + 11571.599609375 + ], + "percentiles_MT": [ + 85.0 + ], + "ic50s_WT": [ + 5425.5 + ], + "percentiles_WT": [ + 69.0 + ], + "hla_types": [ + "HLA-DRB1*11:01" + ], + "mutation_position": "9", + "problematic_positions": "None", + "anchor_fails": "None", + "individual_ic50_calls": { + "algorithms": [ + "NNalign" + ], + "MT": { + "HLA-DRB1*11:01": [ + 11571.6 + ] + }, + "WT": { + "HLA-DRB1*11:01": [ + 5425.5 + ] + } + }, + "individual_ic50_percentile_calls": { + "algorithms": [ + "NNalign" + ], + "MT": { + "HLA-DRB1*11:01": [ + 85.0 + ] + }, + "WT": { + "HLA-DRB1*11:01": [ + 69.0 + ] + } + }, + "individual_el_calls": { + "algorithms": [], + "MT": { + "HLA-DRB1*11:01": [] + }, + "WT": { + "HLA-DRB1*11:01": [] + } + }, + "individual_el_percentile_calls": { + "algorithms": [], + "MT": { + "HLA-DRB1*11:01": [] + }, + "WT": { + "HLA-DRB1*11:01": [] + } + }, + "individual_percentile_calls": { + "algorithms": [ + "NNalign" + ], + "MT": { + "HLA-DRB1*11:01": [ + 85.0 + ] + }, + "WT": { + "HLA-DRB1*11:01": [ + 69.0 + ] + } + }, + "wt_peptide": "KSVNEALNHLLTEEE" + } + }, + "transcripts": [ + "ENST00000263200.10-CLTCL1-H/N-1469" + ], + "transcript_expr": [ + "NA" + ], + "tsl": [ + "Not Supported" + ], + "biotype": [ + "protein_coding" + ], + "transcript_length": [ + 1640 + ], + "transcript_count": 1, + "peptide_count": 1, + "total_expr": 0 + } + }, + "sets": [ + "Transcript Set 1" + ], + "transcript_counts": [ + 1 + ], + "peptide_counts": [ + 1 + ], + "set_expr": [ + 0 + ], "DNA VAF": 0.1, "RNA VAF": "NA", "gene_expr": "NA", @@ -2618,11 +2848,126 @@ } }, "22-20709231-20709232-G-C": { - "good_binders": {}, - "sets": [], - "transcript_counts": [], - "peptide_counts": [], - "set_expr": [], + "good_binders": { + "Transcript Set 1": { + "peptides": { + "VQGIANQDAAQGIAK": { + "ic50s_MT": [ + 6577.2001953125 + ], + "percentiles_MT": [ + 73.0 + ], + "ic50s_WT": [ + 9312.4 + ], + "percentiles_WT": [ + 81.0 + ], + "hla_types": [ + "HLA-DRB1*11:01" + ], + "mutation_position": "7", + "problematic_positions": "None", + "anchor_fails": "None", + "individual_ic50_calls": { + "algorithms": [ + "NNalign" + ], + "MT": { + "HLA-DRB1*11:01": [ + 6577.2 + ] + }, + "WT": { + "HLA-DRB1*11:01": [ + 9312.4 + ] + } + }, + "individual_ic50_percentile_calls": { + "algorithms": [ + "NNalign" + ], + "MT": { + "HLA-DRB1*11:01": [ + 73.0 + ] + }, + "WT": { + "HLA-DRB1*11:01": [ + 81.0 + ] + } + }, + "individual_el_calls": { + "algorithms": [], + "MT": { + "HLA-DRB1*11:01": [] + }, + "WT": { + "HLA-DRB1*11:01": [] + } + }, + "individual_el_percentile_calls": { + "algorithms": [], + "MT": { + "HLA-DRB1*11:01": [] + }, + "WT": { + "HLA-DRB1*11:01": [] + } + }, + "individual_percentile_calls": { + "algorithms": [ + "NNalign" + ], + "MT": { + "HLA-DRB1*11:01": [ + 73.0 + ] + }, + "WT": { + "HLA-DRB1*11:01": [ + 81.0 + ] + } + }, + "wt_peptide": "VQGIANEDAAQGIAK" + } + }, + "transcripts": [ + "ENST00000434783.3-FAM230A-E/Q-322" + ], + "transcript_expr": [ + "NA" + ], + "tsl": [ + "Not Supported" + ], + "biotype": [ + "protein_coding" + ], + "transcript_length": [ + 905 + ], + "transcript_count": 1, + "peptide_count": 1, + "total_expr": 0 + } + }, + "sets": [ + "Transcript Set 1" + ], + "transcript_counts": [ + 1 + ], + "peptide_counts": [ + 1 + ], + "set_expr": [ + 0 + ], "DNA VAF": 0.5, "RNA VAF": "NA", "gene_expr": "NA", @@ -5651,21 +5996,154 @@ }, "SLLHTVSPEPARPPQ": { "ic50s_MT": [ - 4019.300048828125 + 4019.300048828125 + ], + "percentiles_MT": [ + 63.0 + ], + "ic50s_WT": [ + 8706.6 + ], + "percentiles_WT": [ + 79.0 + ], + "hla_types": [ + "HLA-DRB1*11:01" + ], + "mutation_position": "11", + "problematic_positions": "None", + "anchor_fails": "None", + "individual_ic50_calls": { + "algorithms": [ + "NNalign" + ], + "MT": { + "HLA-DRB1*11:01": [ + 4019.3 + ] + }, + "WT": { + "HLA-DRB1*11:01": [ + 8706.6 + ] + } + }, + "individual_ic50_percentile_calls": { + "algorithms": [ + "NNalign" + ], + "MT": { + "HLA-DRB1*11:01": [ + 63.0 + ] + }, + "WT": { + "HLA-DRB1*11:01": [ + 79.0 + ] + } + }, + "individual_el_calls": { + "algorithms": [], + "MT": { + "HLA-DRB1*11:01": [] + }, + "WT": { + "HLA-DRB1*11:01": [] + } + }, + "individual_el_percentile_calls": { + "algorithms": [], + "MT": { + "HLA-DRB1*11:01": [] + }, + "WT": { + "HLA-DRB1*11:01": [] + } + }, + "individual_percentile_calls": { + "algorithms": [ + "NNalign" + ], + "MT": { + "HLA-DRB1*11:01": [ + 63.0 + ] + }, + "WT": { + "HLA-DRB1*11:01": [ + 79.0 + ] + } + }, + "wt_peptide": "SLLHTVSPEPPRPPQ" + } + }, + "transcripts": [ + "ENST00000343632.4-GGA1-P/A-484" + ], + "transcript_expr": [ + "NA" + ], + "tsl": [ + "Not Supported" + ], + "biotype": [ + "protein_coding" + ], + "transcript_length": [ + 639 + ], + "transcript_count": 1, + "peptide_count": 5, + "total_expr": 0 + } + }, + "sets": [ + "Transcript Set 1" + ], + "transcript_counts": [ + 1 + ], + "peptide_counts": [ + 5 + ], + "set_expr": [ + 0 + ], + "DNA VAF": 0.486, + "RNA VAF": "NA", + "gene_expr": "NA", + "best_peptide_mt": "TSLLHTVSPEPARPP", + "best_peptide_wt": "TSLLHTVSPEPPRPP", + "best_hla_allele": "HLA-DRB1*11:01", + "reference_matches": { + "count": 0, + "query_peptide": "HTVSPEPARPPQQPV", + "matches": [] + } + }, + "22-38119219-38119220-GA-G": { + "good_binders": { + "Transcript Set 1": { + "peptides": { + "SGEKAGCPWSGTGQH": { + "ic50s_MT": [ + 11805.0 ], "percentiles_MT": [ - 63.0 + 86.0 ], "ic50s_WT": [ - 8706.6 + "NA" ], "percentiles_WT": [ - 79.0 + "NA" ], "hla_types": [ "HLA-DRB1*11:01" ], - "mutation_position": "11", + "mutation_position": "1-15", "problematic_positions": "None", "anchor_fails": "None", "individual_ic50_calls": { @@ -5674,12 +6152,12 @@ ], "MT": { "HLA-DRB1*11:01": [ - 4019.3 + 11805.0 ] }, "WT": { "HLA-DRB1*11:01": [ - 8706.6 + "NA" ] } }, @@ -5689,12 +6167,12 @@ ], "MT": { "HLA-DRB1*11:01": [ - 63.0 + 86.0 ] }, "WT": { "HLA-DRB1*11:01": [ - 79.0 + "NA" ] } }, @@ -5722,20 +6200,20 @@ ], "MT": { "HLA-DRB1*11:01": [ - 63.0 + 86.0 ] }, "WT": { "HLA-DRB1*11:01": [ - 79.0 + "NA" ] } }, - "wt_peptide": "SLLHTVSPEPPRPPQ" + "wt_peptide": "FS-NA" } }, "transcripts": [ - "ENST00000343632.4-GGA1-P/A-484" + "ENST00000406386.3-TRIOBP-G/X-219" ], "transcript_expr": [ "NA" @@ -5747,10 +6225,10 @@ "protein_coding" ], "transcript_length": [ - 639 + 2365 ], "transcript_count": 1, - "peptide_count": 5, + "peptide_count": 1, "total_expr": 0 } }, @@ -5761,29 +6239,11 @@ 1 ], "peptide_counts": [ - 5 + 1 ], "set_expr": [ 0 ], - "DNA VAF": 0.486, - "RNA VAF": "NA", - "gene_expr": "NA", - "best_peptide_mt": "TSLLHTVSPEPARPP", - "best_peptide_wt": "TSLLHTVSPEPPRPP", - "best_hla_allele": "HLA-DRB1*11:01", - "reference_matches": { - "count": 0, - "query_peptide": "HTVSPEPARPPQQPV", - "matches": [] - } - }, - "22-38119219-38119220-GA-G": { - "good_binders": {}, - "sets": [], - "transcript_counts": [], - "peptide_counts": [], - "set_expr": [], "DNA VAF": 0.768, "RNA VAF": "NA", "gene_expr": "NA", @@ -13028,11 +13488,126 @@ } }, "22-50869713-50869714-C-A": { - "good_binders": {}, - "sets": [], - "transcript_counts": [], - "peptide_counts": [], - "set_expr": [], + "good_binders": { + "Transcript Set 1": { + "peptides": { + "LSHAAREERTEASGY": { + "ic50s_MT": [ + 14140.7998046875 + ], + "percentiles_MT": [ + 89.0 + ], + "ic50s_WT": [ + 13690.0 + ], + "percentiles_WT": [ + 88.0 + ], + "hla_types": [ + "HLA-DRB1*11:01" + ], + "mutation_position": "15", + "problematic_positions": "None", + "anchor_fails": "None", + "individual_ic50_calls": { + "algorithms": [ + "NNalign" + ], + "MT": { + "HLA-DRB1*11:01": [ + 14140.8 + ] + }, + "WT": { + "HLA-DRB1*11:01": [ + 13690.0 + ] + } + }, + "individual_ic50_percentile_calls": { + "algorithms": [ + "NNalign" + ], + "MT": { + "HLA-DRB1*11:01": [ + 89.0 + ] + }, + "WT": { + "HLA-DRB1*11:01": [ + 88.0 + ] + } + }, + "individual_el_calls": { + "algorithms": [], + "MT": { + "HLA-DRB1*11:01": [] + }, + "WT": { + "HLA-DRB1*11:01": [] + } + }, + "individual_el_percentile_calls": { + "algorithms": [], + "MT": { + "HLA-DRB1*11:01": [] + }, + "WT": { + "HLA-DRB1*11:01": [] + } + }, + "individual_percentile_calls": { + "algorithms": [ + "NNalign" + ], + "MT": { + "HLA-DRB1*11:01": [ + 89.0 + ] + }, + "WT": { + "HLA-DRB1*11:01": [ + 88.0 + ] + } + }, + "wt_peptide": "LSHAAREERTEASGS" + } + }, + "transcripts": [ + "ENST00000395741.3-PPP6R2-S/Y-414" + ], + "transcript_expr": [ + "NA" + ], + "tsl": [ + "Not Supported" + ], + "biotype": [ + "protein_coding" + ], + "transcript_length": [ + 933 + ], + "transcript_count": 1, + "peptide_count": 1, + "total_expr": 0 + } + }, + "sets": [ + "Transcript Set 1" + ], + "transcript_counts": [ + 1 + ], + "peptide_counts": [ + 1 + ], + "set_expr": [ + 0 + ], "DNA VAF": 0.043, "RNA VAF": "NA", "gene_expr": "NA", @@ -13046,11 +13621,126 @@ } }, "4-40434704-40434725-AGCGGCTGCGGCGGCTGCGGCC-A": { - "good_binders": {}, - "sets": [], - "transcript_counts": [], - "peptide_counts": [], - "set_expr": [], + "good_binders": { + "Transcript Set 1": { + "peptides": { + "SAAAAAAAVIPTVST": { + "ic50s_MT": [ + 14537.0 + ], + "percentiles_MT": [ + 89.0 + ], + "ic50s_WT": [ + 14673.4 + ], + "percentiles_WT": [ + 89.0 + ], + "hla_types": [ + "HLA-DRB1*11:01" + ], + "mutation_position": "8-9", + "problematic_positions": "None", + "anchor_fails": "None", + "individual_ic50_calls": { + "algorithms": [ + "NNalign" + ], + "MT": { + "HLA-DRB1*11:01": [ + 14537.0 + ] + }, + "WT": { + "HLA-DRB1*11:01": [ + 14673.4 + ] + } + }, + "individual_ic50_percentile_calls": { + "algorithms": [ + "NNalign" + ], + "MT": { + "HLA-DRB1*11:01": [ + 89.0 + ] + }, + "WT": { + "HLA-DRB1*11:01": [ + 89.0 + ] + } + }, + "individual_el_calls": { + "algorithms": [], + "MT": { + "HLA-DRB1*11:01": [] + }, + "WT": { + "HLA-DRB1*11:01": [] + } + }, + "individual_el_percentile_calls": { + "algorithms": [], + "MT": { + "HLA-DRB1*11:01": [] + }, + "WT": { + "HLA-DRB1*11:01": [] + } + }, + "individual_percentile_calls": { + "algorithms": [ + "NNalign" + ], + "MT": { + "HLA-DRB1*11:01": [ + 89.0 + ] + }, + "WT": { + "HLA-DRB1*11:01": [ + 89.0 + ] + } + }, + "wt_peptide": "AAAAAAAAVIPTVST" + } + }, + "transcripts": [ + "ENST00000381793.2-RBM47-AAAAAAAA/A-495-502" + ], + "transcript_expr": [ + "NA" + ], + "tsl": [ + "Not Supported" + ], + "biotype": [ + "protein_coding" + ], + "transcript_length": [ + 593 + ], + "transcript_count": 1, + "peptide_count": 1, + "total_expr": 0 + } + }, + "sets": [ + "Transcript Set 1" + ], + "transcript_counts": [ + 1 + ], + "peptide_counts": [ + 1 + ], + "set_expr": [ + 0 + ], "DNA VAF": 0.977, "RNA VAF": "NA", "gene_expr": "NA", diff --git a/tests/test_data/pvacseq/MHC_Class_II/Test.all_epitopes.aggregated.tsv b/tests/test_data/pvacseq/MHC_Class_II/Test.all_epitopes.aggregated.tsv index 54c607da..8c36a50c 100644 --- a/tests/test_data/pvacseq/MHC_Class_II/Test.all_epitopes.aggregated.tsv +++ b/tests/test_data/pvacseq/MHC_Class_II/Test.all_epitopes.aggregated.tsv @@ -16,9 +16,9 @@ ID Index DRB1*11:01 Gene AA Change Num Passing Transcripts Best Peptide Best Tra 22-22550449-22550450-C-G 9.IGLV6-57.ENST00000390285.3.missense.43R/G 3 IGLV6-57 R43G 1 PGKTVTISCTGSSGS ENST00000390285.3 Not Supported HLA-DRB1*11:01 11 None 3 0 2994.600 726.800 56.000 30.000 NA NA NA NA 1.000 Poor True Pending 22-38027027-38027028-C-G 15.GGA1.ENST00000343632.4.missense.484P/A 5 GGA1 P484A 1 TSLLHTVSPEPARPP ENST00000343632.4 Not Supported HLA-DRB1*11:01 12 None 5 0 3433.300 6964.200 59.000 75.000 NA NA NA NA 0.486 Poor False Pending 22-29886116-29886117-C-A 12.NEFH.ENST00000310624.6.missense.830P/T 1 NEFH P830T 1 KTQEVKVKEPPKKAE ENST00000310624.6 Not Supported HLA-DRB1*11:01 2 None 1 0 4730.400 4999.500 66.000 68.000 NA NA NA NA 0.038 Poor False Pending -22-18020271-18020272-G-A 5.CECR2.ENST00000262608.8.missense.535R/H CECR2 R535H 0 GGSHVWTHSRDPEGS ENST00000262608.8 Not Supported HLA-DRB1*11:01 8 None 0 0 6419.700 1915.000 73.000 47.000 NA NA NA NA 0.071 Poor False Pending -22-20709231-20709232-G-C 8.FAM230A.ENST00000434783.3.missense.322E/Q FAM230A E322Q 0 VQGIANQDAAQGIAK ENST00000434783.3 Not Supported HLA-DRB1*11:01 7 None 0 0 6577.200 9312.400 73.000 81.000 NA NA NA NA 0.500 Poor False Pending -22-19175521-19175522-G-T 7.CLTCL1.ENST00000263200.10.missense.1469H/N CLTCL1 H1469N 0 KSVNEALNNLLTEEE ENST00000263200.10 Not Supported HLA-DRB1*11:01 9 None 0 0 11571.600 5425.500 85.000 69.000 NA NA NA NA 0.100 Poor False Pending -22-38119219-38119220-GA-G 16.TRIOBP.ENST00000406386.3.FS.219GA/G TRIOBP FS219 0 SGEKAGCPWSGTGQH ENST00000406386.3 Not Supported HLA-DRB1*11:01 1-15 None 0 0 11805.000 NA 86.000 NA NA NA NA NA 0.768 Poor False Pending -22-50869713-50869714-C-A 24.PPP6R2.ENST00000395741.3.missense.414S/Y PPP6R2 S414Y 0 LSHAAREERTEASGY ENST00000395741.3 Not Supported HLA-DRB1*11:01 15 None 0 0 14140.800 13690.000 89.000 88.000 NA NA NA NA 0.043 Poor False Pending -4-40434704-40434725-AGCGGCTGCGGCGGCTGCGGCC-A 2.RBM47.ENST00000381793.2.inframe_del.495-502AAAAAAAA/A RBM47 AAAAAAAA495-502A 0 SAAAAAAAVIPTVST ENST00000381793.2 Not Supported HLA-DRB1*11:01 8-9 None 0 0 14537.000 14673.400 89.000 89.000 NA NA NA NA 0.977 Poor True Pending +22-18020271-18020272-G-A 5.CECR2.ENST00000262608.8.missense.535R/H 1 CECR2 R535H 1 GGSHVWTHSRDPEGS ENST00000262608.8 Not Supported HLA-DRB1*11:01 8 None 1 0 6419.700 1915.000 73.000 47.000 NA NA NA NA 0.071 Poor False Pending +22-20709231-20709232-G-C 8.FAM230A.ENST00000434783.3.missense.322E/Q 1 FAM230A E322Q 1 VQGIANQDAAQGIAK ENST00000434783.3 Not Supported HLA-DRB1*11:01 7 None 1 0 6577.200 9312.400 73.000 81.000 NA NA NA NA 0.500 Poor False Pending +22-19175521-19175522-G-T 7.CLTCL1.ENST00000263200.10.missense.1469H/N 1 CLTCL1 H1469N 1 KSVNEALNNLLTEEE ENST00000263200.10 Not Supported HLA-DRB1*11:01 9 None 1 0 11571.600 5425.500 85.000 69.000 NA NA NA NA 0.100 Poor False Pending +22-38119219-38119220-GA-G 16.TRIOBP.ENST00000406386.3.FS.219GA/G 1 TRIOBP FS219 1 SGEKAGCPWSGTGQH ENST00000406386.3 Not Supported HLA-DRB1*11:01 1-15 None 1 0 11805.000 NA 86.000 NA NA NA NA NA 0.768 Poor False Pending +22-50869713-50869714-C-A 24.PPP6R2.ENST00000395741.3.missense.414S/Y 1 PPP6R2 S414Y 1 LSHAAREERTEASGY ENST00000395741.3 Not Supported HLA-DRB1*11:01 15 None 1 0 14140.800 13690.000 89.000 88.000 NA NA NA NA 0.043 Poor False Pending +4-40434704-40434725-AGCGGCTGCGGCGGCTGCGGCC-A 2.RBM47.ENST00000381793.2.inframe_del.495-502AAAAAAAA/A 1 RBM47 AAAAAAAA495-502A 1 SAAAAAAAVIPTVST ENST00000381793.2 Not Supported HLA-DRB1*11:01 8-9 None 1 0 14537.000 14673.400 89.000 89.000 NA NA NA NA 0.977 Poor True Pending diff --git a/tests/test_data/pvacseq/phased/MHC_Class_I/Test.all_epitopes.aggregated.tsv b/tests/test_data/pvacseq/phased/MHC_Class_I/Test.all_epitopes.aggregated.tsv index 93bb28b8..dd6ce4ff 100644 --- a/tests/test_data/pvacseq/phased/MHC_Class_I/Test.all_epitopes.aggregated.tsv +++ b/tests/test_data/pvacseq/phased/MHC_Class_I/Test.all_epitopes.aggregated.tsv @@ -1,409 +1,409 @@ ID Index E*01:01 Gene AA Change Num Passing Transcripts Best Peptide Best Transcript TSL Allele Pos Prob Pos Num Included Peptides Num Passing Peptides IC50 MT IC50 WT %ile MT %ile WT RNA Expr RNA VAF Allele Expr RNA Depth DNA VAF Tier Evaluation -chr14-55180753-55180754-G-A 263.DLGAP5.ENST00000247191.6.missense.202S/L DLGAP5 S202L 0 VMPTLLRM ENST00000247191.6 1 HLA-E*01:01 5 None 0 0 5857.400 2658.680 0.120 0.030 NA NA NA NA 0.239 Poor Pending -chr14-91235009-91235029-GGTACAGCTCATCGAGGAGTT-G 266.GPR68.ENST00000531499.2.FS.8-14GGTACAGCTCATCGAGGAGTT/G GPR68 FS8-14 0 LPGCGPSL ENST00000531499.2 1 HLA-E*01:01 1-8 None 0 0 7028.130 NA 0.170 NA NA NA NA NA 0.127 Poor Pending -chr19-14049194-14049195-C-T 339.IL27RA.ENST00000263379.3.missense.428A/V IL27RA A428V 0 VPPGTPAI ENST00000263379.3 1 HLA-E*01:01 1 None 0 0 7518.130 13004.510 0.200 0.750 NA NA NA NA 0.301 Poor Pending -chr1-45058674-45058675-G-A 12.ZSWIM5.ENST00000359600.5.missense.396L/F ZSWIM5 L396F 0 VADPRFTL ENST00000359600.5 1 HLA-E*01:01 6 None 0 0 7602.960 11507.390 0.210 0.550 NA NA NA NA 0.360 Poor Pending -chr4-108650681-108650682-C-G 76.OSTC.ENST00000512478.2.missense.9F/L OSTC F9L 0 TLYRVPLL ENST00000512478.2 5 HLA-E*01:01 7 None 0 0 8394.910 11601.650 0.270 0.560 NA NA NA NA 0.465 Poor Pending -chr6-27312072-27312073-T-C 111.POM121L2.ENST00000444565.1.missense.33Q/R POM121L2 Q33R 0 RRPPRPLH ENST00000444565.1 NA HLA-E*01:01 5 None 0 0 9499.730 15005.710 0.340 1.200 NA NA NA NA 0.669 Poor Pending -chr13-25541936-25541937-G-C 250.ATP8A2.ENST00000381655.6.missense.224D/H ATP8A2 D224H 0 LMQTREVL ENST00000381655.6 1 HLA-E*01:01 1 None 0 0 9985.260 18778.930 0.380 2.300 NA NA NA NA 0.317 Poor Pending -chr13-25541937-25541938-A-T 251.ATP8A2.ENST00000381655.6.missense.224D/V ATP8A2 D224V 0 LMQTREVL ENST00000381655.6 1 HLA-E*01:01 1 None 0 0 9985.260 18778.930 0.380 2.300 NA NA NA NA 0.317 Poor Pending -chr2-222689427-222689428-G-T 52.MOGAT1.ENST00000446656.3.missense.146W/L MOGAT1 W146L 0 LLFWCPVF ENST00000446656.3 5 HLA-E*01:01 2 None 0 0 10003.530 19835.920 0.380 2.600 NA NA NA NA 0.343 Poor Pending -chr17-7588499-7588500-G-C 316.SOX15.ENST00000250055.2.missense.194Q/E SOX15 Q194E 0 LPESDPRL ENST00000250055.2 1 HLA-E*01:01 3 None 0 0 10054.100 8090.820 0.390 0.250 NA NA NA NA 0.712 Poor Pending -chr4-40808808-40808809-A-G 72.NSUN7.ENST00000381782.6.missense.676Y/C NSUN7 Y676C 0 RMPTQHLC ENST00000381782.6 1 HLA-E*01:01 8 None 0 0 11124.570 8084.780 0.520 0.250 NA NA NA NA 0.466 Poor Pending -chr1-43432295-43432296-G-C 11.SZT2.ENST00000562955.2.missense.1710G/R SZT2 G1710R 0 HLPRHVLL ENST00000562955.2 5 HLA-E*01:01 4 None 0 0 11567.430 17027.460 0.560 1.700 NA NA NA NA 0.309 Poor Pending -chr11-63290369-63290370-G-A 235.SLC22A10.ENST00000332793.10.missense.69E/K SLC22A10 E69K 0 ILSKDALL ENST00000332793.10 1 HLA-E*01:01 4 None 0 0 12068.340 15757.820 0.600 1.400 NA NA NA NA 0.544 Poor Pending -chr15-62819536-62819537-G-A 277.TLN2.ENST00000561311.5.missense.2265E/K TLN2 E2265K 0 LQKPTPKF ENST00000561311.5 5 HLA-E*01:01 7 None 0 0 12103.650 14467.010 0.610 1.000 NA NA NA NA 0.458 Poor Pending -chr3-184239802-184239803-C-T 69.VWA5B2.ENST00000426955.6.missense.836A/V VWA5B2 A836V 0 VPPQVPRC ENST00000426955.6 1 HLA-E*01:01 5 None 0 0 12634.200 6168.640 0.700 0.140 NA NA NA NA 0.430 Poor Pending -chr6-33315988-33315989-T-C 135.ZBTB22.ENST00000431845.2.missense.310T/A ZBTB22 T310A 0 NCPAPAPL ENST00000431845.2 1 HLA-E*01:01 6 None 0 0 12664.580 15601.230 0.700 1.400 NA NA NA NA 0.734 Poor Pending -chr5-145817966-145817967-A-G 91.PRELID2.ENST00000334744.8.missense.111C/R PRELID2 C111R 0 MAIRSHRL ENST00000334744.8 2 HLA-E*01:01 7 None 0 0 12791.130 13626.930 0.720 0.810 NA NA NA NA 0.330 Poor Pending -chr11-64593669-64593670-G-C 238.SLC22A12.ENST00000377574.5.missense.233V/L SLC22A12 V233L 0 AARARPLL ENST00000377574.5 1 HLA-E*01:01 8 None 0 0 12864.840 27811.220 0.730 7.300 NA NA NA NA 0.161 Poor Pending -chrX-3027435-3027436-C-T 369.ARSH.ENST00000381130.2.missense.387T/M ARSH T387M 0 LMDIYPML ENST00000381130.2 1 HLA-E*01:01 7 None 0 0 13539.050 17374.370 0.800 1.800 NA NA NA NA 0.494 Poor Pending -chr7-47833094-47833095-G-A 173.PKD1L1.ENST00000289672.6.missense.2111T/I PKD1L1 T2111I 0 IQAPSSGL ENST00000289672.6 1 HLA-E*01:01 1 None 0 0 13758.790 17418.780 0.850 1.800 NA NA NA NA 0.301 Poor Pending -chr6-31636813-31636814-C-T 126.PRRC2A.ENST00000376033.2.missense.2006P/S PRRC2A P2006S 0 PPPAPPSL ENST00000376033.2 1 HLA-E*01:01 7 None 0 0 13771.150 13218.430 0.850 0.770 NA NA NA NA 0.682 Poor Pending -chr8-125436370-125436371-C-T 198.TRIB1.ENST00000311922.3.missense.340S/F TRIB1 S340F 0 HPWFEFVL ENST00000311922.3 1 HLA-E*01:01 6 None 0 0 14102.880 31337.800 0.920 13.000 NA NA NA NA 0.136 Poor Pending -chr16-81268088-81268089-A-T 305.BCO1.ENST00000258168.6.missense.267R/S BCO1 R267S 0 SMSWASCL ENST00000258168.6 1 HLA-E*01:01 1 None 0 0 14379.620 8166.810 0.980 0.260 NA NA NA NA 0.484 Poor Pending -chr9-4286160-4286161-G-T 202.GLIS3.ENST00000381971.7.missense.89Q/K GLIS3 Q89K 0 LSPRRKML ENST00000381971.7 5 HLA-E*01:01 6 None 0 0 14545.490 13435.150 1.000 0.790 NA NA NA NA 0.152 Poor Pending -chr9-81992222-81992223-C-G 205.SPATA31D1.ENST00000344803.2.missense.585Q/E SPATA31D1 Q585E 0 ESPFRALL ENST00000344803.2 2 HLA-E*01:01 1 None 0 0 14823.360 11381.450 1.200 0.540 NA NA NA NA 0.699 Poor Pending -chr8-132948805-132948806-C-G 200.TG.ENST00000220616.8.missense.1755P/R TG P1755R 0 LLSSRSVL ENST00000220616.8 1 HLA-E*01:01 5 None 0 0 15188.490 25844.630 1.300 5.700 NA NA NA NA 0.994 Poor Pending -chr16-87417563-87417564-G-C 308.ZCCHC14.ENST00000268616.8.missense.290L/V ZCCHC14 L290V 0 LMPSSVQT ENST00000268616.8 1 HLA-E*01:01 6 None 0 0 15487.540 10813.630 1.300 0.490 NA NA NA NA 0.297 Poor Pending -chr5-115130597-115130604-ACTAACTG-A 85.TRIM36.ENST00000282369.7.FS.607-609ACTAACTG/A TRIM36 FS607-609 0 VRMPVLIL ENST00000282369.7 1 HLA-E*01:01 1-8 None 0 0 15517.220 NA 1.300 NA NA NA NA NA 1.000 Poor Pending -chr16-57915319-57915320-G-T 294.CNGB1.ENST00000251102.12.missense.745L/I CNGB1 L745I 0 ILPLDFLY ENST00000251102.12 1 HLA-E*01:01 1 None 0 0 15571.710 18325.300 1.300 2.100 NA NA NA NA 0.639 Poor Pending -chr3-38698510-38698511-G-A 56.SCN10A.ENST00000449082.3.missense.1570T/M SCN10A T1570M 0 MLFRVIRL ENST00000449082.3 1 HLA-E*01:01 1 None 0 0 15876.410 22247.940 1.400 3.600 NA NA NA NA 0.290 Poor Pending -chr3-52395054-52395055-C-T 59.DNAH1.ENST00000420323.6.missense.3655P/L DNAH1 P3655L 0 LEPRFIEL ENST00000420323.6 1 HLA-E*01:01 8 None 0 0 16004.560 38708.930 1.400 34.000 NA NA NA NA 0.273 Poor Pending -chr6-29112672-29112673-G-A 113.OR2J3.ENST00000641960.1.missense.261M/I OR2J3 M261I 0 IPAMCIYL ENST00000641960.1 NA HLA-E*01:01 6 None 0 0 16263.610 14399.080 1.500 0.990 NA NA NA NA 0.657 Poor Pending -chrX-101235943-101235944-G-C 397.DRP2.ENST00000395209.7.missense.68V/L DRP2 V68L 0 SLGASGPL ENST00000395209.7 1 HLA-E*01:01 2 None 0 0 16655.920 24114.770 1.600 4.500 NA NA NA NA 1.000 Poor Pending -chrX-3713125-3713126-A-G 370.PRKX.ENST00000262848.5.missense.43V/A PRKX V43A 0 PEPPAYSL ENST00000262848.5 1 HLA-E*01:01 5 None 0 0 16811.080 24683.630 1.600 4.900 NA NA NA NA 1.000 Poor Pending -chr2-102015965-102015966-C-T 41.IL1R2.ENST00000332549.7.missense.143T/I IL1R2 T143I 0 ILSTSGVL ENST00000332549.7 1 HLA-E*01:01 1 None 0 0 16993.600 20737.240 1.700 2.900 NA NA NA NA 0.196 Poor Pending -chr6-4068931-4068932-C-T 97.FAM217A.ENST00000274673.7.missense.431V/I FAM217A V431I 0 KMISTRCL ENST00000274673.7 1 HLA-E*01:01 3 None 0 0 17088.189 16982.940 1.700 1.700 NA NA NA NA 0.463 Poor Pending -chrX-107601385-107601386-G-T 400.FRMPD3.ENST00000276185.8.missense.1149S/I FRMPD3 S1149I 0 STPKRIKL ENST00000276185.8 5 HLA-E*01:01 6 None 0 0 17641.830 19563.110 1.900 2.500 NA NA NA NA 0.404 Poor Pending -chr12-80495233-80495234-C-A 247.PTPRQ.ENST00000614701.5.missense.582S/Y PTPRQ S582Y 0 ISYSSILL ENST00000614701.5 5 HLA-E*01:01 3 None 0 0 17645.461 17405.410 1.900 1.800 NA NA NA NA 0.984 Poor Pending -chr8-22566400-22566401-G-C 192.SORBS3.ENST00000240123.11.missense.336R/P SORBS3 R336P 0 YLGSAPSL ENST00000240123.11 1 HLA-E*01:01 6 None 0 0 17850.350 32012.930 1.900 14.000 NA NA NA NA 0.436 Poor Pending -chr1-120160392-120160393-C-T 18.SEC22B.ENST00000578049.3.missense.162A/T SEC22B A162T 0 VLQRGETL ENST00000578049.3 1 HLA-E*01:01 7 None 0 0 17886.510 20986.210 2.000 3.000 NA NA NA NA 0.403 Poor Pending -chr6-42592187-42592188-G-A 142.UBR2.ENST00000372899.5.missense.126E/K UBR2 E126K 0 VLCMKCFL ENST00000372899.5 1 HLA-E*01:01 5 None 0 0 18422.510 22958.820 2.100 3.900 NA NA NA NA 0.625 Poor Pending -chr6-16306519-16306520-G-A 103.ATXN1.ENST00000244769.8.missense.753P/S ATXN1 P753S 0 GLSAAPFL ENST00000244769.8 1 HLA-E*01:01 3 None 0 0 18507.830 5841.450 2.200 0.120 NA NA NA NA 0.952 Poor Pending -chr17-11784434-11784435-G-C 319.DNAH9.ENST00000262442.8.missense.2653D/H DNAH9 D2653H 0 SIPPLIHL ENST00000262442.8 1 HLA-E*01:01 7 None 0 0 18983.430 21258.170 2.300 3.100 NA NA NA NA 0.362 Poor Pending -chr6-33801119-33801120-A-G 136.MLN.ENST00000430124.6.missense.15V/A MLN V15A 0 VVHAAAML ENST00000430124.6 1 HLA-E*01:01 4 None 0 0 19243.590 28056.940 2.400 7.600 NA NA NA NA 0.735 Poor Pending -chr15-40622779-40622780-C-T 272.KNL1.ENST00000346991.9.missense.865P/L KNL1 P865L 0 VQKPKFLK ENST00000346991.9 1 HLA-E*01:01 7 None 0 0 19302.801 22026.630 2.400 3.500 NA NA NA NA 0.475 Poor Pending -chr15-40622778-40622779-C-T 271.KNL1.ENST00000346991.9.missense.865P/S KNL1 P865S 0 VQKPKFLK ENST00000346991.9 1 HLA-E*01:01 7 None 0 0 19302.801 22026.630 2.400 3.500 NA NA NA NA 0.475 Poor Pending -chr10-125859825-125859826-G-C 221.DHX32.ENST00000284690.3.missense.209P/R DHX32 P209R 0 VLLARREL ENST00000284690.3 1 HLA-E*01:01 6 None 0 0 19601.881 7349.710 2.500 0.190 NA NA NA NA 1.000 Poor Pending -chr10-115241629-115241630-G-A 219.ATRNL1.ENST00000355044.7.missense.531G/E ATRNL1 G531E 0 VLINEAML ENST00000355044.7 1 HLA-E*01:01 5 None 0 0 19989.971 20984.170 2.700 3.000 NA NA NA NA 0.441 Poor Pending -chr15-50643416-50643417-T-G 276.TRPM7.ENST00000313478.11.missense.153K/T TRPM7 K153T 0 LHPRITQL ENST00000313478.11 1 