diff --git a/micall/core/aln2counts.py b/micall/core/aln2counts.py
index e82ac72bd..90dcfdda0 100755
--- a/micall/core/aln2counts.py
+++ b/micall/core/aln2counts.py
@@ -411,7 +411,8 @@ def _create_amino_writer(amino_file):
                    'query.nuc.pos',
                    'refseq.aa.pos']
         columns.extend(AMINO_ALPHABET)
-        columns.extend(('X', 'partial', 'del', 'ins', 'clip', 'g2p_overlap'))
+        columns.extend(
+            ('X', 'partial', 'del', 'ins', 'clip', 'g2p_overlap', 'coverage'))
         return csv.DictWriter(amino_file,
                               columns,
                               lineterminator=os.linesep)
@@ -446,11 +447,13 @@ def write_amino_counts(self, amino_writer=None, coverage_summary=None):
                        'del': seed_amino.deletions,
                        'ins': report_amino.insertion_count,
                        'clip': report_amino.max_clip_count,
-                       'g2p_overlap': seed_amino.g2p_overlap}
+                       'g2p_overlap': seed_amino.g2p_overlap,
+                       'coverage': seed_amino.deletions}
                 for letter in AMINO_ALPHABET:
                     letter_count = seed_amino.counts[letter]
                     row[letter] = letter_count
                     coverage_sum += letter_count
+                    row['coverage'] += letter_count
                 amino_writer.writerow(row)
                 pos_count += 1
             if coverage_summary is not None and pos_count > 0:
@@ -477,7 +480,8 @@ def _create_nuc_writer(nuc_file):
                                'del',
                                'ins',
                                'clip',
-                               'g2p_overlap'],
+                               'g2p_overlap',
+                               'coverage'],
                               lineterminator=os.linesep)
 
     def write_nuc_header(self, nuc_file):
@@ -521,9 +525,13 @@ def write_counts(self, region, seed_amino, report_amino, nuc_writer):
                    'del': seed_nuc.counts['-'],
                    'ins': insertion_count,
                    'clip': clip_count,
-                   'g2p_overlap': seed_nuc.g2p_overlap}
+                   'g2p_overlap': seed_nuc.g2p_overlap,
+                   'coverage': seed_nuc.counts['-']}
             for base in 'ACTGN':
-                row[base] = seed_nuc.counts[base]
+                nuc_count = seed_nuc.counts[base]
+                row[base] = nuc_count
+                if base != 'N':
+                    row['coverage'] += nuc_count
             nuc_writer.writerow(row)
         if report_amino is not None:
             report_amino.max_clip_count = max_clip_count
diff --git a/micall/hivdb/genreport.py b/micall/hivdb/genreport.py
index efcc32747..1b04624aa 100755
--- a/micall/hivdb/genreport.py
+++ b/micall/hivdb/genreport.py
@@ -6,6 +6,8 @@
 
 from argparse import ArgumentParser, FileType
 import csv
+from collections import defaultdict
+
 import yaml
 
 try:
@@ -142,7 +144,7 @@ def read_mutations(cfg_dct, csv_file):
     Returns a list of dictionaries.
     """
     err_string = "Error in mutations file '{}'".format(csv_file.name)
-    exp_set = frozenset("drug_class,mutation".split(","))
+    exp_set = frozenset("drug_class,mutation,prevalence".split(","))
     try:
         data_lst = list(csv.DictReader(csv_file, restkey="dummy"))
     except csv.Error:
@@ -154,7 +156,7 @@ def read_mutations(cfg_dct, csv_file):
     # simple sanity check of the fields
     # generate a dict of drug_class -> string of mutations
     # also set the strings to 'NONE' if appropriate
-    tmp_dct = {}
+    tmp_dct = defaultdict(list)
     known_drug_class_set = cfg_dct['known_drug_classes']
     glob_err = False
     for od_num, od in enumerate(data_lst):
@@ -167,7 +169,9 @@ def read_mutations(cfg_dct, csv_file):
             print("{}: dataset {}: error with {}\n\n".format(
                 err_string, od_num + 1, od))
             glob_err = True
-        tmp_dct.setdefault(d_class, []).append(mut_str)
+        tmp_dct[d_class].append('{}({:.0f}%)'.format(
+            mut_str,
+            100*float(od['prevalence'])))
     if glob_err:
         raise RuntimeError(
             "{}: fatal error(s) detected: giving up...".format(err_string))
diff --git a/micall/hivdb/hivdb.py b/micall/hivdb/hivdb.py
index 356175921..0f9c4b635 100644
--- a/micall/hivdb/hivdb.py
+++ b/micall/hivdb/hivdb.py
@@ -70,14 +70,14 @@ def read_aminos(amino_csv, min_fraction, reported_regions=None):
         aminos = []
         for row in rows:
             counts = list(map(int, (row[f] for f in coverage_columns)))
-            coverage = sum(counts)
+            coverage = int(row['coverage'])
             min_count = max(1, coverage * min_fraction)  # needs at least 1
-            pos_aminos = [report_names[i]
+            pos_aminos = {report_names[i]: count/coverage
                           for i, count in enumerate(counts)
-                          if count >= min_count and report_names[i] != '*']
+                          if count >= min_count and report_names[i] != '*'}
             ins_count = int(row['ins'])
             if ins_count >= min_count:
-                pos_aminos.append('i')
+                pos_aminos['i'] = ins_count / coverage
             aminos.append(pos_aminos)
         yield translated_region, aminos
     for region in missing_regions:
@@ -109,7 +109,7 @@ def write_resistance(aminos, resistance_csv, mutations_csv):
         lineterminator=os.linesep)
     resistance_writer.writeheader()
     mutations_writer = DictWriter(mutations_csv,
-                                  ['drug_class', 'mutation'],
+                                  ['drug_class', 'mutation', 'prevalence'],
                                   lineterminator=os.linesep)
     mutations_writer.writeheader()
     asi = AsiAlgorithm(RULES_PATH)
@@ -128,8 +128,13 @@ def write_resistance(aminos, resistance_csv, mutations_csv):
                                             score=drug_result.score))
         for drug_class, class_mutations in result.mutations.items():
             for mutation in class_mutations:
+                amino = mutation[-1]
+                pos = int(mutation[1:-1])
+                pos_aminos = amino_seq[pos-1]
+                prevalence = pos_aminos[amino]
                 mutations_writer.writerow(dict(drug_class=drug_class,
-                                               mutation=mutation))
+                                               mutation=mutation,
+                                               prevalence=prevalence))
 
