diff --git a/workflow/scripts/format_pileup.py b/workflow/scripts/format_pileup.py
index 94c3f19..c84cde4 100644
--- a/workflow/scripts/format_pileup.py
+++ b/workflow/scripts/format_pileup.py
@@ -12,7 +12,7 @@
 
 print("\t".join(["contig", "position", "depth", "ref_base", "count_A", "count_C", "count_G", "count_T", "count_del", "alt_frequency"]))
 for pc in samfile.pileup(ignore_orphans=False):
-    freqs = {'A': 0, 'T': 0, 'G': 0, 'C': 0, '-': 0, 'R': 0 }
+    freqs = {'A': 0, 'T': 0, 'G': 0, 'C': 0, '-': 0, 'R': 0, 'N': 0 }
     for pr in pc.pileups:
         if pr.is_del:
             freqs['-'] += 1
diff --git a/workflow/scripts/plot/plot_qc_sequencing.R b/workflow/scripts/plot/plot_qc_sequencing.R
index dd99e10..79d4d94 100644
--- a/workflow/scripts/plot/plot_qc_sequencing.R
+++ b/workflow/scripts/plot/plot_qc_sequencing.R
@@ -122,6 +122,9 @@ if(!interactive()) {
 
     if(args$metadata != "") {
         metadata.raw <- read.table(args$metadata, header=T, sep="\t")
+        if(all(is.na(metadata.raw$ct))) {
+          metadata.raw$ct <- 0
+        }
 
         # clean metadata of unknown Cts
         metadata = subset(metadata.raw, ct != "unknown")