HLA-E*01:01 6 None 0 0 20026.119 20003.380 2.700 2.700 NA NA NA NA 0.500 Poor Pending -chr2-160107761-160107762-T-A 44.ITGB6.ENST00000283249.6.missense.729I/F ITGB6 I729F 0 VLLCFWKL ENST00000283249.6 1 HLA-E*01:01 5 None 0 0 20240.480 21906.830 2.800 3.400 NA NA NA NA 0.230 Poor Pending -chr1-168179177-168179178-A-T 22.TIPRL.ENST00000367833.6.missense.34E/V TIPRL E34V 0 IMKSADVV ENST00000367833.6 1 HLA-E*01:01 8 None 0 0 20390.820 30433.900 2.800 12.000 NA NA NA NA 0.273 Poor Pending -chr19-8955983-8955984-G-A 335.MUC16.ENST00000397910.8.missense.6929S/F MUC16 S6929F 0 TMGHTTVF ENST00000397910.8 5 HLA-E*01:01 8 None 0 0 20594.141 37488.050 2.900 28.000 NA NA NA NA 0.479 Poor Pending -chr22-37631020-37631021-C-G 359.GGA1.ENST00000343632.8.missense.484P/A GGA1 P484A 0 ARPPQQPV ENST00000343632.8 1 HLA-E*01:01 1 None 0 0 21060.600 28549.960 3.000 8.100 NA NA NA NA 0.455 Poor Pending -chrX-40655057-40655058-G-T 383.MED14.ENST00000324817.5.missense.1325F/L MED14 F1325L 0 LPDQATQL ENST00000324817.5 1 HLA-E*01:01 1 None 0 0 21278.881 29909.640 3.100 9.700 NA NA NA NA 1.000 Poor Pending -chr5-14507134-14507135-C-T 83.TRIO.ENST00000344204.8.missense.2876R/C TRIO R2876C 0 MADQGCLL ENST00000344204.8 1 HLA-E*01:01 6 None 0 0 21522.461 19763.520 3.200 2.600 NA NA NA NA 0.254 Poor Pending -chr19-51136070-51136071-A-T 346.SIGLEC9.ENST00000440804.7.missense.438H/L SIGLEC9 H438L 0 YLFSHFRL ENST00000440804.7 2 HLA-E*01:01 2 None 0 0 21590.109 29276.650 3.300 8.900 NA NA NA NA 0.110 Poor Pending -chr13-113425167-113425168-G-T 255.ADPRHL1.ENST00000375418.7.missense.220H/N ADPRHL1 H220N 0 YQENWFYF ENST00000375418.7 1 HLA-E*01:01 4 None 0 0 21600.391 25523.940 3.300 5.500 NA NA NA NA 0.527 Poor Pending -chr9-133354714-133354715-G-C 210.SURF1.ENST00000371974.7.missense.89N/K SURF1 N89K 0 RRKWKLKL ENST00000371974.7 1 HLA-E*01:01 7 None 0 0 21972.830 26468.360 3.500 6.200 NA NA NA NA 0.706 Poor Pending -chr3-33053544-33053545-G-T 55.GLB1.ENST00000307363.9.missense.246S/R GLB1 S246R 0 RNITDAFL ENST00000307363.9 1 HLA-E*01:01 1 None 0 0 22152.330 30372.390 3.600 12.000 NA NA NA NA 0.335 Poor Pending -chr8-23368189-23368210-TGGCCACGTTGGCGGGGGCCTG-T 193.LOXL2.ENST00000389131.7.inframe_del.48-54QAPANVA/- LOXL2 QAPANVA48-54- 0 QPKIQLRL ENST00000389131.7 1 HLA-E*01:01 2-3 None 0 0 22410.039 29604.110 3.700 9.300 NA NA NA NA 0.992 Poor Pending -chr16-25246937-25246938-C-T 286.ZKSCAN2.ENST00000328086.11.missense.420E/K ZKSCAN2 E420K 0 LEPCAFFK ENST00000328086.11 1 HLA-E*01:01 8 None 0 0 23166.680 22030.680 4.000 3.500 NA NA NA NA 0.471 Poor Pending -chr2-190982493-190982494-G-C 46.STAT1.ENST00000361099.7.missense.491P/A STAT1 P491A 0 LTPACARW ENST00000361099.7 1 HLA-E*01:01 4 None 0 0 23220.881 15735.500 4.000 1.400 NA NA NA NA 0.583 Poor Pending -chr11-862686-862687-C-G 224.TSPAN4.ENST00000397404.5.missense.67I/M TSPAN4 I67M 0 VMAMGFVG ENST00000397404.5 5 HLA-E*01:01 4 None 0 0 23293.100 25066.890 4.100 5.100 NA NA NA NA 1.000 Poor Pending -chr10-132163376-132163377-C-G 222.JAKMIP3.ENST00000298622.8.missense.795R/G JAKMIP3 R795G 0 ILGERMEL ENST00000298622.8 5 HLA-E*01:01 3 None 0 0 23368.830 20365.250 4.100 2.800 NA NA NA NA 0.467 Poor Pending -chr6-109451607-109451608-G-T 168.MICAL1.ENST00000630715.2.missense.328L/M MICAL1 L328M 0 VMRQDWPD ENST00000630715.2 2 HLA-E*01:01 2 None 0 0 23437.971 34203.750 4.100 19.000 NA NA NA NA 0.980 Poor Pending -chr1-204125889-204125890-C-T 27.SOX13.ENST00000367204.5.missense.542S/L SOX13 S542L 0 QMSSLDVL ENST00000367204.5 1 HLA-E*01:01 5 None 0 0 23594.189 14811.500 4.200 1.200 NA NA NA NA 0.328 Poor Pending -chr6-46168246-46168247-G-T 154.ENPP5.ENST00000371383.6.missense.6L/I ENPP5 L6I 0 MTSKFILV ENST00000371383.6 1 HLA-E*01:01 6 None 0 0 23693.961 20937.900 4.300 3.000 NA NA NA NA 0.750 Poor Pending -chr6-24828261-24828262-C-T 109.RIPOR2.ENST00000644685.1.missense.868R/Q RIPOR2 R868Q 0 LDQAEPLL ENST00000644685.1 NA HLA-E*01:01 3 None 0 0 23900.211 22239.510 4.400 3.600 NA NA NA NA 0.639 Poor Pending -chrX-130013396-130013397-G-A 402.BCORL1.ENST00000540052.5.missense.209G/S BCORL1 G209S 0 ICPPAPSS ENST00000540052.5 1 HLA-E*01:01 7 None 0 0 23967.270 24918.700 4.500 5.000 NA NA NA NA 1.000 Poor Pending -chr4-154491218-154491219-G-C 80.DCHS2.ENST00000339452.2.missense.46S/C DCHS2 S46C 0 TQRCLLWL ENST00000339452.2 1 HLA-E*01:01 4 None 0 0 23973.240 23372.370 4.500 4.100 NA NA NA NA 0.968 Poor Pending -chrX-102463004-102463005-G-A 399.TCP11X2.ENST00000453326.2.missense.223R/W TCP11X2 R223W 0 LLMDRIWL ENST00000453326.2 2 HLA-E*01:01 7 None 0 0 23985.160 24889.330 4.500 5.000 NA NA NA NA 0.514 Poor Pending -chr1-22576425-22576426-C-A 3.EPHA8.ENST00000166244.7.missense.123N/K EPHA8 N123K 0 TCKETFKL ENST00000166244.7 2 HLA-E*01:01 7 None 0 0 24012.699 27923.990 4.500 7.400 NA NA NA NA 0.270 Poor Pending -chr4-114833618-114833619-A-G 78.NDST4.ENST00000264363.6.missense.795S/P NDST4 S795P 0 NYPEALTF ENST00000264363.6 1 HLA-E*01:01 3 None 0 0 24291.789 35703.800 4.600 23.000 NA NA NA NA 0.197 Poor Pending -chr6-6250886-6250887-T-A 99.F13A1.ENST00000264870.7.missense.205Y/F F13A1 Y205F 0 KEREEFVL ENST00000264870.7 1 HLA-E*01:01 6 None 0 0 24316.770 28767.960 4.600 8.300 NA NA NA NA 0.451 Poor Pending -chr1-16972417-16972418-C-G 2.CROCC.ENST00000375541.9.missense.2009S/C CROCC S2009C 0 CPPSGPPE ENST00000375541.9 5 HLA-E*01:01 1 None 0 0 24326.240 23610.790 4.600 4.200 NA NA NA NA 0.988 Poor Pending -chr20-35384131-35384132-C-G 351.UQCC1.ENST00000374385.9.missense.44W/S UQCC1 W44S 0 RTSQSPQM ENST00000374385.9 1 HLA-E*01:01 5 None 0 0 24459.250 23032.970 4.700 3.900 NA NA NA NA 0.445 Poor Pending -chrX-136230874-136230875-T-G 407.MAP7D3.ENST00000316077.13.missense.502E/A MAP7D3 E502A 0 SPANACGL ENST00000316077.13 1 HLA-E*01:01 3 None 0 0 24585.289 31036.810 4.800 13.000 NA NA NA NA 1.000 Poor Pending -chr6-42923283-42923284-G-A 143.PTCRA.ENST00000616441.2.missense.106V/I PTCRA V106I 0 LASWEPLI ENST00000616441.2 2 HLA-E*01:01 8 None 0 0 25056.859 28339.470 5.100 7.900 NA NA NA NA 0.685 Poor Pending -chr6-36426038-36426039-A-G 138.PXT1.ENST00000454782.2.missense.15V/A PXT1 V15A 0 ALNPSPKV ENST00000454782.2 1 HLA-E*01:01 1 None 0 0 25142.949 18390.260 5.200 2.100 NA NA NA NA 0.685 Poor Pending -chr7-87424004-87424005-A-C 177.ABCB4.ENST00000265723.8.missense.704N/K ABCB4 N704K 0 KKTEWPYF ENST00000265723.8 1 HLA-E*01:01 1 None 0 0 25413.711 32195.650 5.400 15.000 NA NA NA NA 0.189 Poor Pending -chr2-106830076-106830077-G-C 42.ST6GAL2.ENST00000409382.7.missense.436S/C ST6GAL2 S436C 0 IQPNPPSC ENST00000409382.7 1 HLA-E*01:01 8 None 0 0 26054.090 33838.230 5.900 18.000 NA NA NA NA 0.700 Poor Pending -chr1-39429921-39429922-G-C 9.MACF1.ENST00000361689.6.missense.3600E/Q MACF1 E3600Q 0 TLQQARQL ENST00000361689.6 5 HLA-E*01:01 3 None 0 0 26217.820 27609.750 6.000 7.100 NA NA NA NA 0.342 Poor Pending -chr6-44172317-44172317-T-TGGCTGCC 150.CAPN11.ENST00000398776.1.FS.142T/TGGCTGCC CAPN11 FS142 0 LAAGCHRL ENST00000398776.1 1 HLA-E*01:01 4-8 None 0 0 26505.320 NA 6.200 NA NA NA NA NA 0.655 Poor Pending -chr19-8969814-8969831-ACGTGGAATTTCCTTGTG-A 336.MUC16.ENST00000397910.8.FS.3175-3180ACGTGGAATTTCCTTGTG/A MUC16 FS3175-3180 0 VHCEKFSL ENST00000397910.8 5 HLA-E*01:01 1-8 None 0 0 26571.660 NA 6.300 NA NA NA NA NA 1.000 Poor Pending -chr7-112342710-112342711-G-C 183.ZNF277.ENST00000361822.7.missense.445L/F ZNF277 L445F 0 ALKQSSIF ENST00000361822.7 1 HLA-E*01:01 8 None 0 0 26705.109 20485.910 6.400 2.800 NA NA NA NA 0.446 Poor Pending -chrX-78015862-78015863-G-C 392.ATP7A.ENST00000341514.10.missense.870D/H ATP7A D870H 0 SMVHESLI ENST00000341514.10 1 HLA-E*01:01 4 None 0 0 27036.539 31415.540 6.600 13.000 NA NA NA NA 0.979 Poor Pending -chr9-137255473-137255474-G-C 212.NELFB.ENST00000343053.4.missense.37G/R NELFB G37R 0 RAPSRAVA ENST00000343053.4 1 HLA-E*01:01 1 None 0 0 27088.650 37200.370 6.700 27.000 NA NA NA NA 0.600 Poor Pending -chr18-60371739-60371740-T-G 328.MC4R.ENST00000299766.5.missense.204M/L MC4R M204L 0 MFFTLLAL ENST00000299766.5 NA HLA-E*01:01 5 None 0 0 27139.990 24335.460 6.700 4.600 NA NA NA NA 1.000 Poor Pending -chr16-72008782-72008783-A-C 301.DHODH.ENST00000219240.8.missense.7K/Q DHODH K7Q 0 MAWRHLQK ENST00000219240.8 1 HLA-E*01:01 7 None 0 0 27308.490 28009.020 6.800 7.500 NA NA NA NA 0.633 Poor Pending -chr1-243164805-243164806-G-C 32.CEP170.ENST00000366542.5.missense.1052H/D CEP170 H1052D 0 KPDGRTPL ENST00000366542.5 5 HLA-E*01:01 3 None 0 0 27511.939 26446.600 7.000 6.200 NA NA NA NA 0.117 Poor Pending -chr17-41771694-41771736-GTGTACTGGCGCCCGCAGGCCTCATCCTCCTCCATGATGCCCT-G 321.JUP.ENST00000393931.7.inframe_del.40-54KGIMEEDEACGRQYT/T JUP KGIMEEDEACGRQYT40-54T 0 VPSVSSTL ENST00000393931.7 1 HLA-E*01:01 6-7 None 0 0 27543.500 43475.560 7.000 67.000 NA NA NA NA 1.000 Poor Pending -chr22-41524890-41524891-G-C 360.ACO2.ENST00000216254.8.missense.510E/Q ACO2 E510Q 0 FNPQTDYL ENST00000216254.8 1 HLA-E*01:01 4 None 0 0 27748.410 29823.670 7.200 9.600 NA NA NA NA 0.208 Poor Pending -chr1-52961569-52961570-C-A 13.SCP2.ENST00000371514.7.missense.155A/D SCP2 A155D 0 DHPVAPQM ENST00000371514.7 1 HLA-E*01:01 1 None 0 0 27992.350 19991.270 7.500 2.700 NA NA NA NA 0.458 Poor Pending -chr13-45399008-45399009-C-T 253.SLC25A30.ENST00000519676.5.missense.228M/I SLC25A30 M228I 0 IMNQRVLR ENST00000519676.5 1 HLA-E*01:01 1 None 0 0 28018.410 29075.570 7.500 8.700 NA NA NA NA 0.450 Poor Pending -chr6-24174792-24174793-T-A 105.DCDC2.ENST00000378454.7.missense.456K/N DCDC2 K456N 0 RPPRPEVN ENST00000378454.7 1 HLA-E*01:01 8 None 0 0 28077.600 25072.860 7.600 5.100 NA NA NA NA 0.667 Poor Pending -chr2-110933496-110933497-G-A 43.ACOXL.ENST00000439055.5.missense.305G/E ACOXL G305E 0 SRYAEALL ENST00000439055.5 2 HLA-E*01:01 5 None 0 0 28215.551 28817.800 7.700 8.400 NA NA NA NA 1.000 Poor Pending -chr6-33305077-33305078-G-C 134.TAPBP.ENST00000426633.6.missense.260T/R TAPBP T260R 0 WLPRVQPF ENST00000426633.6 1 HLA-E*01:01 4 None 0 0 28317.400 31248.740 7.900 13.000 NA NA NA NA 0.667 Poor Pending -chr6-4995229-4995230-C-T 98.RPP40.ENST00000380051.6.missense.314V/I RPP40 V314I 0 APWVTLSI ENST00000380051.6 5 HLA-E*01:01 8 None 0 0 28393.779 31338.470 8.000 13.000 NA NA NA NA 0.470 Poor Pending -chr16-87305843-87305844-C-T 307.AC010531.1.ENST00000568879.1.missense.210C/Y AC010531.1 C210Y 0 VMSAYCPS ENST00000568879.1 4 HLA-E*01:01 5 None 0 0 28480.859 19846.440 8.000 2.600 NA NA NA NA 0.449 Poor Pending -chrX-12885539-12885540-A-T 373.TLR7.ENST00000380659.3.missense.11Q/L TLR7 Q11L 0 WTLKRLIL ENST00000380659.3 1 HLA-E*01:01 6 None 0 0 28489.490 34481.310 8.000 19.000 NA NA NA NA 1.000 Poor Pending -chr2-669669-669670-C-T 33.TMEM18.ENST00000281017.7.missense.111M/I TMEM18 M111I 0 VIWVWKTL ENST00000281017.7 1 HLA-E*01:01 2 None 0 0 28613.369 12402.320 8.200 0.660 NA NA NA NA 0.250 Poor Pending -chr22-50243800-50243801-T-C 363.TUBGCP6.ENST00000248846.9.missense.220H/R TUBGCP6 H220R 0 VRSRTYDM ENST00000248846.9 1 HLA-E*01:01 2 None 0 0 28615.221 28221.050 8.200 7.700 NA NA NA NA 0.760 Poor Pending -chr11-92982014-92982015-G-T 240.MTNR1B.ENST00000257068.2.missense.264W/C MTNR1B W264C 0 FAICCAPL ENST00000257068.2 1 HLA-E*01:01 5 None 0 0 28668.840 33665.860 8.200 17.000 NA NA NA NA 0.417 Poor Pending -chr6-32166732-32166733-G-A 128.EGFL8.ENST00000395512.5.missense.86R/K EGFL8 R86K 0 VMWREVKR ENST00000395512.5 1 HLA-E*01:01 7 None 0 0 28713.230 27377.720 8.300 6.900 NA NA NA NA 0.672 Poor Pending -chr6-29100981-29100982-C-A 112.OR2J1.ENST00000377171.3.missense.14L/I OR2J1 L14I 0 SFEDFFIL ENST00000377171.3 NA HLA-E*01:01 7 None 0 0 28726.900 28638.460 8.300 8.200 NA NA NA NA 0.661 Poor Pending -chr6-32332044-32332045-G-A 131.TSBP1.ENST00000447241.6.missense.161P/L TSBP1 P161L 0 VQTLGPIV ENST00000447241.6 5 HLA-E*01:01 4 None 0 0 28818.439 11016.290 8.400 0.510 NA NA NA NA 0.722 Poor Pending -chr1-179109009-179109010-T-C 23.ABL2.ENST00000502732.5.missense.753T/A ABL2 T753A 0 TGFFAPRL ENST00000502732.5 1 HLA-E*01:01 5 None 0 0 28837.770 31057.640 8.400 13.000 NA NA NA NA 0.379 Poor Pending -chrX-15355261-15355262-C-T 374.VEGFD.ENST00000297904.3.missense.177E/K VEGFD E177K 0 PLTSVPKL ENST00000297904.3 1 HLA-E*01:01 7 None 0 0 28853.061 30274.300 8.400 12.000 NA NA NA NA 0.985 Poor Pending -chr19-19336157-19336158-A-C 342.MAU2.ENST00000262815.12.missense.111S/R MAU2 S111R 0 KFEAARLL ENST00000262815.12 1 HLA-E*01:01 6 None 0 0 28879.609 30044.250 8.500 9.900 NA NA NA NA 0.365 Poor Pending -chr6-152325133-152325134-C-T 170.SYNE1.ENST00000367255.9.missense.5203E/K SYNE1 E5203K 0 AQDQKKIL ENST00000367255.9 1 HLA-E*01:01 5 None 0 0 28899.920 32620.270 8.500 15.000 NA NA NA NA 0.339 Poor Pending -chr6-53654806-53654807-C-T 161.KLHL31.ENST00000370905.3.missense.156V/I KLHL31 V156I 0 IKMCSDFL ENST00000370905.3 1 HLA-E*01:01 1 None 0 0 28954.689 27652.190 8.500 7.100 NA NA NA NA 0.450 Poor Pending -chrX-9967396-9967397-G-A 372.CLDN34.ENST00000445307.4.missense.14V/I CLDN34 V14I 0 CQFSIFAL ENST00000445307.4 NA HLA-E*01:01 5 None 0 0 29036.570 27185.560 8.700 6.700 NA NA NA NA 0.989 Poor Pending -chr16-3745299-3745300-G-C 284.CREBBP.ENST00000262367.9.missense.1297H/Q CREBBP H1297Q 0 VLQYDIIW ENST00000262367.9 1 HLA-E*01:01 3 None 0 0 29176.400 30579.800 8.800 12.000 NA NA NA NA 0.246 Poor Pending -chr6-29374537-29374538-G-C 114.OR12D3.ENST00000396806.3.missense.250F/L OR12D3 F250L 0 FMVVCLLY ENST00000396806.3 NA HLA-E*01:01 7 None 0 0 29396.320 32644.640 9.000 15.000 NA NA NA NA 0.423 Poor Pending -chr10-37957500-37957501-C-T 216.ZNF25.ENST00000302609.7.missense.21E/K ZNF25 E21K 0 TKEKWKLL ENST00000302609.7 1 HLA-E*01:01 4 None 0 0 29465.730 33031.190 9.100 16.000 NA NA NA NA 0.460 Poor Pending -chr20-41165771-41165772-C-G 352.PLCG1.ENST00000244007.7.missense.582S/C PLCG1 S582C 0 GAPDGCFL ENST00000244007.7 5 HLA-E*01:01 6 None 0 0 29469.869 28834.010 9.100 8.400 NA NA NA NA 0.448 Poor Pending -chr3-44242057-44242058-G-A 58.TOPAZ1.ENST00000309765.4.missense.2R/Q TOPAZ1 R2Q 0 MQRPPPLG ENST00000309765.4 5 HLA-E*01:01 2 None 0 0 29645.131 33883.300 9.300 18.000 NA NA NA NA 0.318 Poor Pending -chrX-16869531-16869532-C-T 375.RBBP7.ENST00000380084.8.missense.37R/H RBBP7 R37H 0 RLGHAAPV ENST00000380084.8 2 HLA-E*01:01 4 None 0 0 29762.770 26966.120 9.500 6.600 NA NA NA NA 1.000 Poor Pending -chr14-26448937-26448938-G-C 259.NOVA1.ENST00000539517.6.missense.182T/R NOVA1 T182R 0 VPNSRAGL ENST00000539517.6 1 HLA-E*01:01 5 None 0 0 29808.199 23770.230 9.600 4.300 NA NA NA NA 0.451 Poor Pending -chrX-153058184-153058185-C-T 410.PNMA3.ENST00000593810.2.missense.377A/V PNMA3 A377V 0 VRPSQGYR ENST00000593810.2 NA HLA-E*01:01 1 None 0 0 30015.971 35864.100 9.800 23.000 NA NA NA NA 1.000 Poor Pending -chr2-219514658-219514659-C-A 51.ASIC4.ENST00000347842.7.missense.106P/T ASIC4 P106T 0 LGRATGLL ENST00000347842.7 1 HLA-E*01:01 5 None 0 0 30245.480 33615.630 12.000 17.000 NA NA NA NA 0.238 Poor Pending -chr6-122781239-122781240-C-G 169.FABP7.ENST00000356535.4.missense.132P/A FABP7 P132A 0 SAHTSHLL ENST00000356535.4 1 HLA-E*01:01 2 None 0 0 30336.920 17573.070 12.000 1.800 NA NA NA NA 0.371 Poor Pending -chr9-130307565-130307566-G-A 209.HMCN2.ENST00000624552.3.missense.733G/R HMCN2 G733R 0 VIWYRRGL ENST00000624552.3 5 HLA-E*01:01 6 None 0 0 30405.279 26270.630 12.000 6.100 NA NA NA NA 0.290 Poor Pending -chr7-82916602-82916603-C-A 176.PCLO.ENST00000333891.13.missense.3795D/Y PCLO D3795Y 0 IYAKLRYL ENST00000333891.13 2 HLA-E*01:01 2 None 0 0 30408.891 33041.930 12.000 16.000 NA NA NA NA 0.219 Poor Pending -chrX-41344254-41344255-G-C 384.DDX3X.ENST00000644876.1.missense.294R/T DDX3X R294T 0 TVRPCVVY ENST00000644876.1 NA HLA-E*01:01 1 None 0 0 30441.480 27209.680 12.000 6.700 NA NA NA NA 0.983 Poor Pending -chr10-13481023-13481024-C-G 214.BEND7.ENST00000341083.7.missense.261R/T BEND7 R261T 0 TKLVCAFF ENST00000341083.7 2 HLA-E*01:01 1 None 0 0 30462.240 26060.290 12.000 5.900 NA NA NA NA 1.000 Poor Pending -chr11-64320894-64320895-T-C 237.PRDX5.ENST00000265462.8.missense.157F/L PRDX5 F157L 0 LADPTGAL ENST00000265462.8 1 HLA-E*01:01 8 None 0 0 30476.090 36635.570 12.000 26.000 NA NA NA NA 0.425 Poor Pending -chr3-171138369-171138370-G-T 66.TNIK.ENST00000436636.6.missense.477R/S TNIK R477S 0 LEYKSKQL ENST00000436636.6 1 HLA-E*01:01 5 None 0 0 30541.119 33712.890 12.000 18.000 NA NA NA NA 0.278 Poor Pending -chrX-18619961-18619962-A-C 377.CDKL5.ENST00000379989.6.missense.791Q/P CDKL5 Q791P 0 KKKKSPTV ENST00000379989.6 1 HLA-E*01:01 6 None 0 0 30563.600 40041.010 12.000 40.000 NA NA NA NA 1.000 Poor Pending -chr16-87748715-87748716-G-C 309.KLHDC4.ENST00000270583.9.missense.155L/V KLHDC4 L155V 0 HYKDVWVL ENST00000270583.9 1 HLA-E*01:01 5 None 0 0 30580.141 33812.990 12.000 18.000 NA NA NA NA 0.453 Poor Pending -chr16-88736715-88736716-T-C 311.PIEZO1.ENST00000301015.14.missense.407R/G PIEZO1 R407G 0 EPGEASPL ENST00000301015.14 1 HLA-E*01:01 3 None 0 0 30601.330 28600.050 12.000 8.200 NA NA NA NA 0.413 Poor Pending -chrX-88753805-88753806-G-A 394.CPXCR1.ENST00000276127.8.missense.131R/H CPXCR1 R131H 0 NHKTHFRL ENST00000276127.8 1 HLA-E*01:01 5 None 0 0 30822.289 25732.470 12.000 5.700 NA NA NA NA 1.000 Poor Pending -chr6-31112111-31112112-C-G 120.C6orf15.ENST00000259870.3.missense.83A/P C6orf15 A83P 0 SVPPSDGF ENST00000259870.3 1 HLA-E*01:01 4 None 0 0 30839.980 37041.310 12.000 27.000 NA NA NA NA 0.703 Poor Pending -chr11-63544840-63544860-GTGAGCACTTTGTCACCCAGC-G 236.RARRES3.ENST00000255688.7.FS.113-120GTGAGCACTTTGTCACCCAGC/G RARRES3 FS113-120 0 CEIWQVPL ENST00000255688.7 1 HLA-E*01:01 3-8 None 0 0 30936.891 NA 13.000 NA NA NA NA NA 0.149 Poor Pending -chr7-157005551-157005552-G-A 191.MNX1.ENST00000252971.10.missense.392P/S MNX1 P392S 0 SPPSRPSH ENST00000252971.10 1 HLA-E*01:01 4 None 0 0 30996.529 28584.290 13.000 8.200 NA NA NA NA 0.052 Poor Pending -chr16-2295600-2295601-C-G 283.ABCA3.ENST00000301732.9.missense.801E/D ABCA3 E801D 0 ILPRDSTH ENST00000301732.9 1 HLA-E*01:01 5 None 0 0 31053.930 31199.430 13.000 13.000 NA NA NA NA 0.594 Poor Pending -chr8-38428419-38428420-G-A 194.FGFR1.ENST00000425967.7.missense.158S/L FGFR1 S158L 0 VSDALPSL ENST00000425967.7 1 HLA-E*01:01 8 None 0 0 31127.939 43501.930 13.000 67.000 NA NA NA NA 1.000 Poor Pending -chr2-175093191-175093192-C-G 45.ATF2.ENST00000264110.6.missense.352D/H ATF2 D352H 0 HEKRRKFL ENST00000264110.6 1 HLA-E*01:01 1 None 0 0 31205.500 33240.930 13.000 17.000 NA NA NA NA 0.462 Poor Pending -chr16-71998331-71998332-T-A 300.PKD1L3.ENST00000620267.1.missense.120I/F PKD1L3 I120F 0 TYLSRNFF ENST00000620267.1 1 HLA-E*01:01 8 None 0 0 31251.461 33213.980 13.000 17.000 NA NA NA NA 0.620 Poor Pending -chr2-94874875-94874876-T-A 40.TEKT4.ENST00000295201.4.missense.272C/S TEKT4 C272S 0 RVLVDSIL ENST00000295201.4 1 HLA-E*01:01 6 None 0 0 31280.539 33479.160 13.000 17.000 NA NA NA NA 0.444 Poor Pending -chr15-94399982-94399983-G-T 281.MCTP2.ENST00000357742.8.missense.651K/N MCTP2 K651N 0 RNLSKKIL ENST00000357742.8 1 HLA-E*01:01 2 None 0 0 31389.381 29273.800 13.000 8.900 NA NA NA NA 0.199 Poor Pending -chr11-5968293-5968294-G-C 225.OR56A5.ENST00000532411.2.missense.67S/R OR56A5 S67R 0 YLLRLLSL ENST00000532411.2 NA HLA-E*01:01 4 None 0 0 31438.990 34483.550 13.000 19.000 NA NA NA NA 1.000 Poor Pending -chr4-121932625-121932626-C-A 79.TRPC3.ENST00000379645.7.missense.211C/F TRPC3 C211F 0 LSPFEQEL ENST00000379645.7 1 HLA-E*01:01 4 None 0 0 31473.039 26616.250 13.000 6.300 NA NA NA NA 0.306 Poor Pending -chr1-27793606-27793607-C-G 6.STX12.ENST00000373943.8.missense.88P/R STX12 P88R 0 KELGSLRL ENST00000373943.8 1 HLA-E*01:01 7 None 0 0 31534.391 32950.170 14.000 16.000 NA NA NA NA 1.000 Poor Pending -chr2-195816717-195816718-T-G 47.DNAH7.ENST00000312428.10.missense.3224E/A DNAH7 E3224A 0 APMYQYSL ENST00000312428.10 1 HLA-E*01:01 1 None 0 0 31644.100 33951.200 14.000 18.000 NA NA NA NA 0.138 Poor Pending -chr8-66813873-66813874-C-T 195.SGK3.ENST00000396596.2.missense.92A/V SGK3 A92V 0 IKQRRVGL ENST00000396596.2 1 HLA-E*01:01 6 None 0 0 31771.039 26125.230 14.000 5.900 NA NA NA NA 0.230 Poor Pending -chr7-155462475-155462476-A-G 190.EN2.ENST00000297375.4.missense.264Q/R EN2 Q264R 0 RLKAEFRT ENST00000297375.4 1 HLA-E*01:01 7 None 0 0 31778.949 32725.630 14.000 16.000 NA NA NA NA 0.254 Poor Pending -chr4-103145955-103145956-C-G 75.CENPE.ENST00000265148.7.missense.1429R/T CENPE R1429T 0 MLGLSKTL ENST00000265148.7 2 HLA-E*01:01 7 None 0 0 31849.160 31232.870 14.000 13.000 NA NA NA NA 0.238 Poor Pending -chr17-3433668-3433669-G-T 312.OR1E2.ENST00000248384.1.missense.58P/H OR1E2 P58H 0 LHTHVYLF ENST00000248384.1 NA HLA-E*01:01 4 None 0 0 31895.039 23286.060 14.000 4.100 NA NA NA NA 0.317 Poor Pending -chr1-16006133-16006134-G-T 1.SRARP.ENST00000329454.2.missense.100G/W SRARP G100W 0 TPMGWGCL ENST00000329454.2 1 HLA-E*01:01 5 None 0 0 31981.770 32224.230 14.000 15.000 NA NA NA NA 0.989 Poor Pending -chr16-56511262-56511263-T-C 289.BBS2.ENST00000245157.9.missense.123I/V BBS2 I123V 0 DGANAVVL ENST00000245157.9 1 HLA-E*01:01 6 None 0 0 32098.961 30233.060 14.000 11.000 NA NA NA NA 0.719 Poor Pending -chr11-124319973-124319974-G-A 242.OR8D2.ENST00000624618.1.missense.75S/F OR8D2 S75F 0 DLCYSFVI ENST00000624618.1 NA HLA-E*01:01 6 None 0 0 32170.580 38913.840 15.000 34.000 NA NA NA NA 1.000 Poor Pending -chr6-56552746-56552747-T-C 166.DST.ENST00000312431.10.missense.3092T/A DST T3092A 0 KGASDVLL ENST00000312431.10 5 HLA-E*01:01 3 None 0 0 32193.900 35860.210 15.000 23.000 NA NA NA NA 0.308 Poor Pending -chr6-24653044-24653045-G-C 108.TDP2.ENST00000378198.8.missense.249Q/E TDP2 Q249E 0 KMEEAPES ENST00000378198.8 1 HLA-E*01:01 3 None 0 0 32249.320 31134.690 15.000 13.000 NA NA NA NA 0.647 Poor Pending -chr10-104021651-104021652-G-T 218.SLK.ENST00000369755.3.missense.1160E/D SLK E1160D 0 VEHDTQKL ENST00000369755.3 1 HLA-E*01:01 4 None 0 0 32262.949 33078.410 15.000 16.000 NA NA NA NA 0.071 Poor Pending -chr16-67239382-67239411-GCTGCTCTTCCAGGGACAGCTCGGTGTCCA-G 296.FHOD1.ENST00000258201.8.FS.82-91GCTGCTCTTCCAGGGACAGCTCGGTGTCCA/G FHOD1 FS82-91 0 YPGDAGGL ENST00000258201.8 1 HLA-E*01:01 2-8 None 0 0 32355.590 NA 15.000 NA NA NA NA NA 0.231 Poor Pending -chrX-43656385-43656386-C-A 385.MAOA.ENST00000338702.3.missense.15D/E MAOA D15E 0 HMFEVVVI ENST00000338702.3 1 HLA-E*01:01 4 None 0 0 32415.510 32391.670 15.000 15.000 NA NA NA NA 1.000 Poor Pending -chr12-49526214-49526215-G-A 246.SPATS2.ENST00000553127.5.missense.533R/H SPATS2 R533H 0 LPQHKPRT ENST00000553127.5 1 HLA-E*01:01 4 None 0 0 32566.670 24939.750 15.000 5.100 NA NA NA NA 0.966 Poor Pending -chr20-4182496-4182497-C-A 348.SMOX.ENST00000621355.4.missense.340Q/K SMOX Q340K 0 KRKYTSFF ENST00000621355.4 1 HLA-E*01:01 3 None 0 0 32571.609 32326.180 15.000 15.000 NA NA NA NA 0.592 Poor Pending -chr5-7886679-7886680-G-C 82.MTRR.ENST00000264668.6.missense.402E/Q MTRR E402Q 0 IFTWCLQI ENST00000264668.6 1 HLA-E*01:01 7 None 0 0 32691.289 34911.530 16.000 20.000 NA NA NA NA 0.189 Poor Pending -chr10-32567832-32567833-C-T 215.CCDC7.ENST00000362006.11.missense.454S/L CCDC7 S454L 0 LEKETRKL ENST00000362006.11 1 HLA-E*01:01 8 None 0 0 32694.109 44861.830 16.000 81.000 NA NA NA NA 0.378 Poor Pending -chr19-50625545-50625546-G-A 345.SYT3.ENST00000338916.8.missense.474S/F SYT3 S474F 0 PYVKAFLI ENST00000338916.8 1 HLA-E*01:01 6 None 0 0 32797.570 42134.880 16.000 55.000 NA NA NA NA 0.538 Poor Pending -chrX-136228625-136228626-T-C 406.MAP7D3.ENST00000316077.13.missense.628Q/R MAP7D3 Q628R 0 EMQRRVIK ENST00000316077.13 1 HLA-E*01:01 4 None 0 0 32824.551 33688.100 16.000 17.000 NA NA NA NA 1.000 Poor Pending -chr15-84036950-84036951-A-T 280.ADAMTSL3.ENST00000286744.9.missense.1645I/F ADAMTSL3 I1645F 0 VQKKKPFS ENST00000286744.9 1 HLA-E*01:01 7 None 0 0 32843.730 31794.780 16.000 14.000 NA NA NA NA 0.368 Poor Pending -chr5-141332647-141332648-C-T 90.PCDHGA1.ENST00000517417.2.missense.655S/F PCDHGA1 S655F 0 PLFATVTL ENST00000517417.2 1 HLA-E*01:01 3 None 0 0 32859.031 32696.960 16.000 16.000 NA NA NA NA 0.688 Poor Pending -chr11-123943666-123943667-G-C 241.OR6T1.ENST00000321252.2.missense.58Q/E OR6T1 Q58E 0 RLHIEMYF ENST00000321252.2 NA HLA-E*01:01 5 None 0 0 32903.141 32404.620 16.000 15.000 NA NA NA NA 0.441 Poor Pending -chr5-150120064-150120065-G-A 92.PDGFRB.ENST00000261799.8.missense.882T/I PDGFRB T882I 0 ILSDVWSF ENST00000261799.8 1 HLA-E*01:01 1 None 0 0 32915.590 35483.900 16.000 22.000 NA NA NA NA 0.289 Poor Pending -chr19-38802098-38802099-G-A 344.LGALS4.ENST00000307751.8.missense.240R/C LGALS4 R240C 0 CMGNGTVV ENST00000307751.8 1 HLA-E*01:01 1 None 0 0 33176.250 25657.130 16.000 5.600 NA NA NA NA 1.000 Poor Pending -chr6-32335914-32335915-T-A 132.TSBP1.ENST00000447241.6.missense.150I/F TSBP1 I150F 0 IPGATGPF ENST00000447241.6 5 HLA-E*01:01 8 None 0 0 33179.480 34404.190 16.000 19.000 NA NA NA NA 0.638 Poor Pending -chr16-69167146-69167147-C-T 297.UTP4.ENST00000314423.11.missense.636R/C UTP4 R636C 0 CTAHAFKI ENST00000314423.11 1 HLA-E*01:01 1 None 0 0 33189.891 24117.100 16.000 4.500 NA NA NA NA 0.671 Poor Pending -chr15-100900576-100900577-G-T 282.ALDH1A3.ENST00000329841.9.missense.296D/Y ALDH1A3 D296Y 0 CADADLYL ENST00000329841.9 1 HLA-E*01:01 7 None 0 0 33191.680 37026.480 16.000 27.000 NA NA NA NA 0.376 Poor Pending -chr7-39339738-39339739-G-C 172.POU6F2.ENST00000403058.5.missense.203Q/H POU6F2 Q203H 0 HHPQPAPQ ENST00000403058.5 5 HLA-E*01:01 1 None 0 0 33344.309 28399.620 17.000 8.000 NA NA NA NA 0.317 Poor Pending -chr6-31120367-31120368-T-A 123.CDSN.ENST00000376288.2.missense.18M/L CDSN M18L 0 RVGGHGML ENST00000376288.2 1 HLA-E*01:01 8 None 0 0 33357.672 38352.500 17.000 32.000 NA NA NA NA 0.674 Poor Pending -chr4-99654590-99654591-C-T 74.C4orf54.ENST00000511828.1.missense.20V/M C4orf54 V20M 0 SMADGIQT ENST00000511828.1 1 HLA-E*01:01 2 None 0 0 33419.078 43086.880 17.000 63.000 NA NA NA NA 0.216 Poor Pending -chr17-5007046-5007047-C-T 315.KIF1C.ENST00000320785.9.missense.433S/F KIF1C S433F 0 SPNTEFQI ENST00000320785.9 1 HLA-E*01:01 6 None 0 0 33450.539 43334.680 17.000 65.000 NA NA NA NA 0.319 Poor Pending -chr6-36871821-36871822-C-G 139.PPIL1.ENST00000373699.5.missense.36C/S PPIL1 C36S 0 APKTSKNF ENST00000373699.5 1 HLA-E*01:01 5 None 0 0 33461.410 36325.320 17.000 25.000 NA NA NA NA 0.792 Poor Pending -chr10-60186848-60186849-G-T 217.ANK3.ENST00000280772.6.missense.651L/M ANK3 L651M 0 MDIATTLM ENST00000280772.6 1 HLA-E*01:01 8 None 0 0 33462.500 23869.970 17.000 4.400 NA NA NA NA 0.134 Poor Pending -chr16-25221522-25221523-G-C 285.AQP8.ENST00000219660.5.missense.109M/I AQP8 M109I 0 ILLPYWVS ENST00000219660.5 1 HLA-E*01:01 1 None 0 0 33482.051 34471.260 17.000 19.000 NA NA NA NA 0.250 Poor Pending -chr6-44183752-44183753-G-A 151.CAPN11.ENST00000398776.1.missense.728S/N CAPN11 S728N 0 NLEQWLQM ENST00000398776.1 1 HLA-E*01:01 1 None 0 0 33547.320 32082.270 17.000 14.000 NA NA NA NA 0.703 Poor Pending -chr7-102595676-102595677-C-G 181.RASA4.ENST00000262940.11.missense.321K/N RASA4 K321N 0 LANDFLDL ENST00000262940.11 1 HLA-E*01:01 3 None 0 0 33598.551 29908.020 17.000 9.700 NA NA NA NA 0.045 Poor Pending -chr3-172353066-172353067-C-T 67.FNDC3B.ENST00000336824.8.missense.927P/S FNDC3B P927S 0 LSETTYRI ENST00000336824.8 1 HLA-E*01:01 2 None 0 0 33774.219 17406.350 18.000 1.800 NA NA NA NA 0.364 Poor Pending -chr17-80086142-80086143-G-C 324.CCDC40.ENST00000397545.8.missense.792E/D CCDC40 E792D 0 TQEQDEQL ENST00000397545.8 5 HLA-E*01:01 5 None 0 0 33852.500 34255.230 18.000 19.000 NA NA NA NA 0.200 Poor Pending -chr5-134893641-134893642-T-C 87.TXNDC15.ENST00000358387.8.missense.248S/P TXNDC15 S248P 0 DAPQHSSL ENST00000358387.8 1 HLA-E*01:01 3 None 0 0 33915.570 41383.070 18.000 49.000 NA NA NA NA 1.000 Poor Pending -chr3-183179682-183179683-G-A 68.MCF2L2.ENST00000328913.7.missense.1039L/F MCF2L2 L1039F 0 ALSLAGFF ENST00000328913.7 5 HLA-E*01:01 7 None 0 0 33988.680 36417.410 18.000 25.000 NA NA NA NA 0.373 Poor Pending -chr11-58190707-58190708-A-T 232.OR9Q2.ENST00000641291.1.missense.73Y/F OR9Q2 Y73F 0 ICFSSAII ENST00000641291.1 NA HLA-E*01:01 3 None 0 0 34085.148 33436.440 18.000 17.000 NA NA NA NA 0.517 Poor Pending -chr14-21403125-21403126-C-A 256.CHD8.ENST00000646647.1.missense.1202R/L CHD8 R1202L 0 SKPDSDLF ENST00000646647.1 NA HLA-E*01:01 7 None 0 0 34086.270 37387.580 18.000 28.000 NA NA NA NA 0.080 Poor Pending -chr19-16572288-16572289-C-G 341.SLC35E1.ENST00000595753.5.missense.26E/Q SLC35E1 E26Q 0 QGARVAAL ENST00000595753.5 1 HLA-E*01:01 1 None 0 0 34187.828 37517.670 19.000 29.000 NA NA NA NA 0.706 Poor Pending -chr7-112821984-112821985-G-T 184.BMT2.ENST00000297145.8.missense.326T/K BMT2 T326K 0 SLKTKSDL ENST00000297145.8 1 HLA-E*01:01 5 None 0 0 34198.949 35291.310 19.000 21.000 NA NA NA NA 0.181 Poor Pending -chr1-36179727-36179728-G-A 7.MAP7D1.ENST00000373151.6.missense.765E/K MAP7D1 E765K 0 VQKEKPIP ENST00000373151.6 1 HLA-E*01:01 5 None 0 0 34265.621 36615.350 19.000 26.000 NA NA NA NA 0.329 Poor Pending -chr11-6401000-6401001-C-T 226.APBB1.ENST00000609360.5.missense.554A/T APBB1 A554T 0 VPVTKPVG ENST00000609360.5 5 HLA-E*01:01 4 None 0 0 34267.469 35410.270 19.000 22.000 NA NA NA NA 0.989 Poor Pending -chr1-160876800-160876801-C-T 21.ITLN1.ENST00000326245.3.missense.269G/R ITLN1 G269R 0 CIGGRGYF ENST00000326245.3 1 HLA-E*01:01 5 None 0 0 34343.559 40127.730 19.000 41.000 NA NA NA NA 0.258 Poor Pending -chr9-129102403-129102404-T-C 208.CRAT.ENST00000318080.6.missense.209Y/C CRAT Y209C 0 VVHNCQFF ENST00000318080.6 1 HLA-E*01:01 5 None 0 0 34345.422 36746.710 19.000 26.000 NA NA NA NA 0.269 Poor Pending -chr14-32600790-32600791-A-T 260.AKAP6.ENST00000280979.8.missense.910K/M AKAP6 K910M 0 SPMAEVQL ENST00000280979.8 1 HLA-E*01:01 3 None 0 0 34356.180 30222.590 19.000 11.000 NA NA NA NA 0.693 Poor Pending -chr1-154590262-154590263-T-A 20.ADAR.ENST00000647597.1.missense.806E/V ADAR E806V 0 RMGFTVVT ENST00000647597.1 NA HLA-E*01:01 6 None 0 0 34374.398 36267.200 19.000 24.000 NA NA NA NA 0.284 Poor Pending -chrX-48559737-48559738-A-G 386.TBC1D25.ENST00000376771.8.missense.277N/S TBC1D25 N277S 0 ASPEDLEF ENST00000376771.8 1 HLA-E*01:01 2 None 0 0 34379.609 34307.540 19.000 19.000 NA NA NA NA 1.000 Poor Pending -chr14-32773880-32773881-G-T 261.AKAP6.ENST00000280979.8.missense.1192M/I AKAP6 M1192I 0 IGKESETL ENST00000280979.8 1 HLA-E*01:01 1 None 0 0 34390.789 24395.040 19.000 4.700 NA NA NA NA 0.618 Poor Pending -chr6-33286887-33286888-A-G 133.WDR46.ENST00000374617.8.missense.341V/A WDR46 V341A 0 ASLWSPAM ENST00000374617.8 1 HLA-E*01:01 1 None 0 0 34576.969 28534.230 20.000 8.100 NA NA NA NA 0.648 Poor Pending -chr22-50177151-50177152-C-T 362.PANX2.ENST00000395842.2.missense.147S/F PANX2 S147F 0 LGWEFLAF ENST00000395842.2 2 HLA-E*01:01 8 None 0 0 34578.090 44153.450 20.000 74.000 NA NA NA NA 0.996 Poor Pending -chr5-136274698-136274699-C-T 88.TRPC7.ENST00000513104.5.missense.368A/T TRPC7 A368T 0 LPFLAITY ENST00000513104.5 5 HLA-E*01:01 7 None 0 0 34695.762 36612.580 20.000 26.000 NA NA NA NA 0.388 Poor Pending -chr2-63942505-63942506-C-G 38.VPS54.ENST00000272322.8.missense.453D/H VPS54 D453H 0 HIFSKFTI ENST00000272322.8 5 HLA-E*01:01 1 None 0 0 34755.129 36864.580 20.000 26.000 NA NA NA NA 1.000 Poor Pending -chr3-186164997-186164998-C-T 70.DGKG.ENST00000265022.7.missense.706E/K DGKG E706K 0 QLLKVVGL ENST00000265022.7 1 HLA-E*01:01 4 None 0 0 34816.461 37385.560 20.000 28.000 NA NA NA NA 0.523 Poor Pending -chr6-30952346-30952347-G-A 118.MUCL3.ENST00000462446.5.missense.1295E/K MUCL3 E1295K 0 GNKSHPYL ENST00000462446.5 5 HLA-E*01:01 3 None 0 0 34820.621 35846.250 20.000 23.000 NA NA NA NA 0.786 Poor Pending -chr4-48420360-48420361-A-G 73.SLAIN2.ENST00000264313.10.missense.533R/G SLAIN2 R533G 0 AMGSGLPR ENST00000264313.10 1 HLA-E*01:01 3 None 0 0 34921.730 31057.980 20.000 13.000 NA NA NA NA 0.288 Poor Pending -chr5-133103958-133103959-T-C 86.HSPA4.ENST00000304858.6.missense.751L/P HSPA4 L751P 0 NPQNKQSL ENST00000304858.6 1 HLA-E*01:01 2 None 0 0 34947.430 37558.680 21.000 29.000 NA NA NA NA 1.000 Poor Pending -chr1-223264671-223264672-G-C 28.SUSD4.ENST00000343846.7.missense.228L/V SUSD4 L228V 0 VIWSSSPP ENST00000343846.7 2 HLA-E*01:01 1 None 0 0 34948.559 38104.730 21.000 31.000 NA NA NA NA 0.390 Poor Pending -chr19-422192-422193-G-C 331.SHC2.ENST00000264554.10.missense.525H/D SHC2 H525D 0 MDAGQPKH ENST00000264554.10 1 HLA-E*01:01 2 None 0 0 35125.230 34280.820 21.000 19.000 NA NA NA NA 0.109 Poor Pending -chr6-43587456-43587457-G-A 149.POLH.ENST00000372236.8.missense.153G/D POLH G153D 0 GLPQDPTT ENST00000372236.8 1 HLA-E*01:01 5 None 0 0 35141.570 33319.420 21.000 17.000 NA NA NA NA 0.221 Poor Pending -chr3-39188114-39188115-A-T 57.XIRP1.ENST00000340369.3.missense.444L/H XIRP1 L444H 0 NHFETLPL ENST00000340369.3 1 HLA-E*01:01 2 None 0 0 35165.922 29287.100 21.000 8.900 NA NA NA NA 0.655 Poor Pending -chr11-59364558-59364559-T-A 233.OR5AN1.ENST00000641850.1.missense.34V/E OR5AN1 V34E 0 VLFTIFLE ENST00000641850.1 NA HLA-E*01:01 8 None 0 0 35445.160 25935.400 22.000 5.800 NA NA NA NA 0.123 Poor Pending -chr14-70060889-70060890-C-G 265.SLC8A3.ENST00000381269.6.missense.612E/Q SLC8A3 E612Q 0 RQQNFFIA ENST00000381269.6 1 HLA-E*01:01 3 None 0 0 35447.461 36794.460 22.000 26.000 NA NA NA NA 1.000 Poor Pending -chrX-77681732-77681733-T-C 390.ATRX.ENST00000373344.10.missense.1175K/E ATRX K1175E 0 SEKKAVIV ENST00000373344.10 1 HLA-E*01:01 2 None 0 0 35460.500 35081.930 22.000 21.000 NA NA NA NA 1.000 Poor Pending -chr16-84318345-84318346-G-A 306.WFDC1.ENST00000219454.9.missense.138V/M WFDC1 V138M 0 LDGPEEML ENST00000219454.9 1 HLA-E*01:01 7 None 0 0 35467.020 34278.590 22.000 19.000 NA NA NA NA 0.495 Poor Pending -chr7-97006043-97006044-G-C 179.DLX6.ENST00000518156.2.missense.23E/Q DLX6 E23Q 0 SSKSAFMQ ENST00000518156.2 1 HLA-E*01:01 8 None 0 0 35541.551 36933.660 22.000 27.000 NA NA NA NA 0.419 Poor Pending -chr16-56982179-56982180-G-A 290.CETP.ENST00000200676.7.missense.422V/I CETP V422I 0 SESIQSFL ENST00000200676.7 1 HLA-E*01:01 4 None 0 0 35616.988 34878.690 22.000 20.000 NA NA NA NA 0.653 Poor Pending -chr18-36067341-36067342-C-G 327.RPRD1A.ENST00000399022.8.missense.21Q/H RPRD1A Q21H 0 SQHSVQTL ENST00000399022.8 1 HLA-E*01:01 3 None 0 0 35630.500 34801.780 22.000 20.000 NA NA NA NA 0.424 Poor Pending -chr7-102317255-102317256-A-G 180.SH2B2.ENST00000536178.3.missense.462H/R SH2B2 H462R 0 YPWFRGTL ENST00000536178.3 1 HLA-E*01:01 5 None 0 0 35639.738 34199.670 22.000 19.000 NA NA NA NA 0.189 Poor Pending -chr17-4545724-4545725-T-C 313.MYBBP1A.ENST00000381556.6.missense.653E/G MYBBP1A E653G 0 EVLVGILL ENST00000381556.6 5 HLA-E*01:01 5 None 0 0 35641.281 36414.640 22.000 25.000 NA NA NA NA 0.354 Poor Pending -chr1-59858482-59858483-C-T 14.HOOK1.ENST00000371208.3.missense.433S/L HOOK1 S433L 0 LQVQQDHL ENST00000371208.3 1 HLA-E*01:01 1 None 0 0 35676.789 38483.020 23.000 33.000 NA NA NA NA 0.413 Poor Pending -chr2-236392010-236392011-C-T 54.IQCA1.ENST00000431676.6.missense.467E/K IQCA1 E467K 0 RERKRPVK ENST00000431676.6 2 HLA-E*01:01 4 None 0 0 35720.430 37398.120 23.000 28.000 NA NA NA NA 0.237 Poor Pending -chrX-100635206-100635207-C-T 395.TSPAN6.ENST00000373020.8.missense.108A/T TSPAN6 A108T 0 ATIVGFVF ENST00000373020.8 1 HLA-E*01:01 2 None 0 0 35834.230 34206.340 23.000 19.000 NA NA NA NA 1.000 Poor Pending -chr1-66834005-66834006-C-G 15.WDR78.ENST00000371026.7.missense.626G/R WDR78 G626R 0 RLDCYDLM ENST00000371026.7 1 HLA-E*01:01 1 None 0 0 35871.090 42568.820 23.000 58.000 NA NA NA NA 0.598 Poor Pending -chr16-74385694-74385695-C-T 303.NPIPB15.ENST00000429990.1.missense.164T/M NPIPB15 T164M 0 IRKRKVTM ENST00000429990.1 5 HLA-E*01:01 8 None 0 0 35930.121 42376.730 23.000 57.000 NA NA NA NA 0.520 Poor Pending -chr2-71611503-71611504-C-G 39.DYSF.ENST00000410020.7.missense.1367L/V DYSF L1367V 0 RNMKSYQV ENST00000410020.7 1 HLA-E*01:01 8 None 0 0 35932.840 23672.440 23.000 4.300 NA NA NA NA 1.000 Poor Pending -chr12-116009024-116009025-G-C 249.MED13L.ENST00000281928.8.missense.463A/G MED13L A463G 0 SLPPPGSS ENST00000281928.8 1 HLA-E*01:01 6 None 0 0 35938.680 32860.450 23.000 16.000 NA NA NA NA 0.055 Poor Pending -chr1-27359862-27359863-T-G 5.MAP3K6.ENST00000493901.5.missense.772I/L MAP3K6 I772L 0 DLKGDNVL ENST00000493901.5 5 HLA-E*01:01 2 None 0 0 35962.422 38898.290 23.000 34.000 NA NA NA NA 0.265 Poor Pending -chr17-10499040-10499041-G-A 318.MYH1.ENST00000226207.5.missense.1306S/L MYH1 S1306L 0 LLRGKQAF ENST00000226207.5 5 HLA-E*01:01 2 None 0 0 36064.500 41818.770 24.000 52.000 NA NA NA NA 0.987 Poor Pending -chr17-29286059-29286060-C-G 320.NUFIP2.ENST00000225388.8.missense.645R/T NUFIP2 R645T 0 EQRYQTGL ENST00000225388.8 1 HLA-E*01:01 6 None 0 0 36075.430 39007.870 24.000 35.000 NA NA NA NA 1.000 Poor Pending -chr16-57655892-57655893-A-C 293.ADGRG1.ENST00000568909.5.missense.306Q/H ADGRG1 Q306H 0 DKNSSHVL ENST00000568909.5 5 HLA-E*01:01 6 None 0 0 36181.371 37550.160 24.000 29.000 NA NA NA NA 0.664 Poor Pending -chr16-69954568-69954569-C-T 298.CLEC18A.ENST00000615430.4.missense.151T/M CLEC18A T151M 0 TCTHYMQL ENST00000615430.4 5 HLA-E*01:01 6 None 0 0 36307.238 38265.040 25.000 32.000 NA NA NA NA 0.632 Poor Pending -chr1-232805681-232805682-C-T 31.MAP10.ENST00000418460.2.missense.220P/L MAP10 P220L 0 ALAAEPWP ENST00000418460.2 NA HLA-E*01:01 2 None 0 0 36481.301 36155.920 25.000 24.000 NA NA NA NA 0.233 Poor Pending -chr16-72128664-72128665-T-G 302.PMFBP1.ENST00000237353.14.missense.694N/H PMFBP1 N694H 0 DLHKEIAL ENST00000237353.14 1 HLA-E*01:01 3 None 0 0 36530.672 38538.000 25.000 33.000 NA NA NA NA 0.066 Poor Pending -chr1-22660990-22660991-G-A 4.C1QB.ENST00000314933.6.missense.123A/T C1QB A123T 0 KATQKITF ENST00000314933.6 1 HLA-E*01:01 7 None 0 0 36570.199 38473.860 25.000 33.000 NA NA NA NA 1.000 Poor Pending -chr14-94463231-94463232-G-T 269.SERPINA9.ENST00000337425.9.missense.390T/N SERPINA9 T390N 0 ATTNKFIV ENST00000337425.9 1 HLA-E*01:01 4 None 0 0 36626.449 34268.950 26.000 19.000 NA NA NA NA 0.466 Poor Pending -chr3-52517959-52517960-A-C 60.STAB1.ENST00000321725.10.missense.1573H/P STAB1 H1573P 0 APTVGDGL ENST00000321725.10 1 HLA-E*01:01 2 None 0 0 36649.441 42570.660 26.000 58.000 NA NA NA NA 1.000 Poor Pending -chr1-86453473-86453474-G-A 16.CLCA2.ENST00000370565.4.missense.754G/E CLCA2 G754E 0 EVPAGPHP ENST00000370565.4 1 HLA-E*01:01 1 None 0 0 36736.781 39491.560 26.000 37.000 NA NA NA NA 0.576 Poor Pending -chr6-43216393-43216394-A-C 145.CUL9.ENST00000252050.8.missense.2058H/P CUL9 H2058P 0 CVPQAQAV ENST00000252050.8 5 HLA-E*01:01 3 None 0 0 36889.719 43625.400 26.000 68.000 NA NA NA NA 0.656 Poor Pending -chr14-23425383-23425384-T-G 257.MYH7.ENST00000355349.3.missense.774E/A MYH7 E774A 0 AEMRDERL ENST00000355349.3 1 HLA-E*01:01 1 None 0 0 36911.680 38330.090 26.000 32.000 NA NA NA NA 0.200 Poor Pending -chr6-52492272-52492273-A-C 160.EFHC1.ENST00000371068.10.missense.619I/L EFHC1 I619L 0 LVKELLRM ENST00000371068.10 1 HLA-E*01:01 6 None 0 0 36915.281 38360.360 26.000 32.000 NA NA NA NA 0.545 Poor Pending -chr6-43283594-43283595-A-T 146.TTBK1.ENST00000259750.8.missense.952E/V TTBK1 E952V 0 QALRSVEF ENST00000259750.8 1 HLA-E*01:01 6 None 0 0 36960.852 39158.820 27.000 36.000 NA NA NA NA 0.280 Poor Pending -chr14-24068642-24068643-G-A 258.CARMIL3.ENST00000342740.5.missense.1248E/K CARMIL3 E1248K 0 KEEKEGTL ENST00000342740.5 5 HLA-E*01:01 1 None 0 0 36987.250 39158.390 27.000 36.000 NA NA NA NA 0.178 Poor Pending -chr7-140024672-140024681-TCAAAGATCA-T 188.PARP12.ENST00000263549.7.inframe_del.662-665VIFE/E PARP12 VIFE662-665E 0 VSDPSIFE ENST00000263549.7 1 HLA-E*01:01 7-8 None 0 0 36994.449 29973.150 27.000 9.800 NA NA NA NA 0.129 Poor Pending -chrX-131544869-131544870-A-C 403.OR13H1.ENST00000338616.5.missense.266Y/S OR13H1 Y266S 0 TQSKSSPD ENST00000338616.5 NA HLA-E*01:01 6 None 0 0 37047.340 38580.970 27.000 33.000 NA NA NA NA 1.000 Poor Pending -chr16-70146184-70146185-A-T 299.PDPR.ENST00000288050.8.missense.640Y/F PDPR Y640F 0 ELSFAPMT ENST00000288050.8 1 HLA-E*01:01 4 None 0 0 37243.051 35176.950 28.000 21.000 NA NA NA NA 0.405 Poor Pending -chr6-30986467-30986468-T-C 119.MUC21.ENST00000376296.3.missense.98V/A MUC21 V98A 0 TASSGISI ENST00000376296.3 1 HLA-E*01:01 2 None 0 0 37243.871 38206.280 28.000 31.000 NA NA NA NA 0.664 Poor Pending -chr18-80136551-80136552-C-T 329.ADNP2.ENST00000262198.8.missense.380P/L ADNP2 P380L 0 SQPVGLVN ENST00000262198.8 1 HLA-E*01:01 6 None 0 0 37589.191 33988.680 29.000 18.000 NA NA NA NA 0.932 Poor Pending -chr6-14131622-14131623-A-G 102.CD83.ENST00000379153.3.missense.86N/S CD83 N86S 0 PSERPYSL ENST00000379153.3 1 HLA-E*01:01 2 None 0 0 37658.781 39448.440 29.000 37.000 NA NA NA NA 0.979 Poor Pending -chr15-49282070-49282071-G-T 275.GALK2.ENST00000560031.5.missense.197A/S GALK2 A197S 0 SEEGTAKL ENST00000560031.5 1 HLA-E*01:01 1 None 0 0 37666.941 36424.500 29.000 25.000 NA NA NA NA 1.000 Poor Pending -chr3-58210851-58210852-G-C 62.DNASE1L3.ENST00000394549.6.missense.19L/V DNASE1L3 L19V 0 SIHSAVAM ENST00000394549.6 1 HLA-E*01:01 6 None 0 0 37677.121 33961.840 29.000 18.000 NA NA NA NA 1.000 Poor Pending -chr9-35609475-35609476-C-T 203.TESK1.ENST00000620767.4.missense.539H/Y TESK1 H539Y 0 WNRAQYSL ENST00000620767.4 5 HLA-E*01:01 6 None 0 0 37719.160 39565.130 29.000 38.000 NA NA NA NA 1.000 Poor Pending -chr6-52236940-52236941-T-C 159.IL17F.ENST00000336123.4.missense.161H/R IL17F H161R 0 VTPVIHRV ENST00000336123.4 1 HLA-E*01:01 7 None 0 0 37738.328 39105.070 29.000 35.000 NA NA NA NA 0.353 Poor Pending -chr6-31112238-31112239-C-G 121.C6orf15.ENST00000259870.3.missense.40L/F C6orf15 L40F 0 FGTNLPQL ENST00000259870.3 1 HLA-E*01:01 1 None 0 0 37783.289 31669.800 30.000 14.000 NA NA NA NA 0.684 Poor Pending -chr7-122013415-122013416-A-G 185.PTPRZ1.ENST00000393386.6.missense.1457N/S PTPRZ1 N1457S 0 VMSDSDTH ENST00000393386.6 1 HLA-E*01:01 3 None 0 0 37831.539 40080.870 30.000 41.000 NA NA NA NA 0.234 Poor Pending -chr6-3010155-3010156-C-T 95.NQO2.ENST00000380455.8.missense.47L/F NQO2 L47F 0 AMNFEPRA ENST00000380455.8 1 HLA-E*01:01 4 None 0 0 37924.172 39421.960 30.000 37.000 NA NA NA NA 0.451 Poor Pending -chr14-94382907-94382908-C-G 268.SERPINA1.ENST00000448921.5.missense.110E/D SERPINA1 E110D 0 TDIPEAQI ENST00000448921.5 1 HLA-E*01:01 2 None 0 0 37941.000 33259.270 30.000 17.000 NA NA NA NA 0.174 Poor Pending -chr3-122927970-122927971-G-C 64.SEMA5B.ENST00000451055.6.missense.277I/M SEMA5B I277M 0 LSRTTEKM ENST00000451055.6 2 HLA-E*01:01 8 None 0 0 38028.941 39577.960 31.000 38.000 NA NA NA NA 1.000 Poor Pending -chr1-227091907-227091908-T-G 30.CDC42BPA.ENST00000366769.7.missense.778K/T CDC42BPA K778T 0 LTEENKTL ENST00000366769.7 1 HLA-E*01:01 7 None 0 0 38121.219 38545.110 31.000 33.000 NA NA NA NA 0.273 Poor Pending -chr2-201835739-201835740-A-C 48.CDK15.ENST00000450471.6.missense.276E/D CDK15 E276D 0 ATDYSSEL ENST00000450471.6 1 HLA-E*01:01 3 None 0 0 38131.941 37533.910 31.000 29.000 NA NA NA NA 0.568 Poor Pending -chrX-34131149-34131150-C-A 380.FAM47A.ENST00000346193.4.missense.377A/S FAM47A A377S 0 SEPSKTGV ENST00000346193.4 NA HLA-E*01:01 1 None 0 0 38136.070 36913.680 31.000 26.000 NA NA NA NA 0.990 Poor Pending -chr2-216428741-216428742-C-G 49.SMARCAL1.ENST00000357276.8.missense.432L/V SMARCAL1 L432V 0 VVSNLMPF ENST00000357276.8 2 HLA-E*01:01 1 None 0 0 38169.090 39765.110 31.000 39.000 NA NA NA NA 0.457 Poor Pending -chr8-125028638-125028639-T-C 196.WASHC5.ENST00000318410.11.missense.1135Y/C WASHC5 Y1135C 0 DYVRCTKL ENST00000318410.11 1 HLA-E*01:01 5 None 0 0 38188.930 39332.930 31.000 37.000 NA NA NA NA 0.133 Poor Pending -chr6-31161532-31161533-C-T 124.TCF19.ENST00000376257.7.missense.109P/S TCF19 P109S 0 SPGTSPSE ENST00000376257.7 1 HLA-E*01:01 1 None 0 0 38214.980 40371.160 31.000 42.000 NA NA NA NA 0.671 Poor Pending -chrX-2917995-2917996-G-C 368.ARSD.ENST00000381154.5.missense.224S/C ARSD S224C 0 CVSARAVT ENST00000381154.5 1 HLA-E*01:01 1 None 0 0 38246.809 37802.900 32.000 30.000 NA NA NA NA 0.542 Poor Pending -chr19-35841840-35841841-C-A 343.NPHS1.ENST00000378910.9.missense.897G/C NPHS1 G897C 0 CGVHSSLL ENST00000378910.9 1 HLA-E*01:01 1 None 0 0 38257.590 40671.950 32.000 44.000 NA NA NA NA 0.087 Poor Pending -chr6-42104971-42104977-ACTCCTC-A 141.C6orf132.ENST00000341865.8.inframe_del.979-980EE/- C6orf132 EE979-980- 0 REEEEFNF ENST00000341865.8 5 HLA-E*01:01 5-6 None 0 0 38289.059 42149.010 32.000 55.000 NA NA NA NA 0.700 Poor Pending -chr6-24503361-24503362-C-T 106.ALDH5A1.ENST00000348925.2.missense.180H/Y ALDH5A1 H180Y 0 RVYGDIIY ENST00000348925.2 1 HLA-E*01:01 8 None 0 0 38323.031 42243.520 32.000 56.000 NA NA NA NA 0.727 Poor Pending -chr13-98431277-98431278-G-T 254.FARP1.ENST00000627049.2.missense.714R/L FARP1 R714L 0 CLAALAEI ENST00000627049.2 5 HLA-E*01:01 2 None 0 0 38324.289 42429.940 32.000 57.000 NA NA NA NA 1.000 Poor Pending -chrX-77682470-77682471-C-G 391.ATRX.ENST00000373344.10.missense.929E/Q ATRX E929Q 0 KEQSFTSL ENST00000373344.10 1 HLA-E*01:01 3 None 0 0 38332.988 39309.520 32.000 36.000 NA NA NA NA 0.951 Poor Pending -chr18-80138228-80138229-G-T 330.ADNP2.ENST00000262198.8.missense.939R/I ADNP2 R939I 0 VRCISAPK ENST00000262198.8 1 HLA-E*01:01 4 None 0 0 38369.910 35070.160 32.000 21.000 NA NA NA NA 1.000 Poor Pending -chr19-16093698-16093699-G-C 340.TPM4.ENST00000646974.1.missense.240E/Q TPM4 E240Q 0 EAETRAQF ENST00000646974.1 NA HLA-E*01:01 7 None 0 0 38433.070 39585.240 32.000 38.000 NA NA NA NA 0.484 Poor Pending -chrX-38367349-38367350-A-G 381.OTC.ENST00000039007.4.missense.46K/R OTC K46R 0 LLTLRNFT ENST00000039007.4 1 HLA-E*01:01 5 None 0 0 38468.852 40362.440 32.000 42.000 NA NA NA NA 1.000 Poor Pending -chr1-150261628-150261629-G-A 19.CA14.ENST00000369111.8.missense.83G/S CA14 G83S 0 NNSHTVQL ENST00000369111.8 1 HLA-E*01:01 3 None 0 0 38474.262 39769.830 33.000 39.000 NA NA NA NA 0.338 Poor Pending -chrX-32389609-32389610-C-T 379.DMD.ENST00000357033.8.missense.1470R/H DMD R1470H 0 HLQESKMI ENST00000357033.8 1 HLA-E*01:01 1 None 0 0 38547.180 31553.520 33.000 14.000 NA NA NA NA 1.000 Poor Pending -chr6-46662451-46662452-C-G 155.SLC25A27.ENST00000371347.9.missense.154Q/E SLC25A27 Q154E 0 LVKVEMQM ENST00000371347.9 1 HLA-E*01:01 5 None 0 0 38547.602 38098.140 33.000 31.000 NA NA NA NA 0.500 Poor Pending -chr6-17632829-17632830-C-T 104.NUP153.ENST00000537253.5.missense.858A/T NUP153 A858T 0 KPGSSVPT ENST00000537253.5 2 HLA-E*01:01 8 None 0 0 38569.301 40151.630 33.000 41.000 NA NA NA NA 0.967 Poor Pending -chr6-31505783-31505784-A-G 125.MICB.ENST00000252229.6.missense.80K/E MICB K80E 0 VLGAETWD ENST00000252229.6 1 HLA-E*01:01 5 None 0 0 38613.559 36194.670 33.000 24.000 NA NA NA NA 0.750 Poor Pending -chr9-120858190-120858191-G-A 207.PHF19.ENST00000616568.5.missense.518P/L PHF19 P518L 0 AELDGRCL ENST00000616568.5 1 HLA-E*01:01 8 None 0 0 38679.211 45699.580 33.000 91.000 NA NA NA NA 0.500 Poor Pending -chr9-137199427-137199428-T-A 211.TPRN.ENST00000409012.5.missense.428E/D TPRN E428D 0 FLPAASDE ENST00000409012.5 1 HLA-E*01:01 7 None 0 0 38685.070 37201.570 33.000 27.000 NA NA NA NA 0.283 Poor Pending -chr11-56542446-56542447-T-C 231.OR5M11.ENST00000528616.4.missense.271K/E OR5M11 K271E 0 TVEESEII ENST00000528616.4 NA HLA-E*01:01 6 None 0 0 38729.879 38815.870 34.000 34.000 NA NA NA NA 0.280 Poor Pending -chr14-39247882-39247883-G-C 262.MIA2.ENST00000640607.1.missense.437D/H MIA2 D437H 0 IIETEHQI ENST00000640607.1 1 HLA-E*01:01 6 None 0 0 38731.121 42203.760 34.000 55.000 NA NA NA NA 0.983 Poor Pending -chr20-59301546-59301547-G-T 353.EDN3.ENST00000337938.6.missense.64G/W EDN3 G64W 0 AGPGEWTV ENST00000337938.6 1 HLA-E*01:01 6 None 0 0 38794.891 40748.140 34.000 45.000 NA NA NA NA 0.216 Poor Pending -chr14-91783159-91783160-T-A 267.TC2N.ENST00000435962.6.missense.471K/N TC2N K471N 0 NQWNETVI ENST00000435962.6 2 HLA-E*01:01 4 None 0 0 38844.020 35774.570 34.000 23.000 NA NA NA NA 0.154 Poor Pending -chr10-125729432-125729433-C-G 220.EDRF1.ENST00000356792.8.missense.324P/A EDRF1 P324A 0 VGSNMAIF ENST00000356792.8 1 HLA-E*01:01 6 None 0 0 38851.180 28587.990 34.000 8.200 NA NA NA NA 0.163 Poor Pending -chr18-14106118-14106119-G-C 326.ZNF519.ENST00000590202.2.missense.141P/A ZNF519 P141A 0 PTEPCIAM ENST00000590202.2 1 HLA-E*01:01 7 None 0 0 38853.691 34409.380 34.000 19.000 NA NA NA NA 0.445 Poor Pending -chr11-62752450-62752451-G-A 234.ZBTB3.ENST00000394807.3.missense.455S/F ZBTB3 S455F 0 HEPLYLSF ENST00000394807.3 1 HLA-E*01:01 8 None 0 0 38889.430 44254.850 34.000 75.000 NA NA NA NA 0.673 Poor Pending -chr5-141123692-141123693-G-C 89.PCDHB4.ENST00000194152.3.missense.565Q/H PCDHB4 Q565H 0 LHNGSAPC ENST00000194152.3 NA HLA-E*01:01 2 None 0 0 38893.648 34644.000 34.000 20.000 NA NA NA NA 0.327 Poor Pending -chr22-37374977-37374978-G-A 357.ELFN2.ENST00000402918.6.missense.186P/L ELFN2 P186L 0 VCELAGNL ENST00000402918.6 4 HLA-E*01:01 8 None 0 0 38927.750 45509.120 35.000 89.000 NA NA NA NA 0.165 Poor Pending -chr6-31765688-31765689-T-C 127.VWA7.ENST00000375688.4.missense.861T/A VWA7 T861A 0 FSPFTLVA ENST00000375688.4 5 HLA-E*01:01 8 None 0 0 38938.301 37678.360 35.000 29.000 NA NA NA NA 0.700 Poor Pending -chr17-82961144-82961145-G-C 325.B3GNTL1.ENST00000320865.3.missense.213L/V B3GNTL1 L213V 0 VRKGGGVI ENST00000320865.3 1 HLA-E*01:01 1 None 0 0 39052.621 39971.290 35.000 40.000 NA NA NA NA 0.211 Poor Pending -chr16-57025571-57025572-C-T 291.NLRC5.ENST00000262510.10.missense.210S/L NLRC5 S210L 0 ADVSILDL ENST00000262510.10 5 HLA-E*01:01 6 None 0 0 39058.109 43072.440 35.000 63.000 NA NA NA NA 0.633 Poor Pending -chr6-30926163-30926164-G-A 116.VARS2.ENST00000541562.5.missense.1079R/Q VARS2 R1079Q 0 AASHLQQL ENST00000541562.5 2 HLA-E*01:01 6 None 0 0 39096.160 39452.690 35.000 37.000 NA NA NA NA 0.788 Poor Pending -chr19-5928080-5928081-C-G 332.RANBP3.ENST00000340578.10.missense.234E/Q RANBP3 E234Q 0 KQPQKNES ENST00000340578.10 1 HLA-E*01:01 2 None 0 0 39248.750 42874.370 36.000 61.000 NA NA NA NA 0.987 Poor Pending -chr12-889169-889170-C-G 243.WNK1.ENST00000340908.8.missense.2051Q/E WNK1 Q2051E 0 ELRRTLSP ENST00000340908.8 5 HLA-E*01:01 1 None 0 0 39271.691 37697.930 36.000 29.000 NA NA NA NA 0.612 Poor Pending -chrX-2861528-2861529-A-G 367.GYG2.ENST00000381163.7.missense.313H/R GYG2 H313R 0 SPGHTLCR ENST00000381163.7 1 HLA-E*01:01 8 None 0 0 39273.391 38846.550 36.000 34.000 NA NA NA NA 0.508 Poor Pending -chr9-37784015-37784016-T-A 204.EXOSC3.ENST00000327304.9.missense.124K/N EXOSC3 K124N 0 TANSGDIF ENST00000327304.9 1 HLA-E*01:01 3 None 0 0 39297.199 35832.290 36.000 23.000 NA NA NA NA 0.489 Poor Pending -chrX-133304843-133304844-C-A 405.GPC4.ENST00000370828.3.missense.391E/D GPC4 E391D 0 VTDVKDKL ENST00000370828.3 1 HLA-E*01:01 6 None 0 0 39369.980 38082.050 37.000 31.000 NA NA NA NA 1.000 Poor Pending -chr15-74280668-74280669-G-T 279.CCDC33.ENST00000398814.7.missense.297M/I CCDC33 M297I 0 IKGSQPWT ENST00000398814.7 2 HLA-E*01:01 1 None 0 0 39387.020 31761.080 37.000 14.000 NA NA NA NA 0.575 Poor Pending -chr6-26509101-26509102-C-G 110.BTN1A1.ENST00000244513.10.missense.503D/E BTN1A1 D503E 0 MGEESAPR ENST00000244513.10 1 HLA-E*01:01 4 None 0 0 39486.000 41012.200 37.000 47.000 NA NA NA NA 0.719 Poor Pending -chr12-31697921-31697922-G-T 245.AMN1.ENST00000281471.10.missense.118H/N AMN1 H118N 0 SYLNEASL ENST00000281471.10 1 HLA-E*01:01 4 None 0 0 39496.680 38682.550 37.000 33.000 NA NA NA NA 0.441 Poor Pending -chr1-37721680-37721681-G-T 8.EPHA10.ENST00000373048.8.missense.709L/M EPHA10 L709M 0 RMEGVVTR ENST00000373048.8 5 HLA-E*01:01 2 None 0 0 39503.102 43807.500 37.000 70.000 NA NA NA NA 0.388 Poor Pending -chr13-37746421-37746422-C-T 252.TRPC4.ENST00000625583.2.missense.138E/K TRPC4 E138K 0 KQFSKFTP ENST00000625583.2 1 HLA-E*01:01 5 None 0 0 39529.172 41082.380 38.000 47.000 NA NA NA NA 0.516 Poor Pending -chr6-12124353-12124354-C-G 100.HIVEP1.ENST00000379388.6.missense.1520A/G HIVEP1 A1520G 0 HGPPSHQS ENST00000379388.6 1 HLA-E*01:01 2 None 0 0 39551.430 37531.050 38.000 29.000 NA NA NA NA 0.977 Poor Pending -chrX-48560270-48560271-G-A 387.TBC1D25.ENST00000376771.8.missense.455A/T TBC1D25 A455T 0 SQVADTGF ENST00000376771.8 1 HLA-E*01:01 6 None 0 0 39555.281 37701.600 38.000 29.000 NA NA NA NA 0.992 Poor Pending -chrX-2221144-2221145-C-T 365.DHRSX.ENST00000334651.10.missense.297E/K DHRSX E297K 0 NKKETKSL ENST00000334651.10 1 HLA-E*01:01 2 None 0 0 39633.238 39714.370 38.000 39.000 NA NA NA NA 0.515 Poor Pending -chr8-132141242-132141243-C-G 199.KCNQ3.ENST00000388996.9.missense.451D/H KCNQ3 D451H 0 TPLNVHAI ENST00000388996.9 1 HLA-E*01:01 6 None 0 0 39790.512 43193.300 39.000 64.000 NA NA NA NA 0.286 Poor Pending -chr17-7675087-7675088-C-T 317.TP53.ENST00000269305.8.missense.175R/H TP53 R175H 0 VVRHCPHH ENST00000269305.8 1 HLA-E*01:01 4 None 0 0 39844.359 36460.370 39.000 25.000 NA NA NA NA 0.988 Poor Pending -chr6-56552483-56552484-C-T 165.DST.ENST00000312431.10.missense.3179M/I DST M3179I 0 LKKLEALI ENST00000312431.10 5 HLA-E*01:01 8 None 0 0 39897.410 38744.120 40.000 34.000 NA NA NA NA 0.490 Poor Pending -chr7-77600798-77600799-C-T 174.PTPN12.ENST00000248594.10.missense.230H/Y PTPN12 H230Y 0 VPICIYCS ENST00000248594.10 1 HLA-E*01:01 6 None 0 0 39908.648 41222.640 40.000 48.000 NA NA NA NA 0.192 Poor Pending -chr1-183880710-183880711-A-C 24.RGL1.ENST00000304685.8.missense.209Y/S RGL1 Y209S 0 LLDSLTRM ENST00000304685.8 1 HLA-E*01:01 4 None 0 0 39947.090 40501.550 40.000 43.000 NA NA NA NA 0.314 Poor Pending -chr12-112043094-112043095-A-C 248.NAA25.ENST00000261745.8.missense.789S/R NAA25 S789R 0 ELDTRGLE ENST00000261745.8 1 HLA-E*01:01 5 None 0 0 39958.328 41819.680 40.000 52.000 NA NA NA NA 1.000 Poor Pending -chr1-42775287-42775288-A-G 10.C1orf50.ENST00000372525.6.missense.165D/G C1orf50 D165G 0 TPYEGIEK ENST00000372525.6 1 HLA-E*01:01 5 None 0 0 40037.520 43105.530 40.000 63.000 NA NA NA NA 0.111 Poor Pending -chrX-133303308-133303309-G-A 404.GPC4.ENST00000370828.3.missense.442A/V GPC4 A442V 0 AVTGNGLV ENST00000370828.3 1 HLA-E*01:01 8 None 0 0 40088.680 43919.040 41.000 71.000 NA NA NA NA 0.976 Poor Pending -chr9-138120681-138120682-G-A 213.CACNA1B.ENST00000371372.5.missense.2097G/D CACNA1B G2097D 0 PPGEGPTD ENST00000371372.5 5 HLA-E*01:01 8 None 0 0 40113.840 39996.380 41.000 40.000 NA NA NA NA 0.280 Poor Pending -chr11-70087776-70087777-C-T 239.ANO1.ENST00000355303.9.missense.45P/L ANO1 P45L 0 LNSLSVDL ENST00000355303.9 1 HLA-E*01:01 8 None 0 0 40271.699 46282.270 42.000 96.000 NA NA NA NA 0.181 Poor Pending -chr15-45133932-45133933-G-A 274.DUOX1.ENST00000321429.8.missense.43R/K DUOX1 R43K 0 LMEHKWGS ENST00000321429.8 1 HLA-E*01:01 5 None 0 0 40320.531 38077.950 42.000 31.000 NA NA NA NA 1.000 Poor Pending -chr17-4818361-4818376-TGGACAGAATCCTGAA-T 314.PLD2.ENST00000263088.10.inframe_del.662-667VDRILK/V PLD2 VDRILK662-667V 0 VAHKQGWC ENST00000263088.10 1 HLA-E*01:01 1-2 None 0 0 40351.090 42563.300 42.000 58.000 NA NA NA NA 0.310 Poor Pending -chr6-43340177-43340178-C-G 147.ZNF318.ENST00000361428.2.missense.1274G/R ZNF318 G1274R 0 SSFRKFSW ENST00000361428.2 1 HLA-E*01:01 4 None 0 0 40376.422 42620.440 42.000 59.000 NA NA NA NA 0.344 Poor Pending -chr6-49517552-49517553-C-A 158.GLYATL3.ENST00000371197.8.missense.104Q/K GLYATL3 Q104K 0 IKGLQSEL ENST00000371197.8 2 HLA-E*01:01 2 None 0 0 40411.379 36683.960 43.000 26.000 NA NA NA NA 0.442 Poor Pending -chrX-115191629-115191630-G-A 401.RBMXL3.ENST00000424776.4.missense.730R/Q RBMXL3 R730Q 0 CSPDTYSQ ENST00000424776.4 NA HLA-E*01:01 8 None 0 0 40447.680 40925.750 43.000 46.000 NA NA NA NA 1.000 Poor Pending -chr20-23354058-23354059-C-G 350.NXT1.ENST00000254998.2.missense.6F/L NXT1 F6L 0 MASVDLKT ENST00000254998.2 1 HLA-E*01:01 6 None 0 0 40470.012 38652.000 43.000 33.000 NA NA NA NA 0.391 Poor Pending -chr8-138737576-138737577-C-A 201.COL22A1.ENST00000303045.10.missense.696G/W COL22A1 G696W 0 LRWKKGDM ENST00000303045.10 1 HLA-E*01:01 3 None 0 0 40555.500 42445.570 43.000 57.000 NA NA NA NA 0.190 Poor Pending -chr19-13765994-13765995-G-C 338.MRI1.ENST00000040663.7.missense.138R/T MRI1 R138T 0 MLEKDLTD ENST00000040663.7 1 HLA-E*01:01 7 None 0 0 40584.461 40019.760 44.000 40.000 NA NA NA NA 0.228 Poor Pending -chr7-132508196-132508197-C-A 187.PLXNA4.ENST00000359827.7.missense.166S/I PLXNA4 S166I 0 VNEIGSVF ENST00000359827.7 5 HLA-E*01:01 4 None 0 0 40605.090 37032.090 44.000 27.000 NA NA NA NA 0.286 Poor Pending -chr8-125102410-125102411-G-C 197.NSMCE2.ENST00000287437.7.missense.27L/F NSMCE2 L27F 0 ALSSFKNF ENST00000287437.7 1 HLA-E*01:01 5 None 0 0 40633.230 42082.920 44.000 54.000 NA NA NA NA 0.265 Poor Pending -chr6-46167751-46167752-T-C 153.ENPP5.ENST00000371383.6.missense.171I/V ENPP5 I171V 0 RVAKIVEW ENST00000371383.6 1 HLA-E*01:01 6 None 0 0 40633.672 39334.200 44.000 37.000 NA NA NA NA 0.745 Poor Pending -chr7-92077866-92077867-G-C 178.AKAP9.ENST00000356239.7.missense.2313D/H AKAP9 D2313H 0 ITTHNKVI ENST00000356239.7 1 HLA-E*01:01 4 None 0 0 40655.211 40808.600 44.000 45.000 NA NA NA NA 0.413 Poor Pending -chr16-57046615-57046616-C-A 292.NLRC5.ENST00000262510.10.missense.1105Q/K NLRC5 Q1105K 0 RKRCIPRS ENST00000262510.10 5 HLA-E*01:01 2 None 0 0 40685.141 37684.870 44.000 29.000 NA NA NA NA 0.688 Poor Pending -chr19-12580947-12580948-G-A 337.ZNF490.ENST00000311437.10.missense.376S/F ZNF490 S376F 0 AFKSSSFC ENST00000311437.10 1 HLA-E*01:01 7 None 0 0 40687.352 44739.680 44.000 80.000 NA NA NA NA 0.352 Poor Pending -chr4-373601-373602-C-T 71.ZNF141.ENST00000240499.7.missense.389H/Y ZNF141 H389Y 0 IYTGEKPY ENST00000240499.7 1 HLA-E*01:01 2 None 0 0 40691.762 40440.240 44.000 43.000 NA NA NA NA 0.917 Poor Pending -chr6-30931746-30931747-T-C 117.SFTA2.ENST00000359086.3.missense.37N/S SFTA2 N37S 0 FLTSSSYE ENST00000359086.3 1 HLA-E*01:01 4 None 0 0 40710.230 42675.360 44.000 59.000 NA NA NA NA 0.628 Poor Pending -chr15-28843283-28843284-G-T 270.GOLGA6L7.ENST00000567390.6.missense.274Q/K GOLGA6L7 Q274K 0 LREKEQQM ENST00000567390.6 5 HLA-E*01:01 4 None 0 0 40717.719 41971.990 44.000 54.000 NA NA NA NA 0.539 Poor Pending -chr1-119895935-119895936-C-T 17.ADAM30.ENST00000369400.1.missense.134R/Q ADAM30 R134Q 0 MGGLQGVF ENST00000369400.1 NA HLA-E*01:01 5 None 0 0 40801.961 41001.540 45.000 46.000 NA NA NA NA 0.208 Poor Pending -chr6-56463050-56463051-C-T 164.DST.ENST00000312431.10.missense.5408A/T DST A5408T 0 STEGTPIQ ENST00000312431.10 5 HLA-E*01:01 2 None 0 0 40835.078 39458.660 45.000 37.000 NA NA NA NA 0.481 Poor Pending -chrX-100987546-100987547-C-T 396.ARL13A.ENST00000450049.6.missense.215S/L ARL13A S215L 0 CLSHSFST ENST00000450049.6 5 HLA-E*01:01 2 None 0 0 40885.039 43641.920 46.000 68.000 NA NA NA NA 1.000 Poor Pending -chr12-10159995-10159996-G-C 244.OLR1.ENST00000309539.7.missense.236Q/E OLR1 Q236E 0 ETYPSGTC ENST00000309539.7 1 HLA-E*01:01 1 None 0 0 40891.238 39304.860 46.000 36.000 NA NA NA NA 0.195 Poor Pending -chrX-2859943-2859944-C-T 366.GYG2.ENST00000381163.7.missense.270A/V GYG2 A270V 0 VLEQGSVS ENST00000381163.7 1 HLA-E*01:01 7 None 0 0 40939.922 43392.840 46.000 66.000 NA NA NA NA 0.485 Poor Pending -chr7-27130623-27130624-C-T 171.HOXA4.ENST00000360046.9.missense.37G/D HOXA4 G37D 0 GPDGGPGY ENST00000360046.9 1 HLA-E*01:01 3 None 0 0 40944.359 39097.450 46.000 35.000 NA NA NA NA 0.375 Poor Pending -chr20-59944225-59944226-A-G 354.FAM217B.ENST00000358293.7.missense.95S/G FAM217B S95G 0 DEDSAGDL ENST00000358293.7 2 HLA-E*01:01 6 None 0 0 40990.012 41036.170 46.000 47.000 NA NA NA NA 0.563 Poor Pending -chr3-121697676-121697677-G-C 63.GOLGB1.ENST00000393667.7.missense.949A/G GOLGB1 A949G 0 LLSRAEEG ENST00000393667.7 1 HLA-E*01:01 8 None 0 0 41031.301 39998.140 47.000 40.000 NA NA NA NA 1.000 Poor Pending -chr1-196995755-196995756-A-G 25.CFHR5.ENST00000256785.4.missense.216N/S CFHR5 N216S 0 GPPPQLSS ENST00000256785.4 1 HLA-E*01:01 8 None 0 0 41057.480 40998.000 47.000 46.000 NA NA NA NA 0.284 Poor Pending -chr2-219471924-219471925-A-G 50.SPEG.ENST00000312358.11.missense.1258Y/C SPEG Y1258C 0 GPQHAGVC ENST00000312358.11 5 HLA-E*01:01 8 None 0 0 41075.250 40250.360 47.000 42.000 NA NA NA NA 0.340 Poor Pending -chr15-69049033-69049034-G-C 278.NOX5.ENST00000388866.7.missense.659D/H NOX5 D659H 0 EMHQAEEA ENST00000388866.7 1 HLA-E*01:01 3 None 0 0 41082.379 41526.150 47.000 50.000 NA NA NA NA 0.393 Poor Pending -chr6-24576402-24576403-C-T 107.KIAA0319.ENST00000378214.7.missense.567G/S KIAA0319 G567S 0 VLYEWSLS ENST00000378214.7 1 HLA-E*01:01 8 None 0 0 41191.410 41795.680 48.000 52.000 NA NA NA NA 0.668 Poor Pending -chr16-49281350-49281351-C-T 288.CBLN1.ENST00000219197.10.missense.39D/N CBLN1 D39N 0 VVCNSNPT ENST00000219197.10 1 HLA-E*01:01 4 None 0 0 41220.859 41951.550 48.000 53.000 NA NA NA NA 0.213 Poor Pending -chr6-3723707-3723708-C-G 96.PXDC1.ENST00000380283.4.missense.203E/Q PXDC1 E203Q 0 SEFPSQLE ENST00000380283.4 1 HLA-E*01:01 6 None 0 0 41248.059 41680.530 48.000 51.000 NA NA NA NA 0.419 Poor Pending -chr6-30685003-30685004-C-T 115.PPP1R18.ENST00000274853.7.missense.339G/R PPP1R18 G339R 0 RKAREWTP ENST00000274853.7 1 HLA-E*01:01 1 None 0 0 41269.930 44446.800 48.000 77.000 NA NA NA NA 0.750 Poor Pending -chr11-46876561-46876562-C-T 230.LRP4.ENST00000378623.5.missense.1147R/Q LRP4 R1147Q 0 NQIEVGNL ENST00000378623.5 1 HLA-E*01:01 2 None 0 0 41307.898 43377.370 48.000 66.000 NA NA NA NA 0.444 Poor Pending -chr7-102637601-102637602-C-T 182.UPK3BL1.ENST00000340457.8.missense.239G/S UPK3BL1 G239S 0 SPEEAGSV ENST00000340457.8 1 HLA-E*01:01 1 None 0 0 41312.379 43178.340 48.000 64.000 NA NA NA NA 0.364 Poor Pending -chr6-32220605-32220606-T-C 129.NOTCH4.ENST00000375023.3.missense.320T/A NOTCH4 T320A 0 CEAQGPPH ENST00000375023.3 1 HLA-E*01:01 3 None 0 0 41422.020 43308.410 49.000 65.000 NA NA NA NA 0.602 Poor Pending -chr22-37570267-37570268-C-G 358.LGALS2.ENST00000215886.5.missense.132E/Q LGALS2 E132Q 0 MSSFKLKQ ENST00000215886.5 1 HLA-E*01:01 8 None 0 0 41458.801 41910.720 50.000 53.000 NA NA NA NA 0.484 Poor Pending -chr7-128815875-128815876-C-G 186.CCDC136.ENST00000297788.8.missense.1103S/C CCDC136 S1103C 0 EDDADCSL ENST00000297788.8 1 HLA-E*01:01 6 None 0 0 41460.141 41128.630 50.000 47.000 NA NA NA NA 0.205 Poor Pending -chr2-227893862-227893863-C-T 53.DAW1.ENST00000309931.2.missense.129T/M DAW1 T129M 0 NMLEGHRN ENST00000309931.2 1 HLA-E*01:01 2 None 0 0 41462.379 45967.350 50.000 93.000 NA NA NA NA 0.335 Poor Pending -chr6-47000271-47000272-C-T 156.ADGRF1.ENST00000371253.6.missense.895G/R ADGRF1 G895R 0 RDSSDNIM ENST00000371253.6 1 HLA-E*01:01 1 None 0 0 41491.570 44894.360 50.000 82.000 NA NA NA NA 0.491 Poor Pending -chr11-193734-193735-G-A 223.SCGB1C1.ENST00000342878.2.missense.27D/N SCGB1C1 D27N 0 NEFFMDFL ENST00000342878.2 1 HLA-E*01:01 1 None 0 0 41493.359 42301.610 50.000 56.000 NA NA NA NA 0.232 Poor Pending -chr16-87755257-87755258-G-A 310.KLHDC4.ENST00000270583.9.missense.102T/I KLHDC4 T102I 0 IRKDTWTK ENST00000270583.9 1 HLA-E*01:01 1 None 0 0 41526.578 42820.590 50.000 61.000 NA NA NA NA 0.486 Poor Pending -chr2-53901384-53901385-G-C 36.PSME4.ENST00000404125.5.missense.1084H/D PSME4 H1084D 0 IDRQYETI ENST00000404125.5 1 HLA-E*01:01 2 None 0 0 41530.199 40617.840 50.000 44.000 NA NA NA NA 0.364 Poor Pending -chr17-78484882-78484883-A-T 323.DNAH17.ENST00000389840.6.missense.2545M/K DNAH17 M2545K 0 RQHKDHRH ENST00000389840.6 5 HLA-E*01:01 4 None 0 0 41625.551 43069.160 51.000 63.000 NA NA NA NA 0.229 Poor Pending -chrX-9937278-9937279-G-C 371.SHROOM2.ENST00000380913.7.missense.1245D/H SHROOM2 D1245H 0 EKHQIKTL ENST00000380913.7 1 HLA-E*01:01 3 None 0 0 41632.770 42070.630 51.000 54.000 NA NA NA NA 1.000 Poor Pending -chr5-1331835-1331836-C-A 81.CLPTM1L.ENST00000320895.9.missense.313K/N CLPTM1L K313N 0 WNKKKSMI ENST00000320895.9 1 HLA-E*01:01 2 None 0 0 41636.371 40311.820 51.000 42.000 NA NA NA NA 0.374 Poor Pending -chr4-110559663-110559664-G-C 77.ENPEP.ENST00000265162.9.missense.887R/T ENPEP R887T 0 YTLNNTNL ENST00000265162.9 1 HLA-E*01:01 6 None 0 0 41772.641 43359.530 52.000 66.000 NA NA NA NA 0.238 Poor Pending -chr6-55351464-55351465-G-C 163.GFRAL.ENST00000340465.2.missense.195D/H GFRAL D195H 0 AQSHIPCQ ENST00000340465.2 1 HLA-E*01:01 4 None 0 0 41795.250 41059.700 52.000 47.000 NA NA NA NA 0.506 Poor Pending -chr3-130409352-130409353-G-T 65.COL6A5.ENST00000265379.10.missense.1503G/W COL6A5 G1503W 0 RGAPWQYG ENST00000265379.10 5 HLA-E*01:01 5 None 0 0 41799.320 41532.880 52.000 50.000 NA NA NA NA 0.328 Poor Pending -chr2-31366060-31366061-G-C 34.XDH.ENST00000379416.3.missense.791R/G XDH R791G 0 IVVGVKRM ENST00000379416.3 1 HLA-E*01:01 4 None 0 0 41816.961 37928.280 52.000 30.000 NA NA NA NA 1.000 Poor Pending -chrX-38408966-38408967-A-G 382.OTC.ENST00000039007.4.missense.270Q/R OTC Q270R 0 SMGREEEK ENST00000039007.4 1 HLA-E*01:01 4 None 0 0 41831.441 43507.090 52.000 67.000 NA NA NA NA 1.000 Poor Pending -chr6-55331788-55331789-C-T 162.GFRAL.ENST00000340465.2.missense.33R/C GFRAL R33C 0 YLREQCLC ENST00000340465.2 1 HLA-E*01:01 8 None 0 0 41995.602 42393.240 54.000 57.000 NA NA NA NA 0.500 Poor Pending -chr6-32293729-32293730-T-C 130.TSBP1.ENST00000447241.6.missense.315I/V TSBP1 I315V 0 ISEMSVPQ ENST00000447241.6 5 HLA-E*01:01 6 None 0 0 42103.879 42314.870 55.000 56.000 NA NA NA NA 0.647 Poor Pending -chr5-23521053-23521054-C-G 84.PRDM9.ENST00000296682.3.missense.128S/C PRDM9 S128C 0 SFSNECSL ENST00000296682.3 1 HLA-E*01:01 6 None 0 0 42106.621 42132.590 55.000 55.000 NA NA NA NA 0.421 Poor Pending -chr19-6044262-6044263-G-C 333.RFX2.ENST00000303657.9.missense.37A/G RFX2 A37G 0 VQAGSSNP ENST00000303657.9 1 HLA-E*01:01 4 None 0 0 42138.980 39646.960 55.000 38.000 NA NA NA NA 0.988 Poor Pending -chr20-2312957-2312958-C-T 347.TGM3.ENST00000381458.5.missense.201R/C TGM3 R201C 0 RCDAATDV ENST00000381458.5 1 HLA-E*01:01 2 None 0 0 42247.629 42156.320 56.000 55.000 NA NA NA NA 0.652 Poor Pending -chr22-26540809-26540810-G-T 356.TPST2.ENST00000338754.8.missense.274P/H TPST2 P274H 0 GKHGGVSL ENST00000338754.8 1 HLA-E*01:01 3 None 0 0 42291.980 34681.130 56.000 20.000 NA NA NA NA 0.209 Poor Pending -chr16-48231865-48231866-C-T 287.ABCC11.ENST00000394747.5.missense.19R/H ABCC11 R19H 0 LVNHGIDI ENST00000394747.5 1 HLA-E*01:01 4 None 0 0 42307.090 38411.460 56.000 32.000 NA NA NA NA 0.739 Poor Pending -chr6-46140014-46140015-C-G 152.ENPP4.ENST00000321037.4.missense.144H/Q ENPP4 H144Q 0 VPIQDTIS ENST00000321037.4 1 HLA-E*01:01 4 None 0 0 42327.699 42508.990 56.000 58.000 NA NA NA NA 0.729 Poor Pending -chr14-60724007-60724008-C-G 264.SIX4.ENST00000216513.4.missense.23E/Q SIX4 E23Q 0 MQSASEGQ ENST00000216513.4 1 HLA-E*01:01 2 None 0 0 42340.531 42897.100 56.000 61.000 NA NA NA NA 1.000 Poor Pending -chrX-79171490-79171491-T-C 393.GPR174.ENST00000645147.1.missense.162S/P GPR174 S162P 0 TPGNRTKC ENST00000645147.1 NA HLA-E*01:01 2 None 0 0 42355.629 43843.540 57.000 70.000 NA NA NA NA 1.000 Poor Pending -chr11-20638483-20638484-T-A 228.SLC6A5.ENST00000525748.5.missense.632V/E SLC6A5 V632E 0 QLEDTYAA ENST00000525748.5 1 HLA-E*01:01 3 None 0 0 42393.699 42501.180 57.000 58.000 NA NA NA NA 0.468 Poor Pending -chr20-10054508-10054509-G-C 349.ANKEF1.ENST00000378380.4.missense.694K/N ANKEF1 K694N 0 VPTTSEGN ENST00000378380.4 2 HLA-E*01:01 8 None 0 0 42624.121 41710.330 59.000 51.000 NA NA NA NA 0.532 Poor Pending -chr7-82908982-82908983-C-G 175.PCLO.ENST00000333891.13.missense.4444W/S PCLO W4444S 0 REETDSFD ENST00000333891.13 2 HLA-E*01:01 6 None 0 0 42628.270 41961.540 59.000 53.000 NA NA NA NA 0.411 Poor Pending -chr11-46728135-46728136-T-C 229.F2.ENST00000311907.9.missense.424V/A F2 V424A 0 LLARIGKH ENST00000311907.9 1 HLA-E*01:01 3 None 0 0 42660.590 44251.510 59.000 75.000 NA NA NA NA 0.358 Poor Pending -chr6-42938645-42938646-G-T 144.CNPY3.ENST00000372836.4.missense.231S/I CNPY3 S231I 0 IRAKAAGG ENST00000372836.4 1 HLA-E*01:01 1 None 0 0 42668.891 44538.270 59.000 78.000 NA NA NA NA 0.700 Poor Pending -chr6-36301947-36301948-A-G 137.PNPLA1.ENST00000394571.3.missense.288E/G PNPLA1 E288G 0 GCPERSQP ENST00000394571.3 1 HLA-E*01:01 1 None 0 0 42716.000 41259.660 60.000 48.000 NA NA NA NA 0.620 Poor Pending -chr7-151181249-151181250-C-T 189.ASB10.ENST00000420175.2.missense.265D/N ASB10 D265N 0 ITNAEATT ENST00000420175.2 1 HLA-E*01:01 3 None 0 0 42772.898 41994.700 60.000 54.000 NA NA NA NA 0.157 Poor Pending -chr16-74661180-74661181-G-T 304.RFWD3.ENST00000361070.8.missense.90T/N RFWD3 T90N 0 VLGEDNVE ENST00000361070.8 1 HLA-E*01:01 6 None 0 0 42779.359 40537.950 60.000 43.000 NA NA NA NA 0.650 Poor Pending -chrX-149548665-149548666-C-T 408.HSFX3.ENST00000431993.3.missense.243R/H HSFX3 R243H 0 SFRHSGMW ENST00000431993.3 3 HLA-E*01:01 4 None 0 0 42790.469 40876.180 60.000 46.000 NA NA NA NA 1.000 Poor Pending -chrX-154349376-154349377-C-G 411.FLNA.ENST00000369850.8.missense.2581D/H FLNA D2581H 0 QKSSFTVH ENST00000369850.8 1 HLA-E*01:01 8 None 0 0 43084.551 44142.940 63.000 74.000 NA NA NA NA 0.992 Poor Pending -chrX-101277632-101277633-T-C 398.TAF7L.ENST00000372907.7.missense.308S/G TAF7L S308G 0 LISSGMSG ENST00000372907.7 1 HLA-E*01:01 8 None 0 0 43159.660 43143.800 64.000 64.000 NA NA NA NA 1.000 Poor Pending -chr9-113369791-113369792-G-A 206.BSPRY.ENST00000374183.4.missense.287A/T BSPRY A287T 0 NGLHTWMV ENST00000374183.4 1 HLA-E*01:01 5 None 0 0 43286.891 42473.120 65.000 58.000 NA NA NA NA 0.541 Poor Pending -chr22-46257698-46257699-G-A 361.PKDREJ.ENST00000253255.6.missense.1875T/I PKDREJ T1875I 0 IYGSGGYA ENST00000253255.6 NA HLA-E*01:01 1 None 0 0 43359.531 44278.320 66.000 75.000 NA NA NA NA 0.266 Poor Pending -chr2-47806319-47806320-G-A 35.MSH6.ENST00000234420.9.missense.1255D/N MSH6 D1255N 0 VENYSQNV ENST00000234420.9 1 HLA-E*01:01 3 None 0 0 43380.172 42867.870 66.000 61.000 NA NA NA NA 0.330 Poor Pending -chr3-56617278-56617279-G-C 61.CCDC66.ENST00000394672.7.missense.671E/Q CCDC66 E671Q 0 QDKGASLQ ENST00000394672.7 1 HLA-E*01:01 8 None 0 0 43519.801 43893.390 67.000 71.000 NA NA NA NA 1.000 Poor Pending -chrX-26194359-26194360-G-C 378.MAGEB6.ENST00000379034.1.missense.172G/R MAGEB6 G172R 0 VAAEREDE ENST00000379034.1 1 HLA-E*01:01 5 None 0 0 43573.969 43128.860 68.000 63.000 NA NA NA NA 1.000 Poor Pending -chr6-43567280-43567281-C-T 148.XPO5.ENST00000265351.11.missense.241S/N XPO5 S241N 0 SMNHITAE ENST00000265351.11 1 HLA-E*01:01 3 None 0 0 43638.148 42690.120 68.000 59.000 NA NA NA NA 0.787 Poor Pending -chrX-71378281-71378287-GAGATAT-G 389.TAF1.ENST00000423759.5.inframe_del.347-349GDI/G TAF1 GDI347-349G 0 SQSTGDKV ENST00000423759.5 5 HLA-E*01:01 6-7 None 0 0 43641.469 44716.910 68.000 80.000 NA NA NA NA 1.000 Poor Pending -chr6-13611845-13611846-A-G 101.SIRT5.ENST00000606117.1.missense.305E/G SIRT5 E305G 0 ALACHGNE ENST00000606117.1 1 HLA-E*01:01 6 None 0 0 44074.211 44236.190 73.000 75.000 NA NA NA NA 0.983 Poor Pending -chr17-45119014-45119029-TAGACGGTCGTTGTTG-T 322.PLCD3.ENST00000619929.4.inframe_del.233-238SNNDRL/S PLCD3 SNNDRL233-238S 0 DHSEGAEI ENST00000619929.4 1 HLA-E*01:01 3-4 None 0 0 44102.852 44708.210 73.000 80.000 NA NA NA NA 1.000 Poor Pending -chr16-58045222-58045223-A-G 295.MMP15.ENST00000219271.3.missense.596D/G MMP15 D596G 0 VGGGDGDF ENST00000219271.3 1 HLA-E*01:01 3 None 0 0 44138.641 43807.050 74.000 70.000 NA NA NA NA 0.479 Poor Pending -chr6-38805516-38805517-G-A 140.DNAH8.ENST00000327475.10.missense.1024G/E DNAH8 G1024E 0 VVFGSETE ENST00000327475.10 5 HLA-E*01:01 8 None 0 0 44286.941 44829.790 75.000 81.000 NA NA NA NA 0.649 Poor Pending -chr19-6755017-6755018-T-C 334.SH2D3A.ENST00000245908.10.missense.265E/G SH2D3A E265G 0 GEENRCFT ENST00000245908.10 1 HLA-E*01:01 1 None 0 0 44345.441 43094.330 76.000 63.000 NA NA NA NA 0.984 Poor Pending -chrX-151181398-151181399-A-G 409.GPR50.ENST00000218316.3.missense.606I/V GPR50 I606V 0 VDVEDDPD ENST00000218316.3 1 HLA-E*01:01 1 None 0 0 44390.078 44692.750 76.000 80.000 NA NA NA NA 1.000 Poor Pending -chr1-203347717-203347718-G-C 26.FMOD.ENST00000354955.4.missense.185H/D FMOD H185D 0 LHLDDNQI ENST00000354955.4 1 HLA-E*01:01 5 None 0 0 44542.121 44624.610 78.000 79.000 NA NA NA NA 0.298 Poor Pending -chrX-17726698-17726699-G-A 376.NHS.ENST00000380060.7.missense.844A/T NHS A844T 0 KSDGNTDI ENST00000380060.7 1 HLA-E*01:01 6 None 0 0 44746.461 44075.660 80.000 73.000 NA NA NA NA 1.000 Poor Pending -chr6-49492264-49492265-A-G 157.CENPQ.ENST00000335783.3.missense.266D/G CENPQ D266G 0 EEAYKKLG ENST00000335783.3 1 HLA-E*01:01 8 None 0 0 44753.699 44669.040 80.000 79.000 NA NA NA NA 0.421 Poor Pending -chrX-68717715-68717716-G-A 388.STARD8.ENST00000374599.7.missense.268G/S STARD8 G268S 0 ATSASGSG ENST00000374599.7 1 HLA-E*01:01 5 None 0 0 44858.422 45597.340 81.000 89.000 NA NA NA NA 1.000 Poor Pending -chr15-43149136-43149137-G-C 273.TMEM62.ENST00000260403.6.missense.284W/C TMEM62 W284C 0 CKDNRRYR ENST00000260403.6 1 HLA-E*01:01 1 None 0 0 44900.680 45342.980 82.000 87.000 NA NA NA NA 0.961 Poor Pending -chr6-70190343-70190344-G-C 167.COL19A1.ENST00000620364.4.missense.1019K/N COL19A1 K1019N 0 FEEINKYI ENST00000620364.4 1 HLA-E*01:01 5 None 0 0 45054.930 44223.270 84.000 74.000 NA NA NA NA 0.246 Poor Pending -chr2-61348284-61348285-C-G 37.USP34.ENST00000398571.6.missense.624D/H USP34 D624H 0 IEALKEEH ENST00000398571.6 5 HLA-E*01:01 8 None 0 0 45225.879 45620.520 85.000 90.000 NA NA NA NA 0.280 Poor Pending -chr1-227091906-227091907-GC-G 29.CDC42BPA.ENST00000366769.7.FS.778GC/G CDC42BPA FS778 0 LLTEENKN ENST00000366769.7 1 HLA-E*01:01 8 None 0 0 45350.352 44737.740 87.000 80.000 NA NA NA NA 0.273 Poor Pending -chr6-31117165-31117168-GCTT-G 122.CDSN.ENST00000376288.2.inframe_del.149-150GS/G CDSN GS149-150G 0 SHSGSSSH ENST00000376288.2 1 HLA-E*01:01 7-8 None 0 0 45665.461 46080.410 90.000 94.000 NA NA NA NA 0.693 Poor Pending -chr21-30755335-30755336-C-T 355.KRTAP21-1.ENST00000335093.4.missense.15G/S KRTAP21-1 G15S 0 SSCGCGYG ENST00000335093.4 NA HLA-E*01:01 2 None 0 0 45714.410 46070.930 91.000 94.000 NA NA NA NA 0.472 Poor Pending -chr11-6410863-6410864-C-T 227.APBB1.ENST00000609360.5.missense.162E/K APBB1 E162K 0 GEAEEEEK ENST00000609360.5 5 HLA-E*01:01 8 None 0 0 46646.738 46668.980 99.000 99.000 NA NA NA NA 1.000 Poor Pending +chr14-55180753-55180754-G-A 263.DLGAP5.ENST00000247191.6.missense.202S/L 1 DLGAP5 S202L 1 VMPTLLRM ENST00000247191.6 1 HLA-E*01:01 5 None 1 0 5857.400 2658.680 0.120 0.030 NA NA NA NA 0.239 Poor Pending +chr14-91235009-91235029-GGTACAGCTCATCGAGGAGTT-G 266.GPR68.ENST00000531499.2.FS.8-14GGTACAGCTCATCGAGGAGTT/G 1 GPR68 FS8-14 1 LPGCGPSL ENST00000531499.2 1 HLA-E*01:01 1-8 None 1 0 7028.130 NA 0.170 NA NA NA NA NA 0.127 Poor Pending +chr19-14049194-14049195-C-T 339.IL27RA.ENST00000263379.3.missense.428A/V 1 IL27RA A428V 1 VPPGTPAI ENST00000263379.3 1 HLA-E*01:01 1 None 1 0 7518.130 13004.510 0.200 0.750 NA NA NA NA 0.301 Poor Pending +chr1-45058674-45058675-G-A 12.ZSWIM5.ENST00000359600.5.missense.396L/F 1 ZSWIM5 L396F 1 VADPRFTL ENST00000359600.5 1 HLA-E*01:01 6 None 1 0 7602.960 11507.390 0.210 0.550 NA NA NA NA 0.360 Poor Pending +chr4-108650681-108650682-C-G 76.OSTC.ENST00000512478.2.missense.9F/L 1 OSTC F9L 1 TLYRVPLL ENST00000512478.2 5 HLA-E*01:01 7 None 1 0 8394.910 11601.650 0.270 0.560 NA NA NA NA 0.465 Poor Pending +chr6-27312072-27312073-T-C 111.POM121L2.ENST00000444565.1.missense.33Q/R 1 POM121L2 Q33R 1 RRPPRPLH ENST00000444565.1 NA HLA-E*01:01 5 None 1 0 9499.730 15005.710 0.340 1.200 NA NA NA NA 0.669 Poor Pending +chr13-25541936-25541937-G-C 250.ATP8A2.ENST00000381655.6.missense.224D/H 1 ATP8A2 D224H 1 LMQTREVL ENST00000381655.6 1 HLA-E*01:01 1 None 1 0 9985.260 18778.930 0.380 2.300 NA NA NA NA 0.317 Poor Pending +chr13-25541937-25541938-A-T 251.ATP8A2.ENST00000381655.6.missense.224D/V 1 ATP8A2 D224V 1 LMQTREVL ENST00000381655.6 1 HLA-E*01:01 1 None 1 0 9985.260 18778.930 0.380 2.300 NA NA NA NA 0.317 Poor Pending +chr2-222689427-222689428-G-T 52.MOGAT1.ENST00000446656.3.missense.146W/L 1 MOGAT1 W146L 1 LLFWCPVF ENST00000446656.3 5 HLA-E*01:01 2 None 1 0 10003.530 19835.920 0.380 2.600 NA NA NA NA 0.343 Poor Pending +chr17-7588499-7588500-G-C 316.SOX15.ENST00000250055.2.missense.194Q/E 1 SOX15 Q194E 1 LPESDPRL ENST00000250055.2 1 HLA-E*01:01 3 None 1 0 10054.100 8090.820 0.390 0.250 NA NA NA NA 0.712 Poor Pending +chr4-40808808-40808809-A-G 72.NSUN7.ENST00000381782.6.missense.676Y/C 1 NSUN7 Y676C 1 RMPTQHLC ENST00000381782.6 1 HLA-E*01:01 8 None 1 0 11124.570 8084.780 0.520 0.250 NA NA NA NA 0.466 Poor Pending +chr1-43432295-43432296-G-C 11.SZT2.ENST00000562955.2.missense.1710G/R 1 SZT2 G1710R 1 HLPRHVLL ENST00000562955.2 5 HLA-E*01:01 4 None 1 0 11567.430 17027.460 0.560 1.700 NA NA NA NA 0.309 Poor Pending +chr11-63290369-63290370-G-A 235.SLC22A10.ENST00000332793.10.missense.69E/K 1 SLC22A10 E69K 1 ILSKDALL ENST00000332793.10 1 HLA-E*01:01 4 None 1 0 12068.340 15757.820 0.600 1.400 NA NA NA NA 0.544 Poor Pending +chr15-62819536-62819537-G-A 277.TLN2.ENST00000561311.5.missense.2265E/K 1 TLN2 E2265K 1 LQKPTPKF ENST00000561311.5 5 HLA-E*01:01 7 None 1 0 12103.650 14467.010 0.610 1.000 NA NA NA NA 0.458 Poor Pending +chr3-184239802-184239803-C-T 69.VWA5B2.ENST00000426955.6.missense.836A/V 1 VWA5B2 A836V 1 VPPQVPRC ENST00000426955.6 1 HLA-E*01:01 5 None 1 0 12634.200 6168.640 0.700 0.140 NA NA NA NA 0.430 Poor Pending +chr6-33315988-33315989-T-C 135.ZBTB22.ENST00000431845.2.missense.310T/A 1 ZBTB22 T310A 1 NCPAPAPL ENST00000431845.2 1 HLA-E*01:01 6 None 1 0 12664.580 15601.230 0.700 1.400 NA NA NA NA 0.734 Poor Pending +chr5-145817966-145817967-A-G 91.PRELID2.ENST00000334744.8.missense.111C/R 1 PRELID2 C111R 1 MAIRSHRL ENST00000334744.8 2 HLA-E*01:01 7 None 1 0 12791.130 13626.930 0.720 0.810 NA NA NA NA 0.330 Poor Pending +chr11-64593669-64593670-G-C 238.SLC22A12.ENST00000377574.5.missense.233V/L 1 SLC22A12 V233L 1 AARARPLL ENST00000377574.5 1 HLA-E*01:01 8 None 1 0 12864.840 27811.220 0.730 7.300 NA NA NA NA 0.161 Poor Pending +chrX-3027435-3027436-C-T 369.ARSH.ENST00000381130.2.missense.387T/M 1 ARSH T387M 1 LMDIYPML ENST00000381130.2 1 HLA-E*01:01 7 None 1 0 13539.050 17374.370 0.800 1.800 NA NA NA NA 0.494 Poor Pending +chr7-47833094-47833095-G-A 173.PKD1L1.ENST00000289672.6.missense.2111T/I 1 PKD1L1 T2111I 1 IQAPSSGL ENST00000289672.6 1 HLA-E*01:01 1 None 1 0 13758.790 17418.780 0.850 1.800 NA NA NA NA 0.301 Poor Pending +chr6-31636813-31636814-C-T 126.PRRC2A.ENST00000376033.2.missense.2006P/S 1 PRRC2A P2006S 1 PPPAPPSL ENST00000376033.2 1 HLA-E*01:01 7 None 1 0 13771.150 13218.430 0.850 0.770 NA NA NA NA 0.682 Poor Pending +chr8-125436370-125436371-C-T 198.TRIB1.ENST00000311922.3.missense.340S/F 1 TRIB1 S340F 1 HPWFEFVL ENST00000311922.3 1 HLA-E*01:01 6 None 1 0 14102.880 31337.800 0.920 13.000 NA NA NA NA 0.136 Poor Pending +chr16-81268088-81268089-A-T 305.BCO1.ENST00000258168.6.missense.267R/S 1 BCO1 R267S 1 SMSWASCL ENST00000258168.6 1 HLA-E*01:01 1 None 1 0 14379.620 8166.810 0.980 0.260 NA NA NA NA 0.484 Poor Pending +chr9-4286160-4286161-G-T 202.GLIS3.ENST00000381971.7.missense.89Q/K 1 GLIS3 Q89K 1 LSPRRKML ENST00000381971.7 5 HLA-E*01:01 6 None 1 0 14545.490 13435.150 1.000 0.790 NA NA NA NA 0.152 Poor Pending +chr9-81992222-81992223-C-G 205.SPATA31D1.ENST00000344803.2.missense.585Q/E 1 SPATA31D1 Q585E 1 ESPFRALL ENST00000344803.2 2 HLA-E*01:01 1 None 1 0 14823.360 11381.450 1.200 0.540 NA NA NA NA 0.699 Poor Pending +chr8-132948805-132948806-C-G 200.TG.ENST00000220616.8.missense.1755P/R 1 TG P1755R 1 LLSSRSVL ENST00000220616.8 1 HLA-E*01:01 5 None 1 0 15188.490 25844.630 1.300 5.700 NA NA NA NA 0.994 Poor Pending +chr16-87417563-87417564-G-C 308.ZCCHC14.ENST00000268616.8.missense.290L/V 1 ZCCHC14 L290V 1 LMPSSVQT ENST00000268616.8 1 HLA-E*01:01 6 None 1 0 15487.540 10813.630 1.300 0.490 NA NA NA NA 0.297 Poor Pending +chr5-115130597-115130604-ACTAACTG-A 85.TRIM36.ENST00000282369.7.FS.607-609ACTAACTG/A 1 TRIM36 FS607-609 1 VRMPVLIL ENST00000282369.7 1 HLA-E*01:01 1-8 None 1 0 15517.220 NA 1.300 NA NA NA NA NA 1.000 Poor Pending +chr16-57915319-57915320-G-T 294.CNGB1.ENST00000251102.12.missense.745L/I 1 CNGB1 L745I 1 ILPLDFLY ENST00000251102.12 1 HLA-E*01:01 1 None 1 0 15571.710 18325.300 1.300 2.100 NA NA NA NA 0.639 Poor Pending +chr3-38698510-38698511-G-A 56.SCN10A.ENST00000449082.3.missense.1570T/M 1 SCN10A T1570M 1 MLFRVIRL ENST00000449082.3 1 HLA-E*01:01 1 None 1 0 15876.410 22247.940 1.400 3.600 NA NA NA NA 0.290 Poor Pending +chr3-52395054-52395055-C-T 59.DNAH1.ENST00000420323.6.missense.3655P/L 1 DNAH1 P3655L 1 LEPRFIEL ENST00000420323.6 1 HLA-E*01:01 8 None 1 0 16004.560 38708.930 1.400 34.000 NA NA NA NA 0.273 Poor Pending +chr6-29112672-29112673-G-A 113.OR2J3.ENST00000641960.1.missense.261M/I 1 OR2J3 M261I 1 IPAMCIYL ENST00000641960.1 NA HLA-E*01:01 6 None 1 0 16263.610 14399.080 1.500 0.990 NA NA NA NA 0.657 Poor Pending +chrX-101235943-101235944-G-C 397.DRP2.ENST00000395209.7.missense.68V/L 1 DRP2 V68L 1 SLGASGPL ENST00000395209.7 1 HLA-E*01:01 2 None 1 0 16655.920 24114.770 1.600 4.500 NA NA NA NA 1.000 Poor Pending +chrX-3713125-3713126-A-G 370.PRKX.ENST00000262848.5.missense.43V/A 1 PRKX V43A 1 PEPPAYSL ENST00000262848.5 1 HLA-E*01:01 5 None 1 0 16811.080 24683.630 1.600 4.900 NA NA NA NA 1.000 Poor Pending +chr2-102015965-102015966-C-T 41.IL1R2.ENST00000332549.7.missense.143T/I 1 IL1R2 T143I 1 ILSTSGVL ENST00000332549.7 1 HLA-E*01:01 1 None 1 0 16993.600 20737.240 1.700 2.900 NA NA NA NA 0.196 Poor Pending +chr6-4068931-4068932-C-T 97.FAM217A.ENST00000274673.7.missense.431V/I 1 FAM217A V431I 1 KMISTRCL ENST00000274673.7 1 HLA-E*01:01 3 None 1 0 17088.189 16982.940 1.700 1.700 NA NA NA NA 0.463 Poor Pending +chrX-107601385-107601386-G-T 400.FRMPD3.ENST00000276185.8.missense.1149S/I 1 FRMPD3 S1149I 1 STPKRIKL ENST00000276185.8 5 HLA-E*01:01 6 None 1 0 17641.830 19563.110 1.900 2.500 NA NA NA NA 0.404 Poor Pending +chr12-80495233-80495234-C-A 247.PTPRQ.ENST00000614701.5.missense.582S/Y 1 PTPRQ S582Y 1 ISYSSILL ENST00000614701.5 5 HLA-E*01:01 3 None 1 0 17645.461 17405.410 1.900 1.800 NA NA NA NA 0.984 Poor Pending +chr8-22566400-22566401-G-C 192.SORBS3.ENST00000240123.11.missense.336R/P 1 SORBS3 R336P 1 YLGSAPSL ENST00000240123.11 1 HLA-E*01:01 6 None 1 0 17850.350 32012.930 1.900 14.000 NA NA NA NA 0.436 Poor Pending +chr1-120160392-120160393-C-T 18.SEC22B.ENST00000578049.3.missense.162A/T 1 SEC22B A162T 1 VLQRGETL ENST00000578049.3 1 HLA-E*01:01 7 None 1 0 17886.510 20986.210 2.000 3.000 NA NA NA NA 0.403 Poor Pending +chr6-42592187-42592188-G-A 142.UBR2.ENST00000372899.5.missense.126E/K 1 UBR2 E126K 1 VLCMKCFL ENST00000372899.5 1 HLA-E*01:01 5 None 1 0 18422.510 22958.820 2.100 3.900 NA NA NA NA 0.625 Poor Pending +chr6-16306519-16306520-G-A 103.ATXN1.ENST00000244769.8.missense.753P/S 1 ATXN1 P753S 1 GLSAAPFL ENST00000244769.8 1 HLA-E*01:01 3 None 1 0 18507.830 5841.450 2.200 0.120 NA NA NA NA 0.952 Poor Pending +chr17-11784434-11784435-G-C 319.DNAH9.ENST00000262442.8.missense.2653D/H 1 DNAH9 D2653H 1 SIPPLIHL ENST00000262442.8 1 HLA-E*01:01 7 None 1 0 18983.430 21258.170 2.300 3.100 NA NA NA NA 0.362 Poor Pending +chr6-33801119-33801120-A-G 136.MLN.ENST00000430124.6.missense.15V/A 1 MLN V15A 1 VVHAAAML ENST00000430124.6 1 HLA-E*01:01 4 None 1 0 19243.590 28056.940 2.400 7.600 NA NA NA NA 0.735 Poor Pending +chr15-40622779-40622780-C-T 272.KNL1.ENST00000346991.9.missense.865P/L 1 KNL1 P865L 1 VQKPKFLK ENST00000346991.9 1 HLA-E*01:01 7 None 1 0 19302.801 22026.630 2.400 3.500 NA NA NA NA 0.475 Poor Pending +chr15-40622778-40622779-C-T 271.KNL1.ENST00000346991.9.missense.865P/S 1 KNL1 P865S 1 VQKPKFLK ENST00000346991.9 1 HLA-E*01:01 7 None 1 0 19302.801 22026.630 2.400 3.500 NA NA NA NA 0.475 Poor Pending +chr10-125859825-125859826-G-C 221.DHX32.ENST00000284690.3.missense.209P/R 1 DHX32 P209R 1 VLLARREL ENST00000284690.3 1 HLA-E*01:01 6 None 1 0 19601.881 7349.710 2.500 0.190 NA NA NA NA 1.000 Poor Pending +chr10-115241629-115241630-G-A 219.ATRNL1.ENST00000355044.7.missense.531G/E 1 ATRNL1 G531E 1 VLINEAML ENST00000355044.7 1 HLA-E*01:01 5 None 1 0 19989.971 20984.170 2.700 3.000 NA NA NA NA 0.441 Poor Pending +chr15-50643416-50643417-T-G 276.TRPM7.ENST00000313478.11.missense.153K/T 1 TRPM7 K153T 1 LHPRITQL ENST00000313478.11 1 HLA-E*01:01 6 None 1 0 20026.119 20003.380 2.700 2.700 NA NA NA NA 0.500 Poor Pending +chr2-160107761-160107762-T-A 44.ITGB6.ENST00000283249.6.missense.729I/F 1 ITGB6 I729F 1 VLLCFWKL ENST00000283249.6 1 HLA-E*01:01 5 None 1 0 20240.480 21906.830 2.800 3.400 NA NA NA NA 0.230 Poor Pending +chr1-168179177-168179178-A-T 22.TIPRL.ENST00000367833.6.missense.34E/V 1 TIPRL E34V 1 IMKSADVV ENST00000367833.6 1 HLA-E*01:01 8 None 1 0 20390.820 30433.900 2.800 12.000 NA NA NA NA 0.273 Poor Pending +chr19-8955983-8955984-G-A 335.MUC16.ENST00000397910.8.missense.6929S/F 1 MUC16 S6929F 1 TMGHTTVF ENST00000397910.8 5 HLA-E*01:01 8 None 1 0 20594.141 37488.050 2.900 28.000 NA NA NA NA 0.479 Poor Pending +chr22-37631020-37631021-C-G 359.GGA1.ENST00000343632.8.missense.484P/A 1 GGA1 P484A 1 ARPPQQPV ENST00000343632.8 1 HLA-E*01:01 1 None 1 0 21060.600 28549.960 3.000 8.100 NA NA NA NA 0.455 Poor Pending +chrX-40655057-40655058-G-T 383.MED14.ENST00000324817.5.missense.1325F/L 1 MED14 F1325L 1 LPDQATQL ENST00000324817.5 1 HLA-E*01:01 1 None 1 0 21278.881 29909.640 3.100 9.700 NA NA NA NA 1.000 Poor Pending +chr5-14507134-14507135-C-T 83.TRIO.ENST00000344204.8.missense.2876R/C 1 TRIO R2876C 1 MADQGCLL ENST00000344204.8 1 HLA-E*01:01 6 None 1 0 21522.461 19763.520 3.200 2.600 NA NA NA NA 0.254 Poor Pending +chr19-51136070-51136071-A-T 346.SIGLEC9.ENST00000440804.7.missense.438H/L 1 SIGLEC9 H438L 1 YLFSHFRL ENST00000440804.7 2 HLA-E*01:01 2 None 1 0 21590.109 29276.650 3.300 8.900 NA NA NA NA 0.110 Poor Pending +chr13-113425167-113425168-G-T 255.ADPRHL1.ENST00000375418.7.missense.220H/N 1 ADPRHL1 H220N 1 YQENWFYF ENST00000375418.7 1 HLA-E*01:01 4 None 1 0 21600.391 25523.940 3.300 5.500 NA NA NA NA 0.527 Poor Pending +chr9-133354714-133354715-G-C 210.SURF1.ENST00000371974.7.missense.89N/K 1 SURF1 N89K 1 RRKWKLKL ENST00000371974.7 1 HLA-E*01:01 7 None 1 0 21972.830 26468.360 3.500 6.200 NA NA NA NA 0.706 Poor Pending +chr3-33053544-33053545-G-T 55.GLB1.ENST00000307363.9.missense.246S/R 1 GLB1 S246R 1 RNITDAFL ENST00000307363.9 1 HLA-E*01:01 1 None 1 0 22152.330 30372.390 3.600 12.000 NA NA NA NA 0.335 Poor Pending +chr8-23368189-23368210-TGGCCACGTTGGCGGGGGCCTG-T 193.LOXL2.ENST00000389131.7.inframe_del.48-54QAPANVA/- 1 LOXL2 QAPANVA48-54- 1 QPKIQLRL ENST00000389131.7 1 HLA-E*01:01 2-3 None 1 0 22410.039 29604.110 3.700 9.300 NA NA NA NA 0.992 Poor Pending +chr16-25246937-25246938-C-T 286.ZKSCAN2.ENST00000328086.11.missense.420E/K 1 ZKSCAN2 E420K 1 LEPCAFFK ENST00000328086.11 1 HLA-E*01:01 8 None 1 0 23166.680 22030.680 4.000 3.500 NA NA NA NA 0.471 Poor Pending +chr2-190982493-190982494-G-C 46.STAT1.ENST00000361099.7.missense.491P/A 1 STAT1 P491A 1 LTPACARW ENST00000361099.7 1 HLA-E*01:01 4 None 1 0 23220.881 15735.500 4.000 1.400 NA NA NA NA 0.583 Poor Pending +chr11-862686-862687-C-G 224.TSPAN4.ENST00000397404.5.missense.67I/M 1 TSPAN4 I67M 1 VMAMGFVG ENST00000397404.5 5 HLA-E*01:01 4 None 1 0 23293.100 25066.890 4.100 5.100 NA NA NA NA 1.000 Poor Pending +chr10-132163376-132163377-C-G 222.JAKMIP3.ENST00000298622.8.missense.795R/G 1 JAKMIP3 R795G 1 ILGERMEL ENST00000298622.8 5 HLA-E*01:01 3 None 1 0 23368.830 20365.250 4.100 2.800 NA NA NA NA 0.467 Poor Pending +chr6-109451607-109451608-G-T 168.MICAL1.ENST00000630715.2.missense.328L/M 1 MICAL1 L328M 1 VMRQDWPD ENST00000630715.2 2 HLA-E*01:01 2 None 1 0 23437.971 34203.750 4.100 19.000 NA NA NA NA 0.980 Poor Pending +chr1-204125889-204125890-C-T 27.SOX13.ENST00000367204.5.missense.542S/L 1 SOX13 S542L 1 QMSSLDVL ENST00000367204.5 1 HLA-E*01:01 5 None 1 0 23594.189 14811.500 4.200 1.200 NA NA NA NA 0.328 Poor Pending +chr6-46168246-46168247-G-T 154.ENPP5.ENST00000371383.6.missense.6L/I 1 ENPP5 L6I 1 MTSKFILV ENST00000371383.6 1 HLA-E*01:01 6 None 1 0 23693.961 20937.900 4.300 3.000 NA NA NA NA 0.750 Poor Pending +chr6-24828261-24828262-C-T 109.RIPOR2.ENST00000644685.1.missense.868R/Q 1 RIPOR2 R868Q 1 LDQAEPLL ENST00000644685.1 NA HLA-E*01:01 3 None 1 0 23900.211 22239.510 4.400 3.600 NA NA NA NA 0.639 Poor Pending +chrX-130013396-130013397-G-A 402.BCORL1.ENST00000540052.5.missense.209G/S 1 BCORL1 G209S 1 ICPPAPSS ENST00000540052.5 1 HLA-E*01:01 7 None 1 0 23967.270 24918.700 4.500 5.000 NA NA NA NA 1.000 Poor Pending +chr4-154491218-154491219-G-C 80.DCHS2.ENST00000339452.2.missense.46S/C 1 DCHS2 S46C 1 TQRCLLWL ENST00000339452.2 1 HLA-E*01:01 4 None 1 0 23973.240 23372.370 4.500 4.100 NA NA NA NA 0.968 Poor Pending +chrX-102463004-102463005-G-A 399.TCP11X2.ENST00000453326.2.missense.223R/W 1 TCP11X2 R223W 1 LLMDRIWL ENST00000453326.2 2 HLA-E*01:01 7 None 1 0 23985.160 24889.330 4.500 5.000 NA NA NA NA 0.514 Poor Pending +chr1-22576425-22576426-C-A 3.EPHA8.ENST00000166244.7.missense.123N/K 1 EPHA8 N123K 1 TCKETFKL ENST00000166244.7 2 HLA-E*01:01 7 None 1 0 24012.699 27923.990 4.500 7.400 NA NA NA NA 0.270 Poor Pending +chr4-114833618-114833619-A-G 78.NDST4.ENST00000264363.6.missense.795S/P 1 NDST4 S795P 1 NYPEALTF ENST00000264363.6 1 HLA-E*01:01 3 None 1 0 24291.789 35703.800 4.600 23.000 NA NA NA NA 0.197 Poor Pending +chr6-6250886-6250887-T-A 99.F13A1.ENST00000264870.7.missense.205Y/F 1 F13A1 Y205F 1 KEREEFVL ENST00000264870.7 1 HLA-E*01:01 6 None 1 0 24316.770 28767.960 4.600 8.300 NA NA NA NA 0.451 Poor Pending +chr1-16972417-16972418-C-G 2.CROCC.ENST00000375541.9.missense.2009S/C 1 CROCC S2009C 1 CPPSGPPE ENST00000375541.9 5 HLA-E*01:01 1 None 1 0 24326.240 23610.790 4.600 4.200 NA NA NA NA 0.988 Poor Pending +chr20-35384131-35384132-C-G 351.UQCC1.ENST00000374385.9.missense.44W/S 1 UQCC1 W44S 1 RTSQSPQM ENST00000374385.9 1 HLA-E*01:01 5 None 1 0 24459.250 23032.970 4.700 3.900 NA NA NA NA 0.445 Poor Pending +chrX-136230874-136230875-T-G 407.MAP7D3.ENST00000316077.13.missense.502E/A 1 MAP7D3 E502A 1 SPANACGL ENST00000316077.13 1 HLA-E*01:01 3 None 1 0 24585.289 31036.810 4.800 13.000 NA NA NA NA 1.000 Poor Pending +chr6-42923283-42923284-G-A 143.PTCRA.ENST00000616441.2.missense.106V/I 1 PTCRA V106I 1 LASWEPLI ENST00000616441.2 2 HLA-E*01:01 8 None 1 0 25056.859 28339.470 5.100 7.900 NA NA NA NA 0.685 Poor Pending +chr6-36426038-36426039-A-G 138.PXT1.ENST00000454782.2.missense.15V/A 1 PXT1 V15A 1 ALNPSPKV ENST00000454782.2 1 HLA-E*01:01 1 None 1 0 25142.949 18390.260 5.200 2.100 NA NA NA NA 0.685 Poor Pending +chr7-87424004-87424005-A-C 177.ABCB4.ENST00000265723.8.missense.704N/K 1 ABCB4 N704K 1 KKTEWPYF ENST00000265723.8 1 HLA-E*01:01 1 None 1 0 25413.711 32195.650 5.400 15.000 NA NA NA NA 0.189 Poor Pending +chr2-106830076-106830077-G-C 42.ST6GAL2.ENST00000409382.7.missense.436S/C 1 ST6GAL2 S436C 1 IQPNPPSC ENST00000409382.7 1 HLA-E*01:01 8 None 1 0 26054.090 33838.230 5.900 18.000 NA NA NA NA 0.700 Poor Pending +chr1-39429921-39429922-G-C 9.MACF1.ENST00000361689.6.missense.3600E/Q 1 MACF1 E3600Q 1 TLQQARQL ENST00000361689.6 5 HLA-E*01:01 3 None 1 0 26217.820 27609.750 6.000 7.100 NA NA NA NA 0.342 Poor Pending +chr6-44172317-44172317-T-TGGCTGCC 150.CAPN11.ENST00000398776.1.FS.142T/TGGCTGCC 1 CAPN11 FS142 1 LAAGCHRL ENST00000398776.1 1 HLA-E*01:01 4-8 None 1 0 26505.320 NA 6.200 NA NA NA NA NA 0.655 Poor Pending +chr19-8969814-8969831-ACGTGGAATTTCCTTGTG-A 336.MUC16.ENST00000397910.8.FS.3175-3180ACGTGGAATTTCCTTGTG/A 1 MUC16 FS3175-3180 1 VHCEKFSL ENST00000397910.8 5 HLA-E*01:01 1-8 None 1 0 26571.660 NA 6.300 NA NA NA NA NA 1.000 Poor Pending +chr7-112342710-112342711-G-C 183.ZNF277.ENST00000361822.7.missense.445L/F 1 ZNF277 L445F 1 ALKQSSIF ENST00000361822.7 1 HLA-E*01:01 8 None 1 0 26705.109 20485.910 6.400 2.800 NA NA NA NA 0.446 Poor Pending +chrX-78015862-78015863-G-C 392.ATP7A.ENST00000341514.10.missense.870D/H 1 ATP7A D870H 1 SMVHESLI ENST00000341514.10 1 HLA-E*01:01 4 None 1 0 27036.539 31415.540 6.600 13.000 NA NA NA NA 0.979 Poor Pending +chr9-137255473-137255474-G-C 212.NELFB.ENST00000343053.4.missense.37G/R 1 NELFB G37R 1 RAPSRAVA ENST00000343053.4 1 HLA-E*01:01 1 None 1 0 27088.650 37200.370 6.700 27.000 NA NA NA NA 0.600 Poor Pending +chr18-60371739-60371740-T-G 328.MC4R.ENST00000299766.5.missense.204M/L 1 MC4R M204L 1 MFFTLLAL ENST00000299766.5 NA HLA-E*01:01 5 None 1 0 27139.990 24335.460 6.700 4.600 NA NA NA NA 1.000 Poor Pending +chr16-72008782-72008783-A-C 301.DHODH.ENST00000219240.8.missense.7K/Q 1 DHODH K7Q 1 MAWRHLQK ENST00000219240.8 1 HLA-E*01:01 7 None 1 0 27308.490 28009.020 6.800 7.500 NA NA NA NA 0.633 Poor Pending +chr1-243164805-243164806-G-C 32.CEP170.ENST00000366542.5.missense.1052H/D 1 CEP170 H1052D 1 KPDGRTPL ENST00000366542.5 5 HLA-E*01:01 3 None 1 0 27511.939 26446.600 7.000 6.200 NA NA NA NA 0.117 Poor Pending +chr17-41771694-41771736-GTGTACTGGCGCCCGCAGGCCTCATCCTCCTCCATGATGCCCT-G 321.JUP.ENST00000393931.7.inframe_del.40-54KGIMEEDEACGRQYT/T 1 JUP KGIMEEDEACGRQYT40-54T 1 VPSVSSTL ENST00000393931.7 1 HLA-E*01:01 6-7 None 1 0 27543.500 43475.560 7.000 67.000 NA NA NA NA 1.000 Poor Pending +chr22-41524890-41524891-G-C 360.ACO2.ENST00000216254.8.missense.510E/Q 1 ACO2 E510Q 1 FNPQTDYL ENST00000216254.8 1 HLA-E*01:01 4 None 1 0 27748.410 29823.670 7.200 9.600 NA NA NA NA 0.208 Poor Pending +chr1-52961569-52961570-C-A 13.SCP2.ENST00000371514.7.missense.155A/D 1 SCP2 A155D 1 DHPVAPQM ENST00000371514.7 1 HLA-E*01:01 1 None 1 0 27992.350 19991.270 7.500 2.700 NA NA NA NA 0.458 Poor Pending +chr13-45399008-45399009-C-T 253.SLC25A30.ENST00000519676.5.missense.228M/I 1 SLC25A30 M228I 1 IMNQRVLR ENST00000519676.5 1 HLA-E*01:01 1 None 1 0 28018.410 29075.570 7.500 8.700 NA NA NA NA 0.450 Poor Pending +chr6-24174792-24174793-T-A 105.DCDC2.ENST00000378454.7.missense.456K/N 1 DCDC2 K456N 1 RPPRPEVN ENST00000378454.7 1 HLA-E*01:01 8 None 1 0 28077.600 25072.860 7.600 5.100 NA NA NA NA 0.667 Poor Pending +chr2-110933496-110933497-G-A 43.ACOXL.ENST00000439055.5.missense.305G/E 1 ACOXL G305E 1 SRYAEALL ENST00000439055.5 2 HLA-E*01:01 5 None 1 0 28215.551 28817.800 7.700 8.400 NA NA NA NA 1.000 Poor Pending +chr6-33305077-33305078-G-C 134.TAPBP.ENST00000426633.6.missense.260T/R 1 TAPBP T260R 1 WLPRVQPF ENST00000426633.6 1 HLA-E*01:01 4 None 1 0 28317.400 31248.740 7.900 13.000 NA NA NA NA 0.667 Poor Pending +chr6-4995229-4995230-C-T 98.RPP40.ENST00000380051.6.missense.314V/I 1 RPP40 V314I 1 APWVTLSI ENST00000380051.6 5 HLA-E*01:01 8 None 1 0 28393.779 31338.470 8.000 13.000 NA NA NA NA 0.470 Poor Pending +chr16-87305843-87305844-C-T 307.AC010531.1.ENST00000568879.1.missense.210C/Y 1 AC010531.1 C210Y 1 VMSAYCPS ENST00000568879.1 4 HLA-E*01:01 5 None 1 0 28480.859 19846.440 8.000 2.600 NA NA NA NA 0.449 Poor Pending +chrX-12885539-12885540-A-T 373.TLR7.ENST00000380659.3.missense.11Q/L 1 TLR7 Q11L 1 WTLKRLIL ENST00000380659.3 1 HLA-E*01:01 6 None 1 0 28489.490 34481.310 8.000 19.000 NA NA NA NA 1.000 Poor Pending +chr2-669669-669670-C-T 33.TMEM18.ENST00000281017.7.missense.111M/I 1 TMEM18 M111I 1 VIWVWKTL ENST00000281017.7 1 HLA-E*01:01 2 None 1 0 28613.369 12402.320 8.200 0.660 NA NA NA NA 0.250 Poor Pending +chr22-50243800-50243801-T-C 363.TUBGCP6.ENST00000248846.9.missense.220H/R 1 TUBGCP6 H220R 1 VRSRTYDM ENST00000248846.9 1 HLA-E*01:01 2 None 1 0 28615.221 28221.050 8.200 7.700 NA NA NA NA 0.760 Poor Pending +chr11-92982014-92982015-G-T 240.MTNR1B.ENST00000257068.2.missense.264W/C 1 MTNR1B W264C 1 FAICCAPL ENST00000257068.2 1 HLA-E*01:01 5 None 1 0 28668.840 33665.860 8.200 17.000 NA NA NA NA 0.417 Poor Pending +chr6-32166732-32166733-G-A 128.EGFL8.ENST00000395512.5.missense.86R/K 1 EGFL8 R86K 1 VMWREVKR ENST00000395512.5 1 HLA-E*01:01 7 None 1 0 28713.230 27377.720 8.300 6.900 NA NA NA NA 0.672 Poor Pending +chr6-29100981-29100982-C-A 112.OR2J1.ENST00000377171.3.missense.14L/I 1 OR2J1 L14I 1 SFEDFFIL ENST00000377171.3 NA HLA-E*01:01 7 None 1 0 28726.900 28638.460 8.300 8.200 NA NA NA NA 0.661 Poor Pending +chr6-32332044-32332045-G-A 131.TSBP1.ENST00000447241.6.missense.161P/L 1 TSBP1 P161L 1 VQTLGPIV ENST00000447241.6 5 HLA-E*01:01 4 None 1 0 28818.439 11016.290 8.400 0.510 NA NA NA NA 0.722 Poor Pending +chr1-179109009-179109010-T-C 23.ABL2.ENST00000502732.5.missense.753T/A 1 ABL2 T753A 1 TGFFAPRL ENST00000502732.5 1 HLA-E*01:01 5 None 1 0 28837.770 31057.640 8.400 13.000 NA NA NA NA 0.379 Poor Pending +chrX-15355261-15355262-C-T 374.VEGFD.ENST00000297904.3.missense.177E/K 1 VEGFD E177K 1 PLTSVPKL ENST00000297904.3 1 HLA-E*01:01 7 None 1 0 28853.061 30274.300 8.400 12.000 NA NA NA NA 0.985 Poor Pending +chr19-19336157-19336158-A-C 342.MAU2.ENST00000262815.12.missense.111S/R 1 MAU2 S111R 1 KFEAARLL ENST00000262815.12 1 HLA-E*01:01 6 None 1 0 28879.609 30044.250 8.500 9.900 NA NA NA NA 0.365 Poor Pending +chr6-152325133-152325134-C-T 170.SYNE1.ENST00000367255.9.missense.5203E/K 1 SYNE1 E5203K 1 AQDQKKIL ENST00000367255.9 1 HLA-E*01:01 5 None 1 0 28899.920 32620.270 8.500 15.000 NA NA NA NA 0.339 Poor Pending +chr6-53654806-53654807-C-T 161.KLHL31.ENST00000370905.3.missense.156V/I 1 KLHL31 V156I 1 IKMCSDFL ENST00000370905.3 1 HLA-E*01:01 1 None 1 0 28954.689 27652.190 8.500 7.100 NA NA NA NA 0.450 Poor Pending +chrX-9967396-9967397-G-A 372.CLDN34.ENST00000445307.4.missense.14V/I 1 CLDN34 V14I 1 CQFSIFAL ENST00000445307.4 NA HLA-E*01:01 5 None 1 0 29036.570 27185.560 8.700 6.700 NA NA NA NA 0.989 Poor Pending +chr16-3745299-3745300-G-C 284.CREBBP.ENST00000262367.9.missense.1297H/Q 1 CREBBP H1297Q 1 VLQYDIIW ENST00000262367.9 1 HLA-E*01:01 3 None 1 0 29176.400 30579.800 8.800 12.000 NA NA NA NA 0.246 Poor Pending +chr6-29374537-29374538-G-C 114.OR12D3.ENST00000396806.3.missense.250F/L 1 OR12D3 F250L 1 FMVVCLLY ENST00000396806.3 NA HLA-E*01:01 7 None 1 0 29396.320 32644.640 9.000 15.000 NA NA NA NA 0.423 Poor Pending +chr10-37957500-37957501-C-T 216.ZNF25.ENST00000302609.7.missense.21E/K 1 ZNF25 E21K 1 TKEKWKLL ENST00000302609.7 1 HLA-E*01:01 4 None 1 0 29465.730 33031.190 9.100 16.000 NA NA NA NA 0.460 Poor Pending +chr20-41165771-41165772-C-G 352.PLCG1.ENST00000244007.7.missense.582S/C 1 PLCG1 S582C 1 GAPDGCFL ENST00000244007.7 5 HLA-E*01:01 6 None 1 0 29469.869 28834.010 9.100 8.400 NA NA NA NA 0.448 Poor Pending +chr3-44242057-44242058-G-A 58.TOPAZ1.ENST00000309765.4.missense.2R/Q 1 TOPAZ1 R2Q 1 MQRPPPLG ENST00000309765.4 5 HLA-E*01:01 2 None 1 0 29645.131 33883.300 9.300 18.000 NA NA NA NA 0.318 Poor Pending +chrX-16869531-16869532-C-T 375.RBBP7.ENST00000380084.8.missense.37R/H 1 RBBP7 R37H 1 RLGHAAPV ENST00000380084.8 2 HLA-E*01:01 4 None 1 0 29762.770 26966.120 9.500 6.600 NA NA NA NA 1.000 Poor Pending +chr14-26448937-26448938-G-C 259.NOVA1.ENST00000539517.6.missense.182T/R 1 NOVA1 T182R 1 VPNSRAGL ENST00000539517.6 1 HLA-E*01:01 5 None 1 0 29808.199 23770.230 9.600 4.300 NA NA NA NA 0.451 Poor Pending +chrX-153058184-153058185-C-T 410.PNMA3.ENST00000593810.2.missense.377A/V 1 PNMA3 A377V 1 VRPSQGYR ENST00000593810.2 NA HLA-E*01:01 1 None 1 0 30015.971 35864.100 9.800 23.000 NA NA NA NA 1.000 Poor Pending +chr2-219514658-219514659-C-A 51.ASIC4.ENST00000347842.7.missense.106P/T 1 ASIC4 P106T 1 LGRATGLL ENST00000347842.7 1 HLA-E*01:01 5 None 1 0 30245.480 33615.630 12.000 17.000 NA NA NA NA 0.238 Poor Pending +chr6-122781239-122781240-C-G 169.FABP7.ENST00000356535.4.missense.132P/A 1 FABP7 P132A 1 SAHTSHLL ENST00000356535.4 1 HLA-E*01:01 2 None 1 0 30336.920 17573.070 12.000 1.800 NA NA NA NA 0.371 Poor Pending +chr9-130307565-130307566-G-A 209.HMCN2.ENST00000624552.3.missense.733G/R 1 HMCN2 G733R 1 VIWYRRGL ENST00000624552.3 5 HLA-E*01:01 6 None 1 0 30405.279 26270.630 12.000 6.100 NA NA NA NA 0.290 Poor Pending +chr7-82916602-82916603-C-A 176.PCLO.ENST00000333891.13.missense.3795D/Y 1 PCLO D3795Y 1 IYAKLRYL ENST00000333891.13 2 HLA-E*01:01 2 None 1 0 30408.891 33041.930 12.000 16.000 NA NA NA NA 0.219 Poor Pending +chrX-41344254-41344255-G-C 384.DDX3X.ENST00000644876.1.missense.294R/T 1 DDX3X R294T 1 TVRPCVVY ENST00000644876.1 NA HLA-E*01:01 1 None 1 0 30441.480 27209.680 12.000 6.700 NA NA NA NA 0.983 Poor Pending +chr10-13481023-13481024-C-G 214.BEND7.ENST00000341083.7.missense.261R/T 1 BEND7 R261T 1 TKLVCAFF ENST00000341083.7 2 HLA-E*01:01 1 None 1 0 30462.240 26060.290 12.000 5.900 NA NA NA NA 1.000 Poor Pending +chr11-64320894-64320895-T-C 237.PRDX5.ENST00000265462.8.missense.157F/L 1 PRDX5 F157L 1 LADPTGAL ENST00000265462.8 1 HLA-E*01:01 8 None 1 0 30476.090 36635.570 12.000 26.000 NA NA NA NA 0.425 Poor Pending +chr3-171138369-171138370-G-T 66.TNIK.ENST00000436636.6.missense.477R/S 1 TNIK R477S 1 LEYKSKQL ENST00000436636.6 1 HLA-E*01:01 5 None 1 0 30541.119 33712.890 12.000 18.000 NA NA NA NA 0.278 Poor Pending +chrX-18619961-18619962-A-C 377.CDKL5.ENST00000379989.6.missense.791Q/P 1 CDKL5 Q791P 1 KKKKSPTV ENST00000379989.6 1 HLA-E*01:01 6 None 1 0 30563.600 40041.010 12.000 40.000 NA NA NA NA 1.000 Poor Pending +chr16-87748715-87748716-G-C 309.KLHDC4.ENST00000270583.9.missense.155L/V 1 KLHDC4 L155V 1 HYKDVWVL ENST00000270583.9 1 HLA-E*01:01 5 None 1 0 30580.141 33812.990 12.000 18.000 NA NA NA NA 0.453 Poor Pending +chr16-88736715-88736716-T-C 311.PIEZO1.ENST00000301015.14.missense.407R/G 1 PIEZO1 R407G 1 EPGEASPL ENST00000301015.14 1 HLA-E*01:01 3 None 1 0 30601.330 28600.050 12.000 8.200 NA NA NA NA 0.413 Poor Pending +chrX-88753805-88753806-G-A 394.CPXCR1.ENST00000276127.8.missense.131R/H 1 CPXCR1 R131H 1 NHKTHFRL ENST00000276127.8 1 HLA-E*01:01 5 None 1 0 30822.289 25732.470 12.000 5.700 NA NA NA NA 1.000 Poor Pending +chr6-31112111-31112112-C-G 120.C6orf15.ENST00000259870.3.missense.83A/P 1 C6orf15 A83P 1 SVPPSDGF ENST00000259870.3 1 HLA-E*01:01 4 None 1 0 30839.980 37041.310 12.000 27.000 NA NA NA NA 0.703 Poor Pending +chr11-63544840-63544860-GTGAGCACTTTGTCACCCAGC-G 236.RARRES3.ENST00000255688.7.FS.113-120GTGAGCACTTTGTCACCCAGC/G 1 RARRES3 FS113-120 1 CEIWQVPL ENST00000255688.7 1 HLA-E*01:01 3-8 None 1 0 30936.891 NA 13.000 NA NA NA NA NA 0.149 Poor Pending +chr7-157005551-157005552-G-A 191.MNX1.ENST00000252971.10.missense.392P/S 1 MNX1 P392S 1 SPPSRPSH ENST00000252971.10 1 HLA-E*01:01 4 None 1 0 30996.529 28584.290 13.000 8.200 NA NA NA NA 0.052 Poor Pending +chr16-2295600-2295601-C-G 283.ABCA3.ENST00000301732.9.missense.801E/D 1 ABCA3 E801D 1 ILPRDSTH ENST00000301732.9 1 HLA-E*01:01 5 None 1 0 31053.930 31199.430 13.000 13.000 NA NA NA NA 0.594 Poor Pending +chr8-38428419-38428420-G-A 194.FGFR1.ENST00000425967.7.missense.158S/L 1 FGFR1 S158L 1 VSDALPSL ENST00000425967.7 1 HLA-E*01:01 8 None 1 0 31127.939 43501.930 13.000 67.000 NA NA NA NA 1.000 Poor Pending +chr2-175093191-175093192-C-G 45.ATF2.ENST00000264110.6.missense.352D/H 1 ATF2 D352H 1 HEKRRKFL ENST00000264110.6 1 HLA-E*01:01 1 None 1 0 31205.500 33240.930 13.000 17.000 NA NA NA NA 0.462 Poor Pending +chr16-71998331-71998332-T-A 300.PKD1L3.ENST00000620267.1.missense.120I/F 1 PKD1L3 I120F 1 TYLSRNFF ENST00000620267.1 1 HLA-E*01:01 8 None 1 0 31251.461 33213.980 13.000 17.000 NA NA NA NA 0.620 Poor Pending +chr2-94874875-94874876-T-A 40.TEKT4.ENST00000295201.4.missense.272C/S 1 TEKT4 C272S 1 RVLVDSIL ENST00000295201.4 1 HLA-E*01:01 6 None 1 0 31280.539 33479.160 13.000 17.000 NA NA NA NA 0.444 Poor Pending +chr15-94399982-94399983-G-T 281.MCTP2.ENST00000357742.8.missense.651K/N 1 MCTP2 K651N 1 RNLSKKIL ENST00000357742.8 1 HLA-E*01:01 2 None 1 0 31389.381 29273.800 13.000 8.900 NA NA NA NA 0.199 Poor Pending +chr11-5968293-5968294-G-C 225.OR56A5.ENST00000532411.2.missense.67S/R 1 OR56A5 S67R 1 YLLRLLSL ENST00000532411.2 NA HLA-E*01:01 4 None 1 0 31438.990 34483.550 13.000 19.000 NA NA NA NA 1.000 Poor Pending +chr4-121932625-121932626-C-A 79.TRPC3.ENST00000379645.7.missense.211C/F 1 TRPC3 C211F 1 LSPFEQEL ENST00000379645.7 1 HLA-E*01:01 4 None 1 0 31473.039 26616.250 13.000 6.300 NA NA NA NA 0.306 Poor Pending +chr1-27793606-27793607-C-G 6.STX12.ENST00000373943.8.missense.88P/R 1 STX12 P88R 1 KELGSLRL ENST00000373943.8 1 HLA-E*01:01 7 None 1 0 31534.391 32950.170 14.000 16.000 NA NA NA NA 1.000 Poor Pending +chr2-195816717-195816718-T-G 47.DNAH7.ENST00000312428.10.missense.3224E/A 1 DNAH7 E3224A 1 APMYQYSL ENST00000312428.10 1 HLA-E*01:01 1 None 1 0 31644.100 33951.200 14.000 18.000 NA NA NA NA 0.138 Poor Pending +chr8-66813873-66813874-C-T 195.SGK3.ENST00000396596.2.missense.92A/V 1 SGK3 A92V 1 IKQRRVGL ENST00000396596.2 1 HLA-E*01:01 6 None 1 0 31771.039 26125.230 14.000 5.900 NA NA NA NA 0.230 Poor Pending +chr7-155462475-155462476-A-G 190.EN2.ENST00000297375.4.missense.264Q/R 1 EN2 Q264R 1 RLKAEFRT ENST00000297375.4 1 HLA-E*01:01 7 None 1 0 31778.949 32725.630 14.000 16.000 NA NA NA NA 0.254 Poor Pending +chr4-103145955-103145956-C-G 75.CENPE.ENST00000265148.7.missense.1429R/T 1 CENPE R1429T 1 MLGLSKTL ENST00000265148.7 2 HLA-E*01:01 7 None 1 0 31849.160 31232.870 14.000 13.000 NA NA NA NA 0.238 Poor Pending +chr17-3433668-3433669-G-T 312.OR1E2.ENST00000248384.1.missense.58P/H 1 OR1E2 P58H 1 LHTHVYLF ENST00000248384.1 NA HLA-E*01:01 4 None 1 0 31895.039 23286.060 14.000 4.100 NA NA NA NA 0.317 Poor Pending +chr1-16006133-16006134-G-T 1.SRARP.ENST00000329454.2.missense.100G/W 1 SRARP G100W 1 TPMGWGCL ENST00000329454.2 1 HLA-E*01:01 5 None 1 0 31981.770 32224.230 14.000 15.000 NA NA NA NA 0.989 Poor Pending +chr16-56511262-56511263-T-C 289.BBS2.ENST00000245157.9.missense.123I/V 1 BBS2 I123V 1 DGANAVVL ENST00000245157.9 1 HLA-E*01:01 6 None 1 0 32098.961 30233.060 14.000 11.000 NA NA NA NA 0.719 Poor Pending +chr11-124319973-124319974-G-A 242.OR8D2.ENST00000624618.1.missense.75S/F 1 OR8D2 S75F 1 DLCYSFVI ENST00000624618.1 NA HLA-E*01:01 6 None 1 0 32170.580 38913.840 15.000 34.000 NA NA NA NA 1.000 Poor Pending +chr6-56552746-56552747-T-C 166.DST.ENST00000312431.10.missense.3092T/A 1 DST T3092A 1 KGASDVLL ENST00000312431.10 5 HLA-E*01:01 3 None 1 0 32193.900 35860.210 15.000 23.000 NA NA NA NA 0.308 Poor Pending +chr6-24653044-24653045-G-C 108.TDP2.ENST00000378198.8.missense.249Q/E 1 TDP2 Q249E 1 KMEEAPES ENST00000378198.8 1 HLA-E*01:01 3 None 1 0 32249.320 31134.690 15.000 13.000 NA NA NA NA 0.647 Poor Pending +chr10-104021651-104021652-G-T 218.SLK.ENST00000369755.3.missense.1160E/D 1 SLK E1160D 1 VEHDTQKL ENST00000369755.3 1 HLA-E*01:01 4 None 1 0 32262.949 33078.410 15.000 16.000 NA NA NA NA 0.071 Poor Pending +chr16-67239382-67239411-GCTGCTCTTCCAGGGACAGCTCGGTGTCCA-G 296.FHOD1.ENST00000258201.8.FS.82-91GCTGCTCTTCCAGGGACAGCTCGGTGTCCA/G 1 FHOD1 FS82-91 1 YPGDAGGL ENST00000258201.8 1 HLA-E*01:01 2-8 None 1 0 32355.590 NA 15.000 NA NA NA NA NA 0.231 Poor Pending +chrX-43656385-43656386-C-A 385.MAOA.ENST00000338702.3.missense.15D/E 1 MAOA D15E 1 HMFEVVVI ENST00000338702.3 1 HLA-E*01:01 4 None 1 0 32415.510 32391.670 15.000 15.000 NA NA NA NA 1.000 Poor Pending +chr12-49526214-49526215-G-A 246.SPATS2.ENST00000553127.5.missense.533R/H 1 SPATS2 R533H 1 LPQHKPRT ENST00000553127.5 1 HLA-E*01:01 4 None 1 0 32566.670 24939.750 15.000 5.100 NA NA NA NA 0.966 Poor Pending +chr20-4182496-4182497-C-A 348.SMOX.ENST00000621355.4.missense.340Q/K 1 SMOX Q340K 1 KRKYTSFF ENST00000621355.4 1 HLA-E*01:01 3 None 1 0 32571.609 32326.180 15.000 15.000 NA NA NA NA 0.592 Poor Pending +chr5-7886679-7886680-G-C 82.MTRR.ENST00000264668.6.missense.402E/Q 1 MTRR E402Q 1 IFTWCLQI ENST00000264668.6 1 HLA-E*01:01 7 None 1 0 32691.289 34911.530 16.000 20.000 NA NA NA NA 0.189 Poor Pending +chr10-32567832-32567833-C-T 215.CCDC7.ENST00000362006.11.missense.454S/L 1 CCDC7 S454L 1 LEKETRKL ENST00000362006.11 1 HLA-E*01:01 8 None 1 0 32694.109 44861.830 16.000 81.000 NA NA NA NA 0.378 Poor Pending +chr19-50625545-50625546-G-A 345.SYT3.ENST00000338916.8.missense.474S/F 1 SYT3 S474F 1 PYVKAFLI ENST00000338916.8 1 HLA-E*01:01 6 None 1 0 32797.570 42134.880 16.000 55.000 NA NA NA NA 0.538 Poor Pending +chrX-136228625-136228626-T-C 406.MAP7D3.ENST00000316077.13.missense.628Q/R 1 MAP7D3 Q628R 1 EMQRRVIK ENST00000316077.13 1 HLA-E*01:01 4 None 1 0 32824.551 33688.100 16.000 17.000 NA NA NA NA 1.000 Poor Pending +chr15-84036950-84036951-A-T 280.ADAMTSL3.ENST00000286744.9.missense.1645I/F 1 ADAMTSL3 I1645F 1 VQKKKPFS ENST00000286744.9 1 HLA-E*01:01 7 None 1 0 32843.730 31794.780 16.000 14.000 NA NA NA NA 0.368 Poor Pending +chr5-141332647-141332648-C-T 90.PCDHGA1.ENST00000517417.2.missense.655S/F 1 PCDHGA1 S655F 1 PLFATVTL ENST00000517417.2 1 HLA-E*01:01 3 None 1 0 32859.031 32696.960 16.000 16.000 NA NA NA NA 0.688 Poor Pending +chr11-123943666-123943667-G-C 241.OR6T1.ENST00000321252.2.missense.58Q/E 1 OR6T1 Q58E 1 RLHIEMYF ENST00000321252.2 NA HLA-E*01:01 5 None 1 0 32903.141 32404.620 16.000 15.000 NA NA NA NA 0.441 Poor Pending +chr5-150120064-150120065-G-A 92.PDGFRB.ENST00000261799.8.missense.882T/I 1 PDGFRB T882I 1 ILSDVWSF ENST00000261799.8 1 HLA-E*01:01 1 None 1 0 32915.590 35483.900 16.000 22.000 NA NA NA NA 0.289 Poor Pending +chr19-38802098-38802099-G-A 344.LGALS4.ENST00000307751.8.missense.240R/C 1 LGALS4 R240C 1 CMGNGTVV ENST00000307751.8 1 HLA-E*01:01 1 None 1 0 33176.250 25657.130 16.000 5.600 NA NA NA NA 1.000 Poor Pending +chr6-32335914-32335915-T-A 132.TSBP1.ENST00000447241.6.missense.150I/F 1 TSBP1 I150F 1 IPGATGPF ENST00000447241.6 5 HLA-E*01:01 8 None 1 0 33179.480 34404.190 16.000 19.000 NA NA NA NA 0.638 Poor Pending +chr16-69167146-69167147-C-T 297.UTP4.ENST00000314423.11.missense.636R/C 1 UTP4 R636C 1 CTAHAFKI ENST00000314423.11 1 HLA-E*01:01 1 None 1 0 33189.891 24117.100 16.000 4.500 NA NA NA NA 0.671 Poor Pending +chr15-100900576-100900577-G-T 282.ALDH1A3.ENST00000329841.9.missense.296D/Y 1 ALDH1A3 D296Y 1 CADADLYL ENST00000329841.9 1 HLA-E*01:01 7 None 1 0 33191.680 37026.480 16.000 27.000 NA NA NA NA 0.376 Poor Pending +chr7-39339738-39339739-G-C 172.POU6F2.ENST00000403058.5.missense.203Q/H 1 POU6F2 Q203H 1 HHPQPAPQ ENST00000403058.5 5 HLA-E*01:01 1 None 1 0 33344.309 28399.620 17.000 8.000 NA NA NA NA 0.317 Poor Pending +chr6-31120367-31120368-T-A 123.CDSN.ENST00000376288.2.missense.18M/L 1 CDSN M18L 1 RVGGHGML ENST00000376288.2 1 HLA-E*01:01 8 None 1 0 33357.672 38352.500 17.000 32.000 NA NA NA NA 0.674 Poor Pending +chr4-99654590-99654591-C-T 74.C4orf54.ENST00000511828.1.missense.20V/M 1 C4orf54 V20M 1 SMADGIQT ENST00000511828.1 1 HLA-E*01:01 2 None 1 0 33419.078 43086.880 17.000 63.000 NA NA NA NA 0.216 Poor Pending +chr17-5007046-5007047-C-T 315.KIF1C.ENST00000320785.9.missense.433S/F 1 KIF1C S433F 1 SPNTEFQI ENST00000320785.9 1 HLA-E*01:01 6 None 1 0 33450.539 43334.680 17.000 65.000 NA NA NA NA 0.319 Poor Pending +chr6-36871821-36871822-C-G 139.PPIL1.ENST00000373699.5.missense.36C/S 1 PPIL1 C36S 1 APKTSKNF ENST00000373699.5 1 HLA-E*01:01 5 None 1 0 33461.410 36325.320 17.000 25.000 NA NA NA NA 0.792 Poor Pending +chr10-60186848-60186849-G-T 217.ANK3.ENST00000280772.6.missense.651L/M 1 ANK3 L651M 1 MDIATTLM ENST00000280772.6 1 HLA-E*01:01 8 None 1 0 33462.500 23869.970 17.000 4.400 NA NA NA NA 0.134 Poor Pending +chr16-25221522-25221523-G-C 285.AQP8.ENST00000219660.5.missense.109M/I 1 AQP8 M109I 1 ILLPYWVS ENST00000219660.5 1 HLA-E*01:01 1 None 1 0 33482.051 34471.260 17.000 19.000 NA NA NA NA 0.250 Poor Pending +chr6-44183752-44183753-G-A 151.CAPN11.ENST00000398776.1.missense.728S/N 1 CAPN11 S728N 1 NLEQWLQM ENST00000398776.1 1 HLA-E*01:01 1 None 1 0 33547.320 32082.270 17.000 14.000 NA NA NA NA 0.703 Poor Pending +chr7-102595676-102595677-C-G 181.RASA4.ENST00000262940.11.missense.321K/N 1 RASA4 K321N 1 LANDFLDL ENST00000262940.11 1 HLA-E*01:01 3 None 1 0 33598.551 29908.020 17.000 9.700 NA NA NA NA 0.045 Poor Pending +chr3-172353066-172353067-C-T 67.FNDC3B.ENST00000336824.8.missense.927P/S 1 FNDC3B P927S 1 LSETTYRI ENST00000336824.8 1 HLA-E*01:01 2 None 1 0 33774.219 17406.350 18.000 1.800 NA NA NA NA 0.364 Poor Pending +chr17-80086142-80086143-G-C 324.CCDC40.ENST00000397545.8.missense.792E/D 1 CCDC40 E792D 1 TQEQDEQL ENST00000397545.8 5 HLA-E*01:01 5 None 1 0 33852.500 34255.230 18.000 19.000 NA NA NA NA 0.200 Poor Pending +chr5-134893641-134893642-T-C 87.TXNDC15.ENST00000358387.8.missense.248S/P 1 TXNDC15 S248P 1 DAPQHSSL ENST00000358387.8 1 HLA-E*01:01 3 None 1 0 33915.570 41383.070 18.000 49.000 NA NA NA NA 1.000 Poor Pending +chr3-183179682-183179683-G-A 68.MCF2L2.ENST00000328913.7.missense.1039L/F 1 MCF2L2 L1039F 1 ALSLAGFF ENST00000328913.7 5 HLA-E*01:01 7 None 1 0 33988.680 36417.410 18.000 25.000 NA NA NA NA 0.373 Poor Pending +chr11-58190707-58190708-A-T 232.OR9Q2.ENST00000641291.1.missense.73Y/F 1 OR9Q2 Y73F 1 ICFSSAII ENST00000641291.1 NA HLA-E*01:01 3 None 1 0 34085.148 33436.440 18.000 17.000 NA NA NA NA 0.517 Poor Pending +chr14-21403125-21403126-C-A 256.CHD8.ENST00000646647.1.missense.1202R/L 1 CHD8 R1202L 1 SKPDSDLF ENST00000646647.1 NA HLA-E*01:01 7 None 1 0 34086.270 37387.580 18.000 28.000 NA NA NA NA 0.080 Poor Pending +chr19-16572288-16572289-C-G 341.SLC35E1.ENST00000595753.5.missense.26E/Q 1 SLC35E1 E26Q 1 QGARVAAL ENST00000595753.5 1 HLA-E*01:01 1 None 1 0 34187.828 37517.670 19.000 29.000 NA NA NA NA 0.706 Poor Pending +chr7-112821984-112821985-G-T 184.BMT2.ENST00000297145.8.missense.326T/K 1 BMT2 T326K 1 SLKTKSDL ENST00000297145.8 1 HLA-E*01:01 5 None 1 0 34198.949 35291.310 19.000 21.000 NA NA NA NA 0.181 Poor Pending +chr1-36179727-36179728-G-A 7.MAP7D1.ENST00000373151.6.missense.765E/K 1 MAP7D1 E765K 1 VQKEKPIP ENST00000373151.6 1 HLA-E*01:01 5 None 1 0 34265.621 36615.350 19.000 26.000 NA NA NA NA 0.329 Poor Pending +chr11-6401000-6401001-C-T 226.APBB1.ENST00000609360.5.missense.554A/T 1 APBB1 A554T 1 VPVTKPVG ENST00000609360.5 5 HLA-E*01:01 4 None 1 0 34267.469 35410.270 19.000 22.000 NA NA NA NA 0.989 Poor Pending +chr1-160876800-160876801-C-T 21.ITLN1.ENST00000326245.3.missense.269G/R 1 ITLN1 G269R 1 CIGGRGYF ENST00000326245.3 1 HLA-E*01:01 5 None 1 0 34343.559 40127.730 19.000 41.000 NA NA NA NA 0.258 Poor Pending +chr9-129102403-129102404-T-C 208.CRAT.ENST00000318080.6.missense.209Y/C 1 CRAT Y209C 1 VVHNCQFF ENST00000318080.6 1 HLA-E*01:01 5 None 1 0 34345.422 36746.710 19.000 26.000 NA NA NA NA 0.269 Poor Pending +chr14-32600790-32600791-A-T 260.AKAP6.ENST00000280979.8.missense.910K/M 1 AKAP6 K910M 1 SPMAEVQL ENST00000280979.8 1 HLA-E*01:01 3 None 1 0 34356.180 30222.590 19.000 11.000 NA NA NA NA 0.693 Poor Pending +chr1-154590262-154590263-T-A 20.ADAR.ENST00000647597.1.missense.806E/V 1 ADAR E806V 1 RMGFTVVT ENST00000647597.1 NA HLA-E*01:01 6 None 1 0 34374.398 36267.200 19.000 24.000 NA NA NA NA 0.284 Poor Pending +chrX-48559737-48559738-A-G 386.TBC1D25.ENST00000376771.8.missense.277N/S 1 TBC1D25 N277S 1 ASPEDLEF ENST00000376771.8 1 HLA-E*01:01 2 None 1 0 34379.609 34307.540 19.000 19.000 NA NA NA NA 1.000 Poor Pending +chr14-32773880-32773881-G-T 261.AKAP6.ENST00000280979.8.missense.1192M/I 1 AKAP6 M1192I 1 IGKESETL ENST00000280979.8 1 HLA-E*01:01 1 None 1 0 34390.789 24395.040 19.000 4.700 NA NA NA NA 0.618 Poor Pending +chr6-33286887-33286888-A-G 133.WDR46.ENST00000374617.8.missense.341V/A 1 WDR46 V341A 1 ASLWSPAM ENST00000374617.8 1 HLA-E*01:01 1 None 1 0 34576.969 28534.230 20.000 8.100 NA NA NA NA 0.648 Poor Pending +chr22-50177151-50177152-C-T 362.PANX2.ENST00000395842.2.missense.147S/F 1 PANX2 S147F 1 LGWEFLAF ENST00000395842.2 2 HLA-E*01:01 8 None 1 0 34578.090 44153.450 20.000 74.000 NA NA NA NA 0.996 Poor Pending +chr5-136274698-136274699-C-T 88.TRPC7.ENST00000513104.5.missense.368A/T 1 TRPC7 A368T 1 LPFLAITY ENST00000513104.5 5 HLA-E*01:01 7 None 1 0 34695.762 36612.580 20.000 26.000 NA NA NA NA 0.388 Poor Pending +chr2-63942505-63942506-C-G 38.VPS54.ENST00000272322.8.missense.453D/H 1 VPS54 D453H 1 HIFSKFTI ENST00000272322.8 5 HLA-E*01:01 1 None 1 0 34755.129 36864.580 20.000 26.000 NA NA NA NA 1.000 Poor Pending +chr3-186164997-186164998-C-T 70.DGKG.ENST00000265022.7.missense.706E/K 1 DGKG E706K 1 QLLKVVGL ENST00000265022.7 1 HLA-E*01:01 4 None 1 0 34816.461 37385.560 20.000 28.000 NA NA NA NA 0.523 Poor Pending +chr6-30952346-30952347-G-A 118.MUCL3.ENST00000462446.5.missense.1295E/K 1 MUCL3 E1295K 1 GNKSHPYL ENST00000462446.5 5 HLA-E*01:01 3 None 1 0 34820.621 35846.250 20.000 23.000 NA NA NA NA 0.786 Poor Pending +chr4-48420360-48420361-A-G 73.SLAIN2.ENST00000264313.10.missense.533R/G 1 SLAIN2 R533G 1 AMGSGLPR ENST00000264313.10 1 HLA-E*01:01 3 None 1 0 34921.730 31057.980 20.000 13.000 NA NA NA NA 0.288 Poor Pending +chr5-133103958-133103959-T-C 86.HSPA4.ENST00000304858.6.missense.751L/P 1 HSPA4 L751P 1 NPQNKQSL ENST00000304858.6 1 HLA-E*01:01 2 None 1 0 34947.430 37558.680 21.000 29.000 NA NA NA NA 1.000 Poor Pending +chr1-223264671-223264672-G-C 28.SUSD4.ENST00000343846.7.missense.228L/V 1 SUSD4 L228V 1 VIWSSSPP ENST00000343846.7 2 HLA-E*01:01 1 None 1 0 34948.559 38104.730 21.000 31.000 NA NA NA NA 0.390 Poor Pending +chr19-422192-422193-G-C 331.SHC2.ENST00000264554.10.missense.525H/D 1 SHC2 H525D 1 MDAGQPKH ENST00000264554.10 1 HLA-E*01:01 2 None 1 0 35125.230 34280.820 21.000 19.000 NA NA NA NA 0.109 Poor Pending +chr6-43587456-43587457-G-A 149.POLH.ENST00000372236.8.missense.153G/D 1 POLH G153D 1 GLPQDPTT ENST00000372236.8 1 HLA-E*01:01 5 None 1 0 35141.570 33319.420 21.000 17.000 NA NA NA NA 0.221 Poor Pending +chr3-39188114-39188115-A-T 57.XIRP1.ENST00000340369.3.missense.444L/H 1 XIRP1 L444H 1 NHFETLPL ENST00000340369.3 1 HLA-E*01:01 2 None 1 0 35165.922 29287.100 21.000 8.900 NA NA NA NA 0.655 Poor Pending +chr11-59364558-59364559-T-A 233.OR5AN1.ENST00000641850.1.missense.34V/E 1 OR5AN1 V34E 1 VLFTIFLE ENST00000641850.1 NA HLA-E*01:01 8 None 1 0 35445.160 25935.400 22.000 5.800 NA NA NA NA 0.123 Poor Pending +chr14-70060889-70060890-C-G 265.SLC8A3.ENST00000381269.6.missense.612E/Q 1 SLC8A3 E612Q 1 RQQNFFIA ENST00000381269.6 1 HLA-E*01:01 3 None 1 0 35447.461 36794.460 22.000 26.000 NA NA NA NA 1.000 Poor Pending +chrX-77681732-77681733-T-C 390.ATRX.ENST00000373344.10.missense.1175K/E 1 ATRX K1175E 1 SEKKAVIV ENST00000373344.10 1 HLA-E*01:01 2 None 1 0 35460.500 35081.930 22.000 21.000 NA NA NA NA 1.000 Poor Pending +chr16-84318345-84318346-G-A 306.WFDC1.ENST00000219454.9.missense.138V/M 1 WFDC1 V138M 1 LDGPEEML ENST00000219454.9 1 HLA-E*01:01 7 None 1 0 35467.020 34278.590 22.000 19.000 NA NA NA NA 0.495 Poor Pending +chr7-97006043-97006044-G-C 179.DLX6.ENST00000518156.2.missense.23E/Q 1 DLX6 E23Q 1 SSKSAFMQ ENST00000518156.2 1 HLA-E*01:01 8 None 1 0 35541.551 36933.660 22.000 27.000 NA NA NA NA 0.419 Poor Pending +chr16-56982179-56982180-G-A 290.CETP.ENST00000200676.7.missense.422V/I 1 CETP V422I 1 SESIQSFL ENST00000200676.7 1 HLA-E*01:01 4 None 1 0 35616.988 34878.690 22.000 20.000 NA NA NA NA 0.653 Poor Pending +chr18-36067341-36067342-C-G 327.RPRD1A.ENST00000399022.8.missense.21Q/H 1 RPRD1A Q21H 1 SQHSVQTL ENST00000399022.8 1 HLA-E*01:01 3 None 1 0 35630.500 34801.780 22.000 20.000 NA NA NA NA 0.424 Poor Pending +chr7-102317255-102317256-A-G 180.SH2B2.ENST00000536178.3.missense.462H/R 1 SH2B2 H462R 1 YPWFRGTL ENST00000536178.3 1 HLA-E*01:01 5 None 1 0 35639.738 34199.670 22.000 19.000 NA NA NA NA 0.189 Poor Pending +chr17-4545724-4545725-T-C 313.MYBBP1A.ENST00000381556.6.missense.653E/G 1 MYBBP1A E653G 1 EVLVGILL ENST00000381556.6 5 HLA-E*01:01 5 None 1 0 35641.281 36414.640 22.000 25.000 NA NA NA NA 0.354 Poor Pending +chr1-59858482-59858483-C-T 14.HOOK1.ENST00000371208.3.missense.433S/L 1 HOOK1 S433L 1 LQVQQDHL ENST00000371208.3 1 HLA-E*01:01 1 None 1 0 35676.789 38483.020 23.000 33.000 NA NA NA NA 0.413 Poor Pending +chr2-236392010-236392011-C-T 54.IQCA1.ENST00000431676.6.missense.467E/K 1 IQCA1 E467K 1 RERKRPVK ENST00000431676.6 2 HLA-E*01:01 4 None 1 0 35720.430 37398.120 23.000 28.000 NA NA NA NA 0.237 Poor Pending +chrX-100635206-100635207-C-T 395.TSPAN6.ENST00000373020.8.missense.108A/T 1 TSPAN6 A108T 1 ATIVGFVF ENST00000373020.8 1 HLA-E*01:01 2 None 1 0 35834.230 34206.340 23.000 19.000 NA NA NA NA 1.000 Poor Pending +chr1-66834005-66834006-C-G 15.WDR78.ENST00000371026.7.missense.626G/R 1 WDR78 G626R 1 RLDCYDLM ENST00000371026.7 1 HLA-E*01:01 1 None 1 0 35871.090 42568.820 23.000 58.000 NA NA NA NA 0.598 Poor Pending +chr16-74385694-74385695-C-T 303.NPIPB15.ENST00000429990.1.missense.164T/M 1 NPIPB15 T164M 1 IRKRKVTM ENST00000429990.1 5 HLA-E*01:01 8 None 1 0 35930.121 42376.730 23.000 57.000 NA NA NA NA 0.520 Poor Pending +chr2-71611503-71611504-C-G 39.DYSF.ENST00000410020.7.missense.1367L/V 1 DYSF L1367V 1 RNMKSYQV ENST00000410020.7 1 HLA-E*01:01 8 None 1 0 35932.840 23672.440 23.000 4.300 NA NA NA NA 1.000 Poor Pending +chr12-116009024-116009025-G-C 249.MED13L.ENST00000281928.8.missense.463A/G 1 MED13L A463G 1 SLPPPGSS ENST00000281928.8 1 HLA-E*01:01 6 None 1 0 35938.680 32860.450 23.000 16.000 NA NA NA NA 0.055 Poor Pending +chr1-27359862-27359863-T-G 5.MAP3K6.ENST00000493901.5.missense.772I/L 1 MAP3K6 I772L 1 DLKGDNVL ENST00000493901.5 5 HLA-E*01:01 2 None 1 0 35962.422 38898.290 23.000 34.000 NA NA NA NA 0.265 Poor Pending +chr17-10499040-10499041-G-A 318.MYH1.ENST00000226207.5.missense.1306S/L 1 MYH1 S1306L 1 LLRGKQAF ENST00000226207.5 5 HLA-E*01:01 2 None 1 0 36064.500 41818.770 24.000 52.000 NA NA NA NA 0.987 Poor Pending +chr17-29286059-29286060-C-G 320.NUFIP2.ENST00000225388.8.missense.645R/T 1 NUFIP2 R645T 1 EQRYQTGL ENST00000225388.8 1 HLA-E*01:01 6 None 1 0 36075.430 39007.870 24.000 35.000 NA NA NA NA 1.000 Poor Pending +chr16-57655892-57655893-A-C 293.ADGRG1.ENST00000568909.5.missense.306Q/H 1 ADGRG1 Q306H 1 DKNSSHVL ENST00000568909.5 5 HLA-E*01:01 6 None 1 0 36181.371 37550.160 24.000 29.000 NA NA NA NA 0.664 Poor Pending +chr16-69954568-69954569-C-T 298.CLEC18A.ENST00000615430.4.missense.151T/M 1 CLEC18A T151M 1 TCTHYMQL ENST00000615430.4 5 HLA-E*01:01 6 None 1 0 36307.238 38265.040 25.000 32.000 NA NA NA NA 0.632 Poor Pending +chr1-232805681-232805682-C-T 31.MAP10.ENST00000418460.2.missense.220P/L 1 MAP10 P220L 1 ALAAEPWP ENST00000418460.2 NA HLA-E*01:01 2 None 1 0 36481.301 36155.920 25.000 24.000 NA NA NA NA 0.233 Poor Pending +chr16-72128664-72128665-T-G 302.PMFBP1.ENST00000237353.14.missense.694N/H 1 PMFBP1 N694H 1 DLHKEIAL ENST00000237353.14 1 HLA-E*01:01 3 None 1 0 36530.672 38538.000 25.000 33.000 NA NA NA NA 0.066 Poor Pending +chr1-22660990-22660991-G-A 4.C1QB.ENST00000314933.6.missense.123A/T 1 C1QB A123T 1 KATQKITF ENST00000314933.6 1 HLA-E*01:01 7 None 1 0 36570.199 38473.860 25.000 33.000 NA NA NA NA 1.000 Poor Pending +chr14-94463231-94463232-G-T 269.SERPINA9.ENST00000337425.9.missense.390T/N 1 SERPINA9 T390N 1 ATTNKFIV ENST00000337425.9 1 HLA-E*01:01 4 None 1 0 36626.449 34268.950 26.000 19.000 NA NA NA NA 0.466 Poor Pending +chr3-52517959-52517960-A-C 60.STAB1.ENST00000321725.10.missense.1573H/P 1 STAB1 H1573P 1 APTVGDGL ENST00000321725.10 1 HLA-E*01:01 2 None 1 0 36649.441 42570.660 26.000 58.000 NA NA NA NA 1.000 Poor Pending +chr1-86453473-86453474-G-A 16.CLCA2.ENST00000370565.4.missense.754G/E 1 CLCA2 G754E 1 EVPAGPHP ENST00000370565.4 1 HLA-E*01:01 1 None 1 0 36736.781 39491.560 26.000 37.000 NA NA NA NA 0.576 Poor Pending +chr6-43216393-43216394-A-C 145.CUL9.ENST00000252050.8.missense.2058H/P 1 CUL9 H2058P 1 CVPQAQAV ENST00000252050.8 5 HLA-E*01:01 3 None 1 0 36889.719 43625.400 26.000 68.000 NA NA NA NA 0.656 Poor Pending +chr14-23425383-23425384-T-G 257.MYH7.ENST00000355349.3.missense.774E/A 1 MYH7 E774A 1 AEMRDERL ENST00000355349.3 1 HLA-E*01:01 1 None 1 0 36911.680 38330.090 26.000 32.000 NA NA NA NA 0.200 Poor Pending +chr6-52492272-52492273-A-C 160.EFHC1.ENST00000371068.10.missense.619I/L 1 EFHC1 I619L 1 LVKELLRM ENST00000371068.10 1 HLA-E*01:01 6 None 1 0 36915.281 38360.360 26.000 32.000 NA NA NA NA 0.545 Poor Pending +chr6-43283594-43283595-A-T 146.TTBK1.ENST00000259750.8.missense.952E/V 1 TTBK1 E952V 1 QALRSVEF ENST00000259750.8 1 HLA-E*01:01 6 None 1 0 36960.852 39158.820 27.000 36.000 NA NA NA NA 0.280 Poor Pending +chr14-24068642-24068643-G-A 258.CARMIL3.ENST00000342740.5.missense.1248E/K 1 CARMIL3 E1248K 1 KEEKEGTL ENST00000342740.5 5 HLA-E*01:01 1 None 1 0 36987.250 39158.390 27.000 36.000 NA NA NA NA 0.178 Poor Pending +chr7-140024672-140024681-TCAAAGATCA-T 188.PARP12.ENST00000263549.7.inframe_del.662-665VIFE/E 1 PARP12 VIFE662-665E 1 VSDPSIFE ENST00000263549.7 1 HLA-E*01:01 7-8 None 1 0 36994.449 29973.150 27.000 9.800 NA NA NA NA 0.129 Poor Pending +chrX-131544869-131544870-A-C 403.OR13H1.ENST00000338616.5.missense.266Y/S 1 OR13H1 Y266S 1 TQSKSSPD ENST00000338616.5 NA HLA-E*01:01 6 None 1 0 37047.340 38580.970 27.000 33.000 NA NA NA NA 1.000 Poor Pending +chr16-70146184-70146185-A-T 299.PDPR.ENST00000288050.8.missense.640Y/F 1 PDPR Y640F 1 ELSFAPMT ENST00000288050.8 1 HLA-E*01:01 4 None 1 0 37243.051 35176.950 28.000 21.000 NA NA NA NA 0.405 Poor Pending +chr6-30986467-30986468-T-C 119.MUC21.ENST00000376296.3.missense.98V/A 1 MUC21 V98A 1 TASSGISI ENST00000376296.3 1 HLA-E*01:01 2 None 1 0 37243.871 38206.280 28.000 31.000 NA NA NA NA 0.664 Poor Pending +chr18-80136551-80136552-C-T 329.ADNP2.ENST00000262198.8.missense.380P/L 1 ADNP2 P380L 1 SQPVGLVN ENST00000262198.8 1 HLA-E*01:01 6 None 1 0 37589.191 33988.680 29.000 18.000 NA NA NA NA 0.932 Poor Pending +chr6-14131622-14131623-A-G 102.CD83.ENST00000379153.3.missense.86N/S 1 CD83 N86S 1 PSERPYSL ENST00000379153.3 1 HLA-E*01:01 2 None 1 0 37658.781 39448.440 29.000 37.000 NA NA NA NA 0.979 Poor Pending +chr15-49282070-49282071-G-T 275.GALK2.ENST00000560031.5.missense.197A/S 1 GALK2 A197S 1 SEEGTAKL ENST00000560031.5 1 HLA-E*01:01 1 None 1 0 37666.941 36424.500 29.000 25.000 NA NA NA NA 1.000 Poor Pending +chr3-58210851-58210852-G-C 62.DNASE1L3.ENST00000394549.6.missense.19L/V 1 DNASE1L3 L19V 1 SIHSAVAM ENST00000394549.6 1 HLA-E*01:01 6 None 1 0 37677.121 33961.840 29.000 18.000 NA NA NA NA 1.000 Poor Pending +chr9-35609475-35609476-C-T 203.TESK1.ENST00000620767.4.missense.539H/Y 1 TESK1 H539Y 1 WNRAQYSL ENST00000620767.4 5 HLA-E*01:01 6 None 1 0 37719.160 39565.130 29.000 38.000 NA NA NA NA 1.000 Poor Pending +chr6-52236940-52236941-T-C 159.IL17F.ENST00000336123.4.missense.161H/R 1 IL17F H161R 1 VTPVIHRV ENST00000336123.4 1 HLA-E*01:01 7 None 1 0 37738.328 39105.070 29.000 35.000 NA NA NA NA 0.353 Poor Pending +chr6-31112238-31112239-C-G 121.C6orf15.ENST00000259870.3.missense.40L/F 1 C6orf15 L40F 1 FGTNLPQL ENST00000259870.3 1 HLA-E*01:01 1 None 1 0 37783.289 31669.800 30.000 14.000 NA NA NA NA 0.684 Poor Pending +chr7-122013415-122013416-A-G 185.PTPRZ1.ENST00000393386.6.missense.1457N/S 1 PTPRZ1 N1457S 1 VMSDSDTH ENST00000393386.6 1 HLA-E*01:01 3 None 1 0 37831.539 40080.870 30.000 41.000 NA NA NA NA 0.234 Poor Pending +chr6-3010155-3010156-C-T 95.NQO2.ENST00000380455.8.missense.47L/F 1 NQO2 L47F 1 AMNFEPRA ENST00000380455.8 1 HLA-E*01:01 4 None 1 0 37924.172 39421.960 30.000 37.000 NA NA NA NA 0.451 Poor Pending +chr14-94382907-94382908-C-G 268.SERPINA1.ENST00000448921.5.missense.110E/D 1 SERPINA1 E110D 1 TDIPEAQI ENST00000448921.5 1 HLA-E*01:01 2 None 1 0 37941.000 33259.270 30.000 17.000 NA NA NA NA 0.174 Poor Pending +chr3-122927970-122927971-G-C 64.SEMA5B.ENST00000451055.6.missense.277I/M 1 SEMA5B I277M 1 LSRTTEKM ENST00000451055.6 2 HLA-E*01:01 8 None 1 0 38028.941 39577.960 31.000 38.000 NA NA NA NA 1.000 Poor Pending +chr1-227091907-227091908-T-G 30.CDC42BPA.ENST00000366769.7.missense.778K/T 1 CDC42BPA K778T 1 LTEENKTL ENST00000366769.7 1 HLA-E*01:01 7 None 1 0 38121.219 38545.110 31.000 33.000 NA NA NA NA 0.273 Poor Pending +chr2-201835739-201835740-A-C 48.CDK15.ENST00000450471.6.missense.276E/D 1 CDK15 E276D 1 ATDYSSEL ENST00000450471.6 1 HLA-E*01:01 3 None 1 0 38131.941 37533.910 31.000 29.000 NA NA NA NA 0.568 Poor Pending +chrX-34131149-34131150-C-A 380.FAM47A.ENST00000346193.4.missense.377A/S 1 FAM47A A377S 1 SEPSKTGV ENST00000346193.4 NA HLA-E*01:01 1 None 1 0 38136.070 36913.680 31.000 26.000 NA NA NA NA 0.990 Poor Pending +chr2-216428741-216428742-C-G 49.SMARCAL1.ENST00000357276.8.missense.432L/V 1 SMARCAL1 L432V 1 VVSNLMPF ENST00000357276.8 2 HLA-E*01:01 1 None 1 0 38169.090 39765.110 31.000 39.000 NA NA NA NA 0.457 Poor Pending +chr8-125028638-125028639-T-C 196.WASHC5.ENST00000318410.11.missense.1135Y/C 1 WASHC5 Y1135C 1 DYVRCTKL ENST00000318410.11 1 HLA-E*01:01 5 None 1 0 38188.930 39332.930 31.000 37.000 NA NA NA NA 0.133 Poor Pending +chr6-31161532-31161533-C-T 124.TCF19.ENST00000376257.7.missense.109P/S 1 TCF19 P109S 1 SPGTSPSE ENST00000376257.7 1 HLA-E*01:01 1 None 1 0 38214.980 40371.160 31.000 42.000 NA NA NA NA 0.671 Poor Pending +chrX-2917995-2917996-G-C 368.ARSD.ENST00000381154.5.missense.224S/C 1 ARSD S224C 1 CVSARAVT ENST00000381154.5 1 HLA-E*01:01 1 None 1 0 38246.809 37802.900 32.000 30.000 NA NA NA NA 0.542 Poor Pending +chr19-35841840-35841841-C-A 343.NPHS1.ENST00000378910.9.missense.897G/C 1 NPHS1 G897C 1 CGVHSSLL ENST00000378910.9 1 HLA-E*01:01 1 None 1 0 38257.590 40671.950 32.000 44.000 NA NA NA NA 0.087 Poor Pending +chr6-42104971-42104977-ACTCCTC-A 141.C6orf132.ENST00000341865.8.inframe_del.979-980EE/- 1 C6orf132 EE979-980- 1 REEEEFNF ENST00000341865.8 5 HLA-E*01:01 5-6 None 1 0 38289.059 42149.010 32.000 55.000 NA NA NA NA 0.700 Poor Pending +chr6-24503361-24503362-C-T 106.ALDH5A1.ENST00000348925.2.missense.180H/Y 1 ALDH5A1 H180Y 1 RVYGDIIY ENST00000348925.2 1 HLA-E*01:01 8 None 1 0 38323.031 42243.520 32.000 56.000 NA NA NA NA 0.727 Poor Pending +chr13-98431277-98431278-G-T 254.FARP1.ENST00000627049.2.missense.714R/L 1 FARP1 R714L 1 CLAALAEI ENST00000627049.2 5 HLA-E*01:01 2 None 1 0 38324.289 42429.940 32.000 57.000 NA NA NA NA 1.000 Poor Pending +chrX-77682470-77682471-C-G 391.ATRX.ENST00000373344.10.missense.929E/Q 1 ATRX E929Q 1 KEQSFTSL ENST00000373344.10 1 HLA-E*01:01 3 None 1 0 38332.988 39309.520 32.000 36.000 NA NA NA NA 0.951 Poor Pending +chr18-80138228-80138229-G-T 330.ADNP2.ENST00000262198.8.missense.939R/I 1 ADNP2 R939I 1 VRCISAPK ENST00000262198.8 1 HLA-E*01:01 4 None 1 0 38369.910 35070.160 32.000 21.000 NA NA NA NA 1.000 Poor Pending +chr19-16093698-16093699-G-C 340.TPM4.ENST00000646974.1.missense.240E/Q 1 TPM4 E240Q 1 EAETRAQF ENST00000646974.1 NA HLA-E*01:01 7 None 1 0 38433.070 39585.240 32.000 38.000 NA NA NA NA 0.484 Poor Pending +chrX-38367349-38367350-A-G 381.OTC.ENST00000039007.4.missense.46K/R 1 OTC K46R 1 LLTLRNFT ENST00000039007.4 1 HLA-E*01:01 5 None 1 0 38468.852 40362.440 32.000 42.000 NA NA NA NA 1.000 Poor Pending +chr1-150261628-150261629-G-A 19.CA14.ENST00000369111.8.missense.83G/S 1 CA14 G83S 1 NNSHTVQL ENST00000369111.8 1 HLA-E*01:01 3 None 1 0 38474.262 39769.830 33.000 39.000 NA NA NA NA 0.338 Poor Pending +chrX-32389609-32389610-C-T 379.DMD.ENST00000357033.8.missense.1470R/H 1 DMD R1470H 1 HLQESKMI ENST00000357033.8 1 HLA-E*01:01 1 None 1 0 38547.180 31553.520 33.000 14.000 NA NA NA NA 1.000 Poor Pending +chr6-46662451-46662452-C-G 155.SLC25A27.ENST00000371347.9.missense.154Q/E 1 SLC25A27 Q154E 1 LVKVEMQM ENST00000371347.9 1 HLA-E*01:01 5 None 1 0 38547.602 38098.140 33.000 31.000 NA NA NA NA 0.500 Poor Pending +chr6-17632829-17632830-C-T 104.NUP153.ENST00000537253.5.missense.858A/T 1 NUP153 A858T 1 KPGSSVPT ENST00000537253.5 2 HLA-E*01:01 8 None 1 0 38569.301 40151.630 33.000 41.000 NA NA NA NA 0.967 Poor Pending +chr6-31505783-31505784-A-G 125.MICB.ENST00000252229.6.missense.80K/E 1 MICB K80E 1 VLGAETWD ENST00000252229.6 1 HLA-E*01:01 5 None 1 0 38613.559 36194.670 33.000 24.000 NA NA NA NA 0.750 Poor Pending +chr9-120858190-120858191-G-A 207.PHF19.ENST00000616568.5.missense.518P/L 1 PHF19 P518L 1 AELDGRCL ENST00000616568.5 1 HLA-E*01:01 8 None 1 0 38679.211 45699.580 33.000 91.000 NA NA NA NA 0.500 Poor Pending +chr9-137199427-137199428-T-A 211.TPRN.ENST00000409012.5.missense.428E/D 1 TPRN E428D 1 FLPAASDE ENST00000409012.5 1 HLA-E*01:01 7 None 1 0 38685.070 37201.570 33.000 27.000 NA NA NA NA 0.283 Poor Pending +chr11-56542446-56542447-T-C 231.OR5M11.ENST00000528616.4.missense.271K/E 1 OR5M11 K271E 1 TVEESEII ENST00000528616.4 NA HLA-E*01:01 6 None 1 0 38729.879 38815.870 34.000 34.000 NA NA NA NA 0.280 Poor Pending +chr14-39247882-39247883-G-C 262.MIA2.ENST00000640607.1.missense.437D/H 1 MIA2 D437H 1 IIETEHQI ENST00000640607.1 1 HLA-E*01:01 6 None 1 0 38731.121 42203.760 34.000 55.000 NA NA NA NA 0.983 Poor Pending +chr20-59301546-59301547-G-T 353.EDN3.ENST00000337938.6.missense.64G/W 1 EDN3 G64W 1 AGPGEWTV ENST00000337938.6 1 HLA-E*01:01 6 None 1 0 38794.891 40748.140 34.000 45.000 NA NA NA NA 0.216 Poor Pending +chr14-91783159-91783160-T-A 267.TC2N.ENST00000435962.6.missense.471K/N 1 TC2N K471N 1 NQWNETVI ENST00000435962.6 2 HLA-E*01:01 4 None 1 0 38844.020 35774.570 34.000 23.000 NA NA NA NA 0.154 Poor Pending +chr10-125729432-125729433-C-G 220.EDRF1.ENST00000356792.8.missense.324P/A 1 EDRF1 P324A 1 VGSNMAIF ENST00000356792.8 1 HLA-E*01:01 6 None 1 0 38851.180 28587.990 34.000 8.200 NA NA NA NA 0.163 Poor Pending +chr18-14106118-14106119-G-C 326.ZNF519.ENST00000590202.2.missense.141P/A 1 ZNF519 P141A 1 PTEPCIAM ENST00000590202.2 1 HLA-E*01:01 7 None 1 0 38853.691 34409.380 34.000 19.000 NA NA NA NA 0.445 Poor Pending +chr11-62752450-62752451-G-A 234.ZBTB3.ENST00000394807.3.missense.455S/F 1 ZBTB3 S455F 1 HEPLYLSF ENST00000394807.3 1 HLA-E*01:01 8 None 1 0 38889.430 44254.850 34.000 75.000 NA NA NA NA 0.673 Poor Pending +chr5-141123692-141123693-G-C 89.PCDHB4.ENST00000194152.3.missense.565Q/H 1 PCDHB4 Q565H 1 LHNGSAPC ENST00000194152.3 NA HLA-E*01:01 2 None 1 0 38893.648 34644.000 34.000 20.000 NA NA NA NA 0.327 Poor Pending +chr22-37374977-37374978-G-A 357.ELFN2.ENST00000402918.6.missense.186P/L 1 ELFN2 P186L 1 VCELAGNL ENST00000402918.6 4 HLA-E*01:01 8 None 1 0 38927.750 45509.120 35.000 89.000 NA NA NA NA 0.165 Poor Pending +chr6-31765688-31765689-T-C 127.VWA7.ENST00000375688.4.missense.861T/A 1 VWA7 T861A 1 FSPFTLVA ENST00000375688.4 5 HLA-E*01:01 8 None 1 0 38938.301 37678.360 35.000 29.000 NA NA NA NA 0.700 Poor Pending +chr17-82961144-82961145-G-C 325.B3GNTL1.ENST00000320865.3.missense.213L/V 1 B3GNTL1 L213V 1 VRKGGGVI ENST00000320865.3 1 HLA-E*01:01 1 None 1 0 39052.621 39971.290 35.000 40.000 NA NA NA NA 0.211 Poor Pending +chr16-57025571-57025572-C-T 291.NLRC5.ENST00000262510.10.missense.210S/L 1 NLRC5 S210L 1 ADVSILDL ENST00000262510.10 5 HLA-E*01:01 6 None 1 0 39058.109 43072.440 35.000 63.000 NA NA NA NA 0.633 Poor Pending +chr6-30926163-30926164-G-A 116.VARS2.ENST00000541562.5.missense.1079R/Q 1 VARS2 R1079Q 1 AASHLQQL ENST00000541562.5 2 HLA-E*01:01 6 None 1 0 39096.160 39452.690 35.000 37.000 NA NA NA NA 0.788 Poor Pending +chr19-5928080-5928081-C-G 332.RANBP3.ENST00000340578.10.missense.234E/Q 1 RANBP3 E234Q 1 KQPQKNES ENST00000340578.10 1 HLA-E*01:01 2 None 1 0 39248.750 42874.370 36.000 61.000 NA NA NA NA 0.987 Poor Pending +chr12-889169-889170-C-G 243.WNK1.ENST00000340908.8.missense.2051Q/E 1 WNK1 Q2051E 1 ELRRTLSP ENST00000340908.8 5 HLA-E*01:01 1 None 1 0 39271.691 37697.930 36.000 29.000 NA NA NA NA 0.612 Poor Pending +chrX-2861528-2861529-A-G 367.GYG2.ENST00000381163.7.missense.313H/R 1 GYG2 H313R 1 SPGHTLCR ENST00000381163.7 1 HLA-E*01:01 8 None 1 0 39273.391 38846.550 36.000 34.000 NA NA NA NA 0.508 Poor Pending +chr9-37784015-37784016-T-A 204.EXOSC3.ENST00000327304.9.missense.124K/N 1 EXOSC3 K124N 1 TANSGDIF ENST00000327304.9 1 HLA-E*01:01 3 None 1 0 39297.199 35832.290 36.000 23.000 NA NA NA NA 0.489 Poor Pending +chrX-133304843-133304844-C-A 405.GPC4.ENST00000370828.3.missense.391E/D 1 GPC4 E391D 1 VTDVKDKL ENST00000370828.3 1 HLA-E*01:01 6 None 1 0 39369.980 38082.050 37.000 31.000 NA NA NA NA 1.000 Poor Pending +chr15-74280668-74280669-G-T 279.CCDC33.ENST00000398814.7.missense.297M/I 1 CCDC33 M297I 1 IKGSQPWT ENST00000398814.7 2 HLA-E*01:01 1 None 1 0 39387.020 31761.080 37.000 14.000 NA NA NA NA 0.575 Poor Pending +chr6-26509101-26509102-C-G 110.BTN1A1.ENST00000244513.10.missense.503D/E 1 BTN1A1 D503E 1 MGEESAPR ENST00000244513.10 1 HLA-E*01:01 4 None 1 0 39486.000 41012.200 37.000 47.000 NA NA NA NA 0.719 Poor Pending +chr12-31697921-31697922-G-T 245.AMN1.ENST00000281471.10.missense.118H/N 1 AMN1 H118N 1 SYLNEASL ENST00000281471.10 1 HLA-E*01:01 4 None 1 0 39496.680 38682.550 37.000 33.000 NA NA NA NA 0.441 Poor Pending +chr1-37721680-37721681-G-T 8.EPHA10.ENST00000373048.8.missense.709L/M 1 EPHA10 L709M 1 RMEGVVTR ENST00000373048.8 5 HLA-E*01:01 2 None 1 0 39503.102 43807.500 37.000 70.000 NA NA NA NA 0.388 Poor Pending +chr13-37746421-37746422-C-T 252.TRPC4.ENST00000625583.2.missense.138E/K 1 TRPC4 E138K 1 KQFSKFTP ENST00000625583.2 1 HLA-E*01:01 5 None 1 0 39529.172 41082.380 38.000 47.000 NA NA NA NA 0.516 Poor Pending +chr6-12124353-12124354-C-G 100.HIVEP1.ENST00000379388.6.missense.1520A/G 1 HIVEP1 A1520G 1 HGPPSHQS ENST00000379388.6 1 HLA-E*01:01 2 None 1 0 39551.430 37531.050 38.000 29.000 NA NA NA NA 0.977 Poor Pending +chrX-48560270-48560271-G-A 387.TBC1D25.ENST00000376771.8.missense.455A/T 1 TBC1D25 A455T 1 SQVADTGF ENST00000376771.8 1 HLA-E*01:01 6 None 1 0 39555.281 37701.600 38.000 29.000 NA NA NA NA 0.992 Poor Pending +chrX-2221144-2221145-C-T 365.DHRSX.ENST00000334651.10.missense.297E/K 1 DHRSX E297K 1 NKKETKSL ENST00000334651.10 1 HLA-E*01:01 2 None 1 0 39633.238 39714.370 38.000 39.000 NA NA NA NA 0.515 Poor Pending +chr8-132141242-132141243-C-G 199.KCNQ3.ENST00000388996.9.missense.451D/H 1 KCNQ3 D451H 1 TPLNVHAI ENST00000388996.9 1 HLA-E*01:01 6 None 1 0 39790.512 43193.300 39.000 64.000 NA NA NA NA 0.286 Poor Pending +chr17-7675087-7675088-C-T 317.TP53.ENST00000269305.8.missense.175R/H 1 TP53 R175H 1 VVRHCPHH ENST00000269305.8 1 HLA-E*01:01 4 None 1 0 39844.359 36460.370 39.000 25.000 NA NA NA NA 0.988 Poor Pending +chr6-56552483-56552484-C-T 165.DST.ENST00000312431.10.missense.3179M/I 1 DST M3179I 1 LKKLEALI ENST00000312431.10 5 HLA-E*01:01 8 None 1 0 39897.410 38744.120 40.000 34.000 NA NA NA NA 0.490 Poor Pending +chr7-77600798-77600799-C-T 174.PTPN12.ENST00000248594.10.missense.230H/Y 1 PTPN12 H230Y 1 VPICIYCS ENST00000248594.10 1 HLA-E*01:01 6 None 1 0 39908.648 41222.640 40.000 48.000 NA NA NA NA 0.192 Poor Pending +chr1-183880710-183880711-A-C 24.RGL1.ENST00000304685.8.missense.209Y/S 1 RGL1 Y209S 1 LLDSLTRM ENST00000304685.8 1 HLA-E*01:01 4 None 1 0 39947.090 40501.550 40.000 43.000 NA NA NA NA 0.314 Poor Pending +chr12-112043094-112043095-A-C 248.NAA25.ENST00000261745.8.missense.789S/R 1 NAA25 S789R 1 ELDTRGLE ENST00000261745.8 1 HLA-E*01:01 5 None 1 0 39958.328 41819.680 40.000 52.000 NA NA NA NA 1.000 Poor Pending +chr1-42775287-42775288-A-G 10.C1orf50.ENST00000372525.6.missense.165D/G 1 C1orf50 D165G 1 TPYEGIEK ENST00000372525.6 1 HLA-E*01:01 5 None 1 0 40037.520 43105.530 40.000 63.000 NA NA NA NA 0.111 Poor Pending +chrX-133303308-133303309-G-A 404.GPC4.ENST00000370828.3.missense.442A/V 1 GPC4 A442V 1 AVTGNGLV ENST00000370828.3 1 HLA-E*01:01 8 None 1 0 40088.680 43919.040 41.000 71.000 NA NA NA NA 0.976 Poor Pending +chr9-138120681-138120682-G-A 213.CACNA1B.ENST00000371372.5.missense.2097G/D 1 CACNA1B G2097D 1 PPGEGPTD ENST00000371372.5 5 HLA-E*01:01 8 None 1 0 40113.840 39996.380 41.000 40.000 NA NA NA NA 0.280 Poor Pending +chr11-70087776-70087777-C-T 239.ANO1.ENST00000355303.9.missense.45P/L 1 ANO1 P45L 1 LNSLSVDL ENST00000355303.9 1 HLA-E*01:01 8 None 1 0 40271.699 46282.270 42.000 96.000 NA NA NA NA 0.181 Poor Pending +chr15-45133932-45133933-G-A 274.DUOX1.ENST00000321429.8.missense.43R/K 1 DUOX1 R43K 1 LMEHKWGS ENST00000321429.8 1 HLA-E*01:01 5 None 1 0 40320.531 38077.950 42.000 31.000 NA NA NA NA 1.000 Poor Pending +chr17-4818361-4818376-TGGACAGAATCCTGAA-T 314.PLD2.ENST00000263088.10.inframe_del.662-667VDRILK/V 1 PLD2 VDRILK662-667V 1 VAHKQGWC ENST00000263088.10 1 HLA-E*01:01 1-2 None 1 0 40351.090 42563.300 42.000 58.000 NA NA NA NA 0.310 Poor Pending +chr6-43340177-43340178-C-G 147.ZNF318.ENST00000361428.2.missense.1274G/R 1 ZNF318 G1274R 1 SSFRKFSW ENST00000361428.2 1 HLA-E*01:01 4 None 1 0 40376.422 42620.440 42.000 59.000 NA NA NA NA 0.344 Poor Pending +chr6-49517552-49517553-C-A 158.GLYATL3.ENST00000371197.8.missense.104Q/K 1 GLYATL3 Q104K 1 IKGLQSEL ENST00000371197.8 2 HLA-E*01:01 2 None 1 0 40411.379 36683.960 43.000 26.000 NA NA NA NA 0.442 Poor Pending +chrX-115191629-115191630-G-A 401.RBMXL3.ENST00000424776.4.missense.730R/Q 1 RBMXL3 R730Q 1 CSPDTYSQ ENST00000424776.4 NA HLA-E*01:01 8 None 1 0 40447.680 40925.750 43.000 46.000 NA NA NA NA 1.000 Poor Pending +chr20-23354058-23354059-C-G 350.NXT1.ENST00000254998.2.missense.6F/L 1 NXT1 F6L 1 MASVDLKT ENST00000254998.2 1 HLA-E*01:01 6 None 1 0 40470.012 38652.000 43.000 33.000 NA NA NA NA 0.391 Poor Pending +chr8-138737576-138737577-C-A 201.COL22A1.ENST00000303045.10.missense.696G/W 1 COL22A1 G696W 1 LRWKKGDM ENST00000303045.10 1 HLA-E*01:01 3 None 1 0 40555.500 42445.570 43.000 57.000 NA NA NA NA 0.190 Poor Pending +chr19-13765994-13765995-G-C 338.MRI1.ENST00000040663.7.missense.138R/T 1 MRI1 R138T 1 MLEKDLTD ENST00000040663.7 1 HLA-E*01:01 7 None 1 0 40584.461 40019.760 44.000 40.000 NA NA NA NA 0.228 Poor Pending +chr7-132508196-132508197-C-A 187.PLXNA4.ENST00000359827.7.missense.166S/I 1 PLXNA4 S166I 1 VNEIGSVF ENST00000359827.7 5 HLA-E*01:01 4 None 1 0 40605.090 37032.090 44.000 27.000 NA NA NA NA 0.286 Poor Pending +chr8-125102410-125102411-G-C 197.NSMCE2.ENST00000287437.7.missense.27L/F 1 NSMCE2 L27F 1 ALSSFKNF ENST00000287437.7 1 HLA-E*01:01 5 None 1 0 40633.230 42082.920 44.000 54.000 NA NA NA NA 0.265 Poor Pending +chr6-46167751-46167752-T-C 153.ENPP5.ENST00000371383.6.missense.171I/V 1 ENPP5 I171V 1 RVAKIVEW ENST00000371383.6 1 HLA-E*01:01 6 None 1 0 40633.672 39334.200 44.000 37.000 NA NA NA NA 0.745 Poor Pending +chr7-92077866-92077867-G-C 178.AKAP9.ENST00000356239.7.missense.2313D/H 1 AKAP9 D2313H 1 ITTHNKVI ENST00000356239.7 1 HLA-E*01:01 4 None 1 0 40655.211 40808.600 44.000 45.000 NA NA NA NA 0.413 Poor Pending +chr16-57046615-57046616-C-A 292.NLRC5.ENST00000262510.10.missense.1105Q/K 1 NLRC5 Q1105K 1 RKRCIPRS ENST00000262510.10 5 HLA-E*01:01 2 None 1 0 40685.141 37684.870 44.000 29.000 NA NA NA NA 0.688 Poor Pending +chr19-12580947-12580948-G-A 337.ZNF490.ENST00000311437.10.missense.376S/F 1 ZNF490 S376F 1 AFKSSSFC ENST00000311437.10 1 HLA-E*01:01 7 None 1 0 40687.352 44739.680 44.000 80.000 NA NA NA NA 0.352 Poor Pending +chr4-373601-373602-C-T 71.ZNF141.ENST00000240499.7.missense.389H/Y 1 ZNF141 H389Y 1 IYTGEKPY ENST00000240499.7 1 HLA-E*01:01 2 None 1 0 40691.762 40440.240 44.000 43.000 NA NA NA NA 0.917 Poor Pending +chr6-30931746-30931747-T-C 117.SFTA2.ENST00000359086.3.missense.37N/S 1 SFTA2 N37S 1 FLTSSSYE ENST00000359086.3 1 HLA-E*01:01 4 None 1 0 40710.230 42675.360 44.000 59.000 NA NA NA NA 0.628 Poor Pending +chr15-28843283-28843284-G-T 270.GOLGA6L7.ENST00000567390.6.missense.274Q/K 1 GOLGA6L7 Q274K 1 LREKEQQM ENST00000567390.6 5 HLA-E*01:01 4 None 1 0 40717.719 41971.990 44.000 54.000 NA NA NA NA 0.539 Poor Pending +chr1-119895935-119895936-C-T 17.ADAM30.ENST00000369400.1.missense.134R/Q 1 ADAM30 R134Q 1 MGGLQGVF ENST00000369400.1 NA HLA-E*01:01 5 None 1 0 40801.961 41001.540 45.000 46.000 NA NA NA NA 0.208 Poor Pending +chr6-56463050-56463051-C-T 164.DST.ENST00000312431.10.missense.5408A/T 1 DST A5408T 1 STEGTPIQ ENST00000312431.10 5 HLA-E*01:01 2 None 1 0 40835.078 39458.660 45.000 37.000 NA NA NA NA 0.481 Poor Pending +chrX-100987546-100987547-C-T 396.ARL13A.ENST00000450049.6.missense.215S/L 1 ARL13A S215L 1 CLSHSFST ENST00000450049.6 5 HLA-E*01:01 2 None 1 0 40885.039 43641.920 46.000 68.000 NA NA NA NA 1.000 Poor Pending +chr12-10159995-10159996-G-C 244.OLR1.ENST00000309539.7.missense.236Q/E 1 OLR1 Q236E 1 ETYPSGTC ENST00000309539.7 1 HLA-E*01:01 1 None 1 0 40891.238 39304.860 46.000 36.000 NA NA NA NA 0.195 Poor Pending +chrX-2859943-2859944-C-T 366.GYG2.ENST00000381163.7.missense.270A/V 1 GYG2 A270V 1 VLEQGSVS ENST00000381163.7 1 HLA-E*01:01 7 None 1 0 40939.922 43392.840 46.000 66.000 NA NA NA NA 0.485 Poor Pending +chr7-27130623-27130624-C-T 171.HOXA4.ENST00000360046.9.missense.37G/D 1 HOXA4 G37D 1 GPDGGPGY ENST00000360046.9 1 HLA-E*01:01 3 None 1 0 40944.359 39097.450 46.000 35.000 NA NA NA NA 0.375 Poor Pending +chr20-59944225-59944226-A-G 354.FAM217B.ENST00000358293.7.missense.95S/G 1 FAM217B S95G 1 DEDSAGDL ENST00000358293.7 2 HLA-E*01:01 6 None 1 0 40990.012 41036.170 46.000 47.000 NA NA NA NA 0.563 Poor Pending +chr3-121697676-121697677-G-C 63.GOLGB1.ENST00000393667.7.missense.949A/G 1 GOLGB1 A949G 1 LLSRAEEG ENST00000393667.7 1 HLA-E*01:01 8 None 1 0 41031.301 39998.140 47.000 40.000 NA NA NA NA 1.000 Poor Pending +chr1-196995755-196995756-A-G 25.CFHR5.ENST00000256785.4.missense.216N/S 1 CFHR5 N216S 1 GPPPQLSS ENST00000256785.4 1 HLA-E*01:01 8 None 1 0 41057.480 40998.000 47.000 46.000 NA NA NA NA 0.284 Poor Pending +chr2-219471924-219471925-A-G 50.SPEG.ENST00000312358.11.missense.1258Y/C 1 SPEG Y1258C 1 GPQHAGVC ENST00000312358.11 5 HLA-E*01:01 8 None 1 0 41075.250 40250.360 47.000 42.000 NA NA NA NA 0.340 Poor Pending +chr15-69049033-69049034-G-C 278.NOX5.ENST00000388866.7.missense.659D/H 1 NOX5 D659H 1 EMHQAEEA ENST00000388866.7 1 HLA-E*01:01 3 None 1 0 41082.379 41526.150 47.000 50.000 NA NA NA NA 0.393 Poor Pending +chr6-24576402-24576403-C-T 107.KIAA0319.ENST00000378214.7.missense.567G/S 1 KIAA0319 G567S 1 VLYEWSLS ENST00000378214.7 1 HLA-E*01:01 8 None 1 0 41191.410 41795.680 48.000 52.000 NA NA NA NA 0.668 Poor Pending +chr16-49281350-49281351-C-T 288.CBLN1.ENST00000219197.10.missense.39D/N 1 CBLN1 D39N 1 VVCNSNPT ENST00000219197.10 1 HLA-E*01:01 4 None 1 0 41220.859 41951.550 48.000 53.000 NA NA NA NA 0.213 Poor Pending +chr6-3723707-3723708-C-G 96.PXDC1.ENST00000380283.4.missense.203E/Q 1 PXDC1 E203Q 1 SEFPSQLE ENST00000380283.4 1 HLA-E*01:01 6 None 1 0 41248.059 41680.530 48.000 51.000 NA NA NA NA 0.419 Poor Pending +chr6-30685003-30685004-C-T 115.PPP1R18.ENST00000274853.7.missense.339G/R 1 PPP1R18 G339R 1 RKAREWTP ENST00000274853.7 1 HLA-E*01:01 1 None 1 0 41269.930 44446.800 48.000 77.000 NA NA NA NA 0.750 Poor Pending +chr11-46876561-46876562-C-T 230.LRP4.ENST00000378623.5.missense.1147R/Q 1 LRP4 R1147Q 1 NQIEVGNL ENST00000378623.5 1 HLA-E*01:01 2 None 1 0 41307.898 43377.370 48.000 66.000 NA NA NA NA 0.444 Poor Pending +chr7-102637601-102637602-C-T 182.UPK3BL1.ENST00000340457.8.missense.239G/S 1 UPK3BL1 G239S 1 SPEEAGSV ENST00000340457.8 1 HLA-E*01:01 1 None 1 0 41312.379 43178.340 48.000 64.000 NA NA NA NA 0.364 Poor Pending +chr6-32220605-32220606-T-C 129.NOTCH4.ENST00000375023.3.missense.320T/A 1 NOTCH4 T320A 1 CEAQGPPH ENST00000375023.3 1 HLA-E*01:01 3 None 1 0 41422.020 43308.410 49.000 65.000 NA NA NA NA 0.602 Poor Pending +chr22-37570267-37570268-C-G 358.LGALS2.ENST00000215886.5.missense.132E/Q 1 LGALS2 E132Q 1 MSSFKLKQ ENST00000215886.5 1 HLA-E*01:01 8 None 1 0 41458.801 41910.720 50.000 53.000 NA NA NA NA 0.484 Poor Pending +chr7-128815875-128815876-C-G 186.CCDC136.ENST00000297788.8.missense.1103S/C 1 CCDC136 S1103C 1 EDDADCSL ENST00000297788.8 1 HLA-E*01:01 6 None 1 0 41460.141 41128.630 50.000 47.000 NA NA NA NA 0.205 Poor Pending +chr2-227893862-227893863-C-T 53.DAW1.ENST00000309931.2.missense.129T/M 1 DAW1 T129M 1 NMLEGHRN ENST00000309931.2 1 HLA-E*01:01 2 None 1 0 41462.379 45967.350 50.000 93.000 NA NA NA NA 0.335 Poor Pending +chr6-47000271-47000272-C-T 156.ADGRF1.ENST00000371253.6.missense.895G/R 1 ADGRF1 G895R 1 RDSSDNIM ENST00000371253.6 1 HLA-E*01:01 1 None 1 0 41491.570 44894.360 50.000 82.000 NA NA NA NA 0.491 Poor Pending +chr11-193734-193735-G-A 223.SCGB1C1.ENST00000342878.2.missense.27D/N 1 SCGB1C1 D27N 1 NEFFMDFL ENST00000342878.2 1 HLA-E*01:01 1 None 1 0 41493.359 42301.610 50.000 56.000 NA NA NA NA 0.232 Poor Pending +chr16-87755257-87755258-G-A 310.KLHDC4.ENST00000270583.9.missense.102T/I 1 KLHDC4 T102I 1 IRKDTWTK ENST00000270583.9 1 HLA-E*01:01 1 None 1 0 41526.578 42820.590 50.000 61.000 NA NA NA NA 0.486 Poor Pending +chr2-53901384-53901385-G-C 36.PSME4.ENST00000404125.5.missense.1084H/D 1 PSME4 H1084D 1 IDRQYETI ENST00000404125.5 1 HLA-E*01:01 2 None 1 0 41530.199 40617.840 50.000 44.000 NA NA NA NA 0.364 Poor Pending +chr17-78484882-78484883-A-T 323.DNAH17.ENST00000389840.6.missense.2545M/K 1 DNAH17 M2545K 1 RQHKDHRH ENST00000389840.6 5 HLA-E*01:01 4 None 1 0 41625.551 43069.160 51.000 63.000 NA NA NA NA 0.229 Poor Pending +chrX-9937278-9937279-G-C 371.SHROOM2.ENST00000380913.7.missense.1245D/H 1 SHROOM2 D1245H 1 EKHQIKTL ENST00000380913.7 1 HLA-E*01:01 3 None 1 0 41632.770 42070.630 51.000 54.000 NA NA NA NA 1.000 Poor Pending +chr5-1331835-1331836-C-A 81.CLPTM1L.ENST00000320895.9.missense.313K/N 1 CLPTM1L K313N 1 WNKKKSMI ENST00000320895.9 1 HLA-E*01:01 2 None 1 0 41636.371 40311.820 51.000 42.000 NA NA NA NA 0.374 Poor Pending +chr4-110559663-110559664-G-C 77.ENPEP.ENST00000265162.9.missense.887R/T 1 ENPEP R887T 1 YTLNNTNL ENST00000265162.9 1 HLA-E*01:01 6 None 1 0 41772.641 43359.530 52.000 66.000 NA NA NA NA 0.238 Poor Pending +chr6-55351464-55351465-G-C 163.GFRAL.ENST00000340465.2.missense.195D/H 1 GFRAL D195H 1 AQSHIPCQ ENST00000340465.2 1 HLA-E*01:01 4 None 1 0 41795.250 41059.700 52.000 47.000 NA NA NA NA 0.506 Poor Pending +chr3-130409352-130409353-G-T 65.COL6A5.ENST00000265379.10.missense.1503G/W 1 COL6A5 G1503W 1 RGAPWQYG ENST00000265379.10 5 HLA-E*01:01 5 None 1 0 41799.320 41532.880 52.000 50.000 NA NA NA NA 0.328 Poor Pending +chr2-31366060-31366061-G-C 34.XDH.ENST00000379416.3.missense.791R/G 1 XDH R791G 1 IVVGVKRM ENST00000379416.3 1 HLA-E*01:01 4 None 1 0 41816.961 37928.280 52.000 30.000 NA NA NA NA 1.000 Poor Pending +chrX-38408966-38408967-A-G 382.OTC.ENST00000039007.4.missense.270Q/R 1 OTC Q270R 1 SMGREEEK ENST00000039007.4 1 HLA-E*01:01 4 None 1 0 41831.441 43507.090 52.000 67.000 NA NA NA NA 1.000 Poor Pending +chr6-55331788-55331789-C-T 162.GFRAL.ENST00000340465.2.missense.33R/C 1 GFRAL R33C 1 YLREQCLC ENST00000340465.2 1 HLA-E*01:01 8 None 1 0 41995.602 42393.240 54.000 57.000 NA NA NA NA 0.500 Poor Pending +chr6-32293729-32293730-T-C 130.TSBP1.ENST00000447241.6.missense.315I/V 1 TSBP1 I315V 1 ISEMSVPQ ENST00000447241.6 5 HLA-E*01:01 6 None 1 0 42103.879 42314.870 55.000 56.000 NA NA NA NA 0.647 Poor Pending +chr5-23521053-23521054-C-G 84.PRDM9.ENST00000296682.3.missense.128S/C 1 PRDM9 S128C 1 SFSNECSL ENST00000296682.3 1 HLA-E*01:01 6 None 1 0 42106.621 42132.590 55.000 55.000 NA NA NA NA 0.421 Poor Pending +chr19-6044262-6044263-G-C 333.RFX2.ENST00000303657.9.missense.37A/G 1 RFX2 A37G 1 VQAGSSNP ENST00000303657.9 1 HLA-E*01:01 4 None 1 0 42138.980 39646.960 55.000 38.000 NA NA NA NA 0.988 Poor Pending +chr20-2312957-2312958-C-T 347.TGM3.ENST00000381458.5.missense.201R/C 1 TGM3 R201C 1 RCDAATDV ENST00000381458.5 1 HLA-E*01:01 2 None 1 0 42247.629 42156.320 56.000 55.000 NA NA NA NA 0.652 Poor Pending +chr22-26540809-26540810-G-T 356.TPST2.ENST00000338754.8.missense.274P/H 1 TPST2 P274H 1 GKHGGVSL ENST00000338754.8 1 HLA-E*01:01 3 None 1 0 42291.980 34681.130 56.000 20.000 NA NA NA NA 0.209 Poor Pending +chr16-48231865-48231866-C-T 287.ABCC11.ENST00000394747.5.missense.19R/H 1 ABCC11 R19H 1 LVNHGIDI ENST00000394747.5 1 HLA-E*01:01 4 None 1 0 42307.090 38411.460 56.000 32.000 NA NA NA NA 0.739 Poor Pending +chr6-46140014-46140015-C-G 152.ENPP4.ENST00000321037.4.missense.144H/Q 1 ENPP4 H144Q 1 VPIQDTIS ENST00000321037.4 1 HLA-E*01:01 4 None 1 0 42327.699 42508.990 56.000 58.000 NA NA NA NA 0.729 Poor Pending +chr14-60724007-60724008-C-G 264.SIX4.ENST00000216513.4.missense.23E/Q 1 SIX4 E23Q 1 MQSASEGQ ENST00000216513.4 1 HLA-E*01:01 2 None 1 0 42340.531 42897.100 56.000 61.000 NA NA NA NA 1.000 Poor Pending +chrX-79171490-79171491-T-C 393.GPR174.ENST00000645147.1.missense.162S/P 1 GPR174 S162P 1 TPGNRTKC ENST00000645147.1 NA HLA-E*01:01 2 None 1 0 42355.629 43843.540 57.000 70.000 NA NA NA NA 1.000 Poor Pending +chr11-20638483-20638484-T-A 228.SLC6A5.ENST00000525748.5.missense.632V/E 1 SLC6A5 V632E 1 QLEDTYAA ENST00000525748.5 1 HLA-E*01:01 3 None 1 0 42393.699 42501.180 57.000 58.000 NA NA NA NA 0.468 Poor Pending +chr20-10054508-10054509-G-C 349.ANKEF1.ENST00000378380.4.missense.694K/N 1 ANKEF1 K694N 1 VPTTSEGN ENST00000378380.4 2 HLA-E*01:01 8 None 1 0 42624.121 41710.330 59.000 51.000 NA NA NA NA 0.532 Poor Pending +chr7-82908982-82908983-C-G 175.PCLO.ENST00000333891.13.missense.4444W/S 1 PCLO W4444S 1 REETDSFD ENST00000333891.13 2 HLA-E*01:01 6 None 1 0 42628.270 41961.540 59.000 53.000 NA NA NA NA 0.411 Poor Pending +chr11-46728135-46728136-T-C 229.F2.ENST00000311907.9.missense.424V/A 1 F2 V424A 1 LLARIGKH ENST00000311907.9 1 HLA-E*01:01 3 None 1 0 42660.590 44251.510 59.000 75.000 NA NA NA NA 0.358 Poor Pending +chr6-42938645-42938646-G-T 144.CNPY3.ENST00000372836.4.missense.231S/I 1 CNPY3 S231I 1 IRAKAAGG ENST00000372836.4 1 HLA-E*01:01 1 None 1 0 42668.891 44538.270 59.000 78.000 NA NA NA NA 0.700 Poor Pending +chr6-36301947-36301948-A-G 137.PNPLA1.ENST00000394571.3.missense.288E/G 1 PNPLA1 E288G 1 GCPERSQP ENST00000394571.3 1 HLA-E*01:01 1 None 1 0 42716.000 41259.660 60.000 48.000 NA NA NA NA 0.620 Poor Pending +chr7-151181249-151181250-C-T 189.ASB10.ENST00000420175.2.missense.265D/N 1 ASB10 D265N 1 ITNAEATT ENST00000420175.2 1 HLA-E*01:01 3 None 1 0 42772.898 41994.700 60.000 54.000 NA NA NA NA 0.157 Poor Pending +chr16-74661180-74661181-G-T 304.RFWD3.ENST00000361070.8.missense.90T/N 1 RFWD3 T90N 1 VLGEDNVE ENST00000361070.8 1 HLA-E*01:01 6 None 1 0 42779.359 40537.950 60.000 43.000 NA NA NA NA 0.650 Poor Pending +chrX-149548665-149548666-C-T 408.HSFX3.ENST00000431993.3.missense.243R/H 1 HSFX3 R243H 1 SFRHSGMW ENST00000431993.3 3 HLA-E*01:01 4 None 1 0 42790.469 40876.180 60.000 46.000 NA NA NA NA 1.000 Poor Pending +chrX-154349376-154349377-C-G 411.FLNA.ENST00000369850.8.missense.2581D/H 1 FLNA D2581H 1 QKSSFTVH ENST00000369850.8 1 HLA-E*01:01 8 None 1 0 43084.551 44142.940 63.000 74.000 NA NA NA NA 0.992 Poor Pending +chrX-101277632-101277633-T-C 398.TAF7L.ENST00000372907.7.missense.308S/G 1 TAF7L S308G 1 LISSGMSG ENST00000372907.7 1 HLA-E*01:01 8 None 1 0 43159.660 43143.800 64.000 64.000 NA NA NA NA 1.000 Poor Pending +chr9-113369791-113369792-G-A 206.BSPRY.ENST00000374183.4.missense.287A/T 1 BSPRY A287T 1 NGLHTWMV ENST00000374183.4 1 HLA-E*01:01 5 None 1 0 43286.891 42473.120 65.000 58.000 NA NA NA NA 0.541 Poor Pending +chr22-46257698-46257699-G-A 361.PKDREJ.ENST00000253255.6.missense.1875T/I 1 PKDREJ T1875I 1 IYGSGGYA ENST00000253255.6 NA HLA-E*01:01 1 None 1 0 43359.531 44278.320 66.000 75.000 NA NA NA NA 0.266 Poor Pending +chr2-47806319-47806320-G-A 35.MSH6.ENST00000234420.9.missense.1255D/N 1 MSH6 D1255N 1 VENYSQNV ENST00000234420.9 1 HLA-E*01:01 3 None 1 0 43380.172 42867.870 66.000 61.000 NA NA NA NA 0.330 Poor Pending +chr3-56617278-56617279-G-C 61.CCDC66.ENST00000394672.7.missense.671E/Q 1 CCDC66 E671Q 1 QDKGASLQ ENST00000394672.7 1 HLA-E*01:01 8 None 1 0 43519.801 43893.390 67.000 71.000 NA NA NA NA 1.000 Poor Pending +chrX-26194359-26194360-G-C 378.MAGEB6.ENST00000379034.1.missense.172G/R 1 MAGEB6 G172R 1 VAAEREDE ENST00000379034.1 1 HLA-E*01:01 5 None 1 0 43573.969 43128.860 68.000 63.000 NA NA NA NA 1.000 Poor Pending +chr6-43567280-43567281-C-T 148.XPO5.ENST00000265351.11.missense.241S/N 1 XPO5 S241N 1 SMNHITAE ENST00000265351.11 1 HLA-E*01:01 3 None 1 0 43638.148 42690.120 68.000 59.000 NA NA NA NA 0.787 Poor Pending +chrX-71378281-71378287-GAGATAT-G 389.TAF1.ENST00000423759.5.inframe_del.347-349GDI/G 1 TAF1 GDI347-349G 1 SQSTGDKV ENST00000423759.5 5 HLA-E*01:01 6-7 None 1 0 43641.469 44716.910 68.000 80.000 NA NA NA NA 1.000 Poor Pending +chr6-13611845-13611846-A-G 101.SIRT5.ENST00000606117.1.missense.305E/G 1 SIRT5 E305G 1 ALACHGNE ENST00000606117.1 1 HLA-E*01:01 6 None 1 0 44074.211 44236.190 73.000 75.000 NA NA NA NA 0.983 Poor Pending +chr17-45119014-45119029-TAGACGGTCGTTGTTG-T 322.PLCD3.ENST00000619929.4.inframe_del.233-238SNNDRL/S 1 PLCD3 SNNDRL233-238S 1 DHSEGAEI ENST00000619929.4 1 HLA-E*01:01 3-4 None 1 0 44102.852 44708.210 73.000 80.000 NA NA NA NA 1.000 Poor Pending +chr16-58045222-58045223-A-G 295.MMP15.ENST00000219271.3.missense.596D/G 1 MMP15 D596G 1 VGGGDGDF ENST00000219271.3 1 HLA-E*01:01 3 None 1 0 44138.641 43807.050 74.000 70.000 NA NA NA NA 0.479 Poor Pending +chr6-38805516-38805517-G-A 140.DNAH8.ENST00000327475.10.missense.1024G/E 1 DNAH8 G1024E 1 VVFGSETE ENST00000327475.10 5 HLA-E*01:01 8 None 1 0 44286.941 44829.790 75.000 81.000 NA NA NA NA 0.649 Poor Pending +chr19-6755017-6755018-T-C 334.SH2D3A.ENST00000245908.10.missense.265E/G 1 SH2D3A E265G 1 GEENRCFT ENST00000245908.10 1 HLA-E*01:01 1 None 1 0 44345.441 43094.330 76.000 63.000 NA NA NA NA 0.984 Poor Pending +chrX-151181398-151181399-A-G 409.GPR50.ENST00000218316.3.missense.606I/V 1 GPR50 I606V 1 VDVEDDPD ENST00000218316.3 1 HLA-E*01:01 1 None 1 0 44390.078 44692.750 76.000 80.000 NA NA NA NA 1.000 Poor Pending +chr1-203347717-203347718-G-C 26.FMOD.ENST00000354955.4.missense.185H/D 1 FMOD H185D 1 LHLDDNQI ENST00000354955.4 1 HLA-E*01:01 5 None 1 0 44542.121 44624.610 78.000 79.000 NA NA NA NA 0.298 Poor Pending +chrX-17726698-17726699-G-A 376.NHS.ENST00000380060.7.missense.844A/T 1 NHS A844T 1 KSDGNTDI ENST00000380060.7 1 HLA-E*01:01 6 None 1 0 44746.461 44075.660 80.000 73.000 NA NA NA NA 1.000 Poor Pending +chr6-49492264-49492265-A-G 157.CENPQ.ENST00000335783.3.missense.266D/G 1 CENPQ D266G 1 EEAYKKLG ENST00000335783.3 1 HLA-E*01:01 8 None 1 0 44753.699 44669.040 80.000 79.000 NA NA NA NA 0.421 Poor Pending +chrX-68717715-68717716-G-A 388.STARD8.ENST00000374599.7.missense.268G/S 1 STARD8 G268S 1 ATSASGSG ENST00000374599.7 1 HLA-E*01:01 5 None 1 0 44858.422 45597.340 81.000 89.000 NA NA NA NA 1.000 Poor Pending +chr15-43149136-43149137-G-C 273.TMEM62.ENST00000260403.6.missense.284W/C 1 TMEM62 W284C 1 CKDNRRYR ENST00000260403.6 1 HLA-E*01:01 1 None 1 0 44900.680 45342.980 82.000 87.000 NA NA NA NA 0.961 Poor Pending +chr6-70190343-70190344-G-C 167.COL19A1.ENST00000620364.4.missense.1019K/N 1 COL19A1 K1019N 1 FEEINKYI ENST00000620364.4 1 HLA-E*01:01 5 None 1 0 45054.930 44223.270 84.000 74.000 NA NA NA NA 0.246 Poor Pending +chr2-61348284-61348285-C-G 37.USP34.ENST00000398571.6.missense.624D/H 1 USP34 D624H 1 IEALKEEH ENST00000398571.6 5 HLA-E*01:01 8 None 1 0 45225.879 45620.520 85.000 90.000 NA NA NA NA 0.280 Poor Pending +chr1-227091906-227091907-GC-G 29.CDC42BPA.ENST00000366769.7.FS.778GC/G 1 CDC42BPA FS778 1 LLTEENKN ENST00000366769.7 1 HLA-E*01:01 8 None 1 0 45350.352 44737.740 87.000 80.000 NA NA NA NA 0.273 Poor Pending +chr6-31117165-31117168-GCTT-G 122.CDSN.ENST00000376288.2.inframe_del.149-150GS/G 1 CDSN GS149-150G 1 SHSGSSSH ENST00000376288.2 1 HLA-E*01:01 7-8 None 1 0 45665.461 46080.410 90.000 94.000 NA NA NA NA 0.693 Poor Pending +chr21-30755335-30755336-C-T 355.KRTAP21-1.ENST00000335093.4.missense.15G/S 1 KRTAP21-1 G15S 1 SSCGCGYG ENST00000335093.4 NA HLA-E*01:01 2 None 1 0 45714.410 46070.930 91.000 94.000 NA NA NA NA 0.472 Poor Pending +chr11-6410863-6410864-C-T 227.APBB1.ENST00000609360.5.missense.162E/K 1 APBB1 E162K 1 GEAEEEEK ENST00000609360.5 5 HLA-E*01:01 8 None 1 0 46646.738 46668.980 99.000 99.000 NA NA NA NA 1.000 Poor Pending diff --git a/tests/test_data/pvacseq/problematic_amino_acids/MHC_Class_I/Test.all_epitopes.aggregated.tsv b/tests/test_data/pvacseq/problematic_amino_acids/MHC_Class_I/Test.all_epitopes.aggregated.tsv index 6019434d..af7d4984 100644 --- a/tests/test_data/pvacseq/problematic_amino_acids/MHC_Class_I/Test.all_epitopes.aggregated.tsv +++ b/tests/test_data/pvacseq/problematic_amino_acids/MHC_Class_I/Test.all_epitopes.aggregated.tsv @@ -8,17 +8,17 @@ ID Index E*01:01 G*01:09 Gene AA Change Num Passing Transcripts Best Peptide Bes 22-50682229-50682230-T-C 23.TUBGCP6.ENST00000248846.5.missense.220H/R 1 TUBGCP6 H220R 1 RSRTYDMDV ENST00000248846.5 Not Supported HLA-G*01:09 1 None 1 0 4576.120 7609.380 6.300 15.000 NA NA NA NA 0.686 Poor Pending 2-217498305-217498305-T-TGCTGCC 1.IGFBP2.ENST00000233809.4.inframe_ins.20L/LLP 1 1 IGFBP2 L20LLP 1 LLPLLPLLL ENST00000233809.4 Not Supported HLA-E*01:01 6-7 None 1 0 4721.430 6167.260 0.785 1.265 NA NA NA NA 0.891 Poor Pending 22-19175521-19175522-G-T 7.CLTCL1.ENST00000263200.10.missense.1469H/N 1 CLTCL1 H1469N 1 SVNEALNNL ENST00000263200.10 Not Supported HLA-G*01:09 8 None 1 0 4989.870 7775.840 7.300 15.000 NA NA NA NA 0.100 Poor Pending -22-18020271-18020272-G-A 5.CECR2.ENST00000262608.8.missense.535R/H CECR2 R535H 0 WTHSRDPEG ENST00000262608.8 Not Supported HLA-G*01:09 3 None 0 0 5500.220 19932.310 8.400 40.000 NA NA NA NA 0.071 Poor Pending -22-50869713-50869714-C-A 24.PPP6R2.ENST00000395741.3.missense.414S/Y PPP6R2 S414Y 0 GYESRVEPP ENST00000395741.3 Not Supported HLA-G*01:09 2 None 0 0 5620.540 22209.930 8.700 44.000 NA NA NA NA 0.043 Poor Pending -22-20709231-20709232-G-C 8.FAM230A.ENST00000434783.3.missense.322E/Q FAM230A E322Q 0 ANQDAAQGI ENST00000434783.3 Not Supported HLA-G*01:09 3 None 0 0 5681.680 9654.430 8.800 20.000 NA NA NA NA 0.500 Poor Pending -22-38027027-38027028-C-G 15.GGA1.ENST00000343632.4.missense.484P/A GGA1 P484A 0 ARPPQQPVP ENST00000343632.4 Not Supported HLA-E*01:01 1 None 0 0 6693.895 10556.225 0.485 3.200 NA NA NA NA 0.486 Poor Pending -22-29886116-29886117-C-A 12.NEFH.ENST00000310624.6.missense.830P/T NEFH P830T 0 KTQEVKVKE ENST00000310624.6 Not Supported HLA-G*01:09 2 None 0 0 7366.350 25842.400 14.000 50.000 NA NA NA NA 0.038 Poor Pending -22-41895790-41895791-C-A 18.ACO2.ENST00000216254.4.missense.33A/E ACO2 A33E 0 KVEMSHFEP ENST00000216254.4 Not Supported HLA-G*01:09 3 None 0 0 9972.950 31060.990 21.000 56.000 NA NA NA NA 0.044 Poor Pending -22-50555769-50555770-G-A 21.MOV10L1.ENST00000262794.5.missense.482A/T MOV10L1 A482T 0 KTTVVVTTQ ENST00000262794.5 Not Supported HLA-G*01:09 8 None 0 0 10874.650 16763.860 23.000 34.000 NA NA NA NA 0.042 Poor Pending -22-18644672-18644673-C-T 6.USP18.ENST00000215794.7.missense.124A/V 1 USP18 A124V 1 AVRPLELVY ENST00000215794.7 Not Supported HLA-G*01:09 8 None 1 0 14099.070 23444.560 29.000 46.000 NA NA NA NA 0.053 Poor Pending -22-37966274-37966275-C-G 14.LGALS2.ENST00000215886.4.missense.132E/Q LGALS2 E132Q 0 NMSSFKLKQ ENST00000215886.4 Not Supported HLA-E*01:01 9 None 0 0 17113.260 17432.180 8.000 8.450 NA NA NA NA 0.496 Poor Pending -22-26936775-26936776-G-T 11.TPST2.ENST00000338754.4.missense.274P/H TPST2 P274H 0 IGKHGGVSL ENST00000338754.4 Not Supported HLA-E*01:01 4 None 0 0 18405.336 11610.230 14.950 9.650 NA NA NA NA 0.179 Poor Pending -22-38119219-38119220-GA-G 16.TRIOBP.ENST00000406386.3.FS.219GA/G TRIOBP FS219 0 TGQGSGEKA ENST00000406386.3 Not Supported HLA-G*01:09 1-9 None 0 0 21040.320 NA 42.000 NA NA NA NA NA 0.768 Poor Pending -22-22550449-22550450-C-G 9.IGLV6-57.ENST00000390285.3.missense.43R/G IGLV6-57 R43G 0 TGSSGSIAS ENST00000390285.3 Not Supported HLA-E*01:01 2 None 0 0 26618.010 25216.455 42.500 36.500 NA NA NA NA 1.000 Poor Pending -4-40434704-40434725-AGCGGCTGCGGCGGCTGCGGCC-A 2.RBM47.ENST00000381793.2.inframe_del.495-502AAAAAAAA/A RBM47 AAAAAAAA495-502A 0 SAAAAAAAV ENST00000381793.2 Not Supported HLA-E*01:01 8-9 None 0 0 28125.199 29506.670 38.000 42.500 NA NA NA NA 0.977 Poor Pending -22-39994238-39994239-G-A 17.CACNA1I.ENST00000402142.3.missense.107C/Y 1 CACNA1I C107Y 1 DDMDYLSDR ENST00000402142.3 Not Supported HLA-G*01:09 5 None 1 0 38565.121 50000.000 65.000 73.000 NA NA NA NA 0.043 Poor Pending +22-18020271-18020272-G-A 5.CECR2.ENST00000262608.8.missense.535R/H 1 CECR2 R535H 1 WTHSRDPEG ENST00000262608.8 Not Supported HLA-G*01:09 3 None 1 0 5500.220 19932.310 8.400 40.000 NA NA NA NA 0.071 Poor Pending +22-50869713-50869714-C-A 24.PPP6R2.ENST00000395741.3.missense.414S/Y 1 PPP6R2 S414Y 1 GYESRVEPP ENST00000395741.3 Not Supported HLA-G*01:09 2 None 1 0 5620.540 22209.930 8.700 44.000 NA NA NA NA 0.043 Poor Pending +22-20709231-20709232-G-C 8.FAM230A.ENST00000434783.3.missense.322E/Q 1 FAM230A E322Q 1 ANQDAAQGI ENST00000434783.3 Not Supported HLA-G*01:09 3 None 1 0 5681.680 9654.430 8.800 20.000 NA NA NA NA 0.500 Poor Pending +22-38027027-38027028-C-G 15.GGA1.ENST00000343632.4.missense.484P/A 1 GGA1 P484A 1 ARPPQQPVP ENST00000343632.4 Not Supported HLA-E*01:01 1 None 1 0 6693.895 10556.225 0.485 3.200 NA NA NA NA 0.486 Poor Pending +22-29886116-29886117-C-A 12.NEFH.ENST00000310624.6.missense.830P/T 1 NEFH P830T 1 KTQEVKVKE ENST00000310624.6 Not Supported HLA-G*01:09 2 None 1 0 7366.350 25842.400 14.000 50.000 NA NA NA NA 0.038 Poor Pending +22-41895790-41895791-C-A 18.ACO2.ENST00000216254.4.missense.33A/E 1 ACO2 A33E 1 KVEMSHFEP ENST00000216254.4 Not Supported HLA-G*01:09 3 None 1 0 9972.950 31060.990 21.000 56.000 NA NA NA NA 0.044 Poor Pending +22-50555769-50555770-G-A 21.MOV10L1.ENST00000262794.5.missense.482A/T 1 MOV10L1 A482T 1 KTTVVVTTQ ENST00000262794.5 Not Supported HLA-G*01:09 8 None 1 0 10874.650 16763.860 23.000 34.000 NA NA NA NA 0.042 Poor Pending +22-18644672-18644673-C-T 6.USP18.ENST00000215794.7.missense.124A/V 2 USP18 A124V 1 AVRPLELVY ENST00000215794.7 Not Supported HLA-G*01:09 8 None 2 0 14099.070 23444.560 29.000 46.000 NA NA NA NA 0.053 Poor Pending +22-37966274-37966275-C-G 14.LGALS2.ENST00000215886.4.missense.132E/Q 1 LGALS2 E132Q 1 NMSSFKLKQ ENST00000215886.4 Not Supported HLA-E*01:01 9 None 1 0 17113.260 17432.180 8.000 8.450 NA NA NA NA 0.496 Poor Pending +22-26936775-26936776-G-T 11.TPST2.ENST00000338754.4.missense.274P/H 1 TPST2 P274H 1 IGKHGGVSL ENST00000338754.4 Not Supported HLA-E*01:01 4 None 1 0 18405.336 11610.230 14.950 9.650 NA NA NA NA 0.179 Poor Pending +22-38119219-38119220-GA-G 16.TRIOBP.ENST00000406386.3.FS.219GA/G 1 TRIOBP FS219 1 TGQGSGEKA ENST00000406386.3 Not Supported HLA-G*01:09 1-9 None 1 0 21040.320 NA 42.000 NA NA NA NA NA 0.768 Poor Pending +22-22550449-22550450-C-G 9.IGLV6-57.ENST00000390285.3.missense.43R/G 1 IGLV6-57 R43G 1 TGSSGSIAS ENST00000390285.3 Not Supported HLA-E*01:01 2 None 1 0 26618.010 25216.455 42.500 36.500 NA NA NA NA 1.000 Poor Pending +4-40434704-40434725-AGCGGCTGCGGCGGCTGCGGCC-A 2.RBM47.ENST00000381793.2.inframe_del.495-502AAAAAAAA/A 1 RBM47 AAAAAAAA495-502A 1 SAAAAAAAV ENST00000381793.2 Not Supported HLA-E*01:01 8-9 None 1 0 28125.199 29506.670 38.000 42.500 NA NA NA NA 0.977 Poor Pending +22-39994238-39994239-G-A 17.CACNA1I.ENST00000402142.3.missense.107C/Y 2 CACNA1I C107Y 1 DDMDYLSDR ENST00000402142.3 Not Supported HLA-G*01:09 5 None 2 0 38565.121 50000.000 65.000 73.000 NA NA NA NA 0.043 Poor Pending diff --git a/tests/test_data/pvacsplice/results/run/MHC_Class_I/HCC1395_TUMOR_DNA.all_epitopes.aggregated.tsv b/tests/test_data/pvacsplice/results/run/MHC_Class_I/HCC1395_TUMOR_DNA.all_epitopes.aggregated.tsv index ec6c3eb6..3d44363f 100644 --- a/tests/test_data/pvacsplice/results/run/MHC_Class_I/HCC1395_TUMOR_DNA.all_epitopes.aggregated.tsv +++ b/tests/test_data/pvacsplice/results/run/MHC_Class_I/HCC1395_TUMOR_DNA.all_epitopes.aggregated.tsv @@ -1,15 +1,15 @@ ID E*01:01 G*01:09 Gene Transcript Junction Name AA Change Best Peptide TSL Allele Pos Prob Pos Num Included Peptides Num Passing Peptides IC50 MT %ile MT RNA Expr RNA VAF Allele Expr RNA Depth DNA VAF Tier Ref Match Evaluation -TIPRL.ENST00000367830.JUNC00000028.chr1:168179177-168179178.D TIPRL ENST00000367830.3 JUNC00000028 E/V KNPAWVWLW 1 HLA-G*01:09 39 None 0 0 5099.030 7.500 55.745 0.332 18.507 927.000 0.273 Poor False Pending -TIPRL.ENST00000367833.JUNC00000028.chr1:168179177-168179178.D TIPRL ENST00000367833.7 JUNC00000028 E/V KNPAWVWLW 1 HLA-G*01:09 39 None 0 0 5099.030 7.500 55.745 0.332 18.507 927.000 0.273 Poor False Pending -CCDC18.ENST00000343253.JUNC00000011.chr1:93226448-93226449.D CCDC18 ENST00000343253.11 JUNC00000011 E KSEEKELKI 5 HLA-G*01:09 760 None 0 0 9759.450 20.000 18.750 0.300 5.625 20.000 0.628 Poor False Pending -CCDC18.ENST00000370276.JUNC00000011.chr1:93226448-93226449.D CCDC18 ENST00000370276.6 JUNC00000011 E KSEEKELKI 5 HLA-G*01:09 760 None 0 0 9759.450 20.000 18.750 0.300 5.625 20.000 0.628 Poor False Pending -CCDC18.ENST00000401026.JUNC00000011.chr1:93226448-93226449.D CCDC18 ENST00000401026.7 JUNC00000011 E KSEEKELKI 1 HLA-G*01:09 761 None 0 0 9759.450 20.000 18.750 0.300 5.625 20.000 0.628 Poor False Pending -CCDC18.ENST00000690025.JUNC00000011.chr1:93226448-93226449.D CCDC18 ENST00000690025.1 JUNC00000011 E KSEEKELKI NA HLA-G*01:09 761 None 0 0 9759.450 20.000 18.750 0.300 5.625 20.000 0.628 Poor False Pending -TIPRL.ENST00000367830.JUNC00000027.chr1:168179177-168179178.D TIPRL ENST00000367830.3 JUNC00000027 E/V HIMKSADVVN 1 HLA-G*01:09 26 None 0 0 11857.880 6.800 55.745 0.332 18.507 927.000 0.273 Poor False Pending -TIPRL.ENST00000367833.JUNC00000027.chr1:168179177-168179178.D TIPRL ENST00000367833.7 JUNC00000027 E/V HIMKSADVVN 1 HLA-G*01:09 26 None 0 0 11857.880 6.800 55.745 0.332 18.507 927.000 0.273 Poor False Pending -CCDC18.ENST00000343253.JUNC00000006.chr1:93226448-93226449.NDA 1 CCDC18 ENST00000343253.11 JUNC00000006 E VSEETIKVY 5 HLA-G*01:09 718 None 1 1 14882.820 31.000 18.750 0.300 5.625 20.000 0.628 Poor False Pending -CCDC18.ENST00000370276.JUNC00000006.chr1:93226448-93226449.NDA 1 CCDC18 ENST00000370276.6 JUNC00000006 E VSEETIKVY 5 HLA-G*01:09 718 None 1 1 14882.820 31.000 18.750 0.300 5.625 20.000 0.628 Poor False Pending -CCDC18.ENST00000401026.JUNC00000006.chr1:93226448-93226449.NDA 1 CCDC18 ENST00000401026.7 JUNC00000006 E VSEETIKVY 1 HLA-G*01:09 719 None 1 1 14882.820 31.000 18.750 0.300 5.625 20.000 0.628 Poor False Pending -CCDC18.ENST00000690025.JUNC00000006.chr1:93226448-93226449.NDA 1 CCDC18 ENST00000690025.1 JUNC00000006 E VSEETIKVY NA HLA-G*01:09 719 None 1 1 14882.820 31.000 18.750 0.300 5.625 20.000 0.628 Poor False Pending -TIPRL.ENST00000367830.JUNC00000025.chr1:168179177-168179178.D TIPRL ENST00000367830.3 JUNC00000025 E/V IMKSADVVKV 1 HLA-E*01:01 27 None 0 0 19498.205 7.200 55.745 0.332 18.507 927.000 0.273 Poor False Pending -TIPRL.ENST00000367833.JUNC00000025.chr1:168179177-168179178.D TIPRL ENST00000367833.7 JUNC00000025 E/V IMKSADVVKV 1 HLA-E*01:01 27 None 0 0 19498.205 7.200 55.745 0.332 18.507 927.000 0.273 Poor False Pending +TIPRL.ENST00000367830.JUNC00000028.chr1:168179177-168179178.D 1 TIPRL ENST00000367830.3 JUNC00000028 E/V KNPAWVWLW 1 HLA-G*01:09 39 None 1 0 5099.030 7.500 55.745 0.332 18.507 927.000 0.273 Poor False Pending +TIPRL.ENST00000367833.JUNC00000028.chr1:168179177-168179178.D 1 TIPRL ENST00000367833.7 JUNC00000028 E/V KNPAWVWLW 1 HLA-G*01:09 39 None 1 0 5099.030 7.500 55.745 0.332 18.507 927.000 0.273 Poor False Pending +CCDC18.ENST00000343253.JUNC00000011.chr1:93226448-93226449.D 1 CCDC18 ENST00000343253.11 JUNC00000011 E KSEEKELKI 5 HLA-G*01:09 760 None 1 0 9759.450 20.000 18.750 0.300 5.625 20.000 0.628 Poor False Pending +CCDC18.ENST00000370276.JUNC00000011.chr1:93226448-93226449.D 1 CCDC18 ENST00000370276.6 JUNC00000011 E KSEEKELKI 5 HLA-G*01:09 760 None 1 0 9759.450 20.000 18.750 0.300 5.625 20.000 0.628 Poor False Pending +CCDC18.ENST00000401026.JUNC00000011.chr1:93226448-93226449.D 1 CCDC18 ENST00000401026.7 JUNC00000011 E KSEEKELKI 1 HLA-G*01:09 761 None 1 0 9759.450 20.000 18.750 0.300 5.625 20.000 0.628 Poor False Pending +CCDC18.ENST00000690025.JUNC00000011.chr1:93226448-93226449.D 1 CCDC18 ENST00000690025.1 JUNC00000011 E KSEEKELKI NA HLA-G*01:09 761 None 1 0 9759.450 20.000 18.750 0.300 5.625 20.000 0.628 Poor False Pending +TIPRL.ENST00000367830.JUNC00000027.chr1:168179177-168179178.D 1 TIPRL ENST00000367830.3 JUNC00000027 E/V HIMKSADVVN 1 HLA-G*01:09 26 None 1 0 11857.880 6.800 55.745 0.332 18.507 927.000 0.273 Poor False Pending +TIPRL.ENST00000367833.JUNC00000027.chr1:168179177-168179178.D 1 TIPRL ENST00000367833.7 JUNC00000027 E/V HIMKSADVVN 1 HLA-G*01:09 26 None 1 0 11857.880 6.800 55.745 0.332 18.507 927.000 0.273 Poor False Pending +CCDC18.ENST00000343253.JUNC00000006.chr1:93226448-93226449.NDA 2 CCDC18 ENST00000343253.11 JUNC00000006 E VSEETIKVY 5 HLA-G*01:09 718 None 2 1 14882.820 31.000 18.750 0.300 5.625 20.000 0.628 Poor False Pending +CCDC18.ENST00000370276.JUNC00000006.chr1:93226448-93226449.NDA 2 CCDC18 ENST00000370276.6 JUNC00000006 E VSEETIKVY 5 HLA-G*01:09 718 None 2 1 14882.820 31.000 18.750 0.300 5.625 20.000 0.628 Poor False Pending +CCDC18.ENST00000401026.JUNC00000006.chr1:93226448-93226449.NDA 2 CCDC18 ENST00000401026.7 JUNC00000006 E VSEETIKVY 1 HLA-G*01:09 719 None 2 1 14882.820 31.000 18.750 0.300 5.625 20.000 0.628 Poor False Pending +CCDC18.ENST00000690025.JUNC00000006.chr1:93226448-93226449.NDA 2 CCDC18 ENST00000690025.1 JUNC00000006 E VSEETIKVY NA HLA-G*01:09 719 None 2 1 14882.820 31.000 18.750 0.300 5.625 20.000 0.628 Poor False Pending +TIPRL.ENST00000367830.JUNC00000025.chr1:168179177-168179178.D 1 TIPRL ENST00000367830.3 JUNC00000025 E/V IMKSADVVKV 1 HLA-E*01:01 27 None 1 0 19498.205 7.200 55.745 0.332 18.507 927.000 0.273 Poor False Pending +TIPRL.ENST00000367833.JUNC00000025.chr1:168179177-168179178.D 1 TIPRL ENST00000367833.7 JUNC00000025 E/V IMKSADVVKV 1 HLA-E*01:01 27 None 1 0 19498.205 7.200 55.745 0.332 18.507 927.000 0.273 Poor False Pending diff --git a/tests/test_data/pvacsplice/results/run/MHC_Class_II/HCC1395_TUMOR_DNA.all_epitopes.aggregated.tsv b/tests/test_data/pvacsplice/results/run/MHC_Class_II/HCC1395_TUMOR_DNA.all_epitopes.aggregated.tsv index 5ede6af7..3ebf8be8 100644 --- a/tests/test_data/pvacsplice/results/run/MHC_Class_II/HCC1395_TUMOR_DNA.all_epitopes.aggregated.tsv +++ b/tests/test_data/pvacsplice/results/run/MHC_Class_II/HCC1395_TUMOR_DNA.all_epitopes.aggregated.tsv @@ -9,7 +9,7 @@ TIPRL.ENST00000367833.JUNC00000027.chr1:168179177-168179178.D 2 TIPRL ENST000003 CCDC18.ENST00000343253.JUNC00000011.chr1:93226448-93226449.D 10 CCDC18 ENST00000343253.11 JUNC00000011 E KEKFEKQLKKKSEEK 5 HLA-DRB1*11:01 750 None 10 9 31.700 3.200 18.750 0.300 5.625 20.000 0.628 Poor False Pending CCDC18.ENST00000370276.JUNC00000011.chr1:93226448-93226449.D 10 CCDC18 ENST00000370276.6 JUNC00000011 E KEKFEKQLKKKSEEK 5 HLA-DRB1*11:01 750 None 10 9 31.700 3.200 18.750 0.300 5.625 20.000 0.628 Poor False Pending CCDC18.ENST00000690025.JUNC00000011.chr1:93226448-93226449.D 10 CCDC18 ENST00000690025.1 JUNC00000011 E KEKFEKQLKKKSEEK NA HLA-DRB1*11:01 751 None 10 9 31.700 3.200 18.750 0.300 5.625 20.000 0.628 Poor False Pending -CCDC18.ENST00000343253.JUNC00000006.chr1:93226448-93226449.NDA 8 CCDC18 ENST00000343253.11 JUNC00000006 E KALQNQVSEETIKVY 5 HLA-DRB1*11:01 712 None 8 6 16019.100 91.000 18.750 0.300 5.625 20.000 0.628 Poor False Pending -CCDC18.ENST00000370276.JUNC00000006.chr1:93226448-93226449.NDA 8 CCDC18 ENST00000370276.6 JUNC00000006 E KALQNQVSEETIKVY 5 HLA-DRB1*11:01 712 None 8 6 16019.100 91.000 18.750 0.300 5.625 20.000 0.628 Poor False Pending -CCDC18.ENST00000401026.JUNC00000006.chr1:93226448-93226449.NDA 8 CCDC18 ENST00000401026.7 JUNC00000006 E KALQNQVSEETIKVY 1 HLA-DRB1*11:01 713 None 8 6 16019.100 91.000 18.750 0.300 5.625 20.000 0.628 Poor False Pending -CCDC18.ENST00000690025.JUNC00000006.chr1:93226448-93226449.NDA 8 CCDC18 ENST00000690025.1 JUNC00000006 E KALQNQVSEETIKVY NA HLA-DRB1*11:01 713 None 8 6 16019.100 91.000 18.750 0.300 5.625 20.000 0.628 Poor False Pending +CCDC18.ENST00000343253.JUNC00000006.chr1:93226448-93226449.NDA 9 CCDC18 ENST00000343253.11 JUNC00000006 E KALQNQVSEETIKVY 5 HLA-DRB1*11:01 712 None 9 6 16019.100 91.000 18.750 0.300 5.625 20.000 0.628 Poor False Pending +CCDC18.ENST00000370276.JUNC00000006.chr1:93226448-93226449.NDA 9 CCDC18 ENST00000370276.6 JUNC00000006 E KALQNQVSEETIKVY 5 HLA-DRB1*11:01 712 None 9 6 16019.100 91.000 18.750 0.300 5.625 20.000 0.628 Poor False Pending +CCDC18.ENST00000401026.JUNC00000006.chr1:93226448-93226449.NDA 9 CCDC18 ENST00000401026.7 JUNC00000006 E KALQNQVSEETIKVY 1 HLA-DRB1*11:01 713 None 9 6 16019.100 91.000 18.750 0.300 5.625 20.000 0.628 Poor False Pending +CCDC18.ENST00000690025.JUNC00000006.chr1:93226448-93226449.NDA 9 CCDC18 ENST00000690025.1 JUNC00000006 E KALQNQVSEETIKVY NA HLA-DRB1*11:01 713 None 9 6 16019.100 91.000 18.750 0.300 5.625 20.000 0.628 Poor False Pending