 
 def hivdb(amino_csv,
diff --git a/micall/tests/aln2counts_test.py b/micall/tests/aln2counts_test.py
index eb5d724ae..c9fd0e838 100644
--- a/micall/tests/aln2counts_test.py
+++ b/micall/tests/aln2counts_test.py
@@ -396,10 +396,10 @@ def testSingleReadAminoReport(self):
 
         expected_text = """\
 seed,region,q-cutoff,query.nuc.pos,refseq.aa.pos,\
-A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y,*,X,partial,del,ins,clip,g2p_overlap
-R1-seed,R1,15,1,1,0,0,0,0,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
-R1-seed,R1,15,4,2,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
-R1-seed,R1,15,,3,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y,*,X,partial,del,ins,clip,g2p_overlap,coverage
+R1-seed,R1,15,1,1,0,0,0,0,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,9
+R1-seed,R1,15,4,2,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,9
+R1-seed,R1,15,,3,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
 """
 
         self.report.write_amino_header(self.report_file)
@@ -421,16 +421,16 @@ def testSingleReadNucleotideReport(self):
 """)
 
         expected_text = """\
-seed,region,q-cutoff,query.nuc.pos,refseq.nuc.pos,A,C,G,T,N,del,ins,clip,g2p_overlap
-R1-seed,R1,15,1,1,9,0,0,0,0,0,0,0,0
-R1-seed,R1,15,2,2,9,0,0,0,0,0,0,0,0
-R1-seed,R1,15,3,3,9,0,0,0,0,0,0,0,0
-R1-seed,R1,15,4,4,0,0,0,9,0,0,0,0,0
-R1-seed,R1,15,5,5,0,0,0,9,0,0,0,0,0
-R1-seed,R1,15,6,6,0,0,0,9,0,0,0,0,0
-R1-seed,R1,15,,7,0,0,0,0,0,0,0,0,0
-R1-seed,R1,15,,8,0,0,0,0,0,0,0,0,0
-R1-seed,R1,15,,9,0,0,0,0,0,0,0,0,0
+seed,region,q-cutoff,query.nuc.pos,refseq.nuc.pos,A,C,G,T,N,del,ins,clip,g2p_overlap,coverage
+R1-seed,R1,15,1,1,9,0,0,0,0,0,0,0,0,9
+R1-seed,R1,15,2,2,9,0,0,0,0,0,0,0,0,9
+R1-seed,R1,15,3,3,9,0,0,0,0,0,0,0,0,9
+R1-seed,R1,15,4,4,0,0,0,9,0,0,0,0,0,9
+R1-seed,R1,15,5,5,0,0,0,9,0,0,0,0,0,9
+R1-seed,R1,15,6,6,0,0,0,9,0,0,0,0,0,9
+R1-seed,R1,15,,7,0,0,0,0,0,0,0,0,0,0
+R1-seed,R1,15,,8,0,0,0,0,0,0,0,0,0,0
+R1-seed,R1,15,,9,0,0,0,0,0,0,0,0,0,0
 """
 
         self.report.write_nuc_header(self.report_file)
@@ -457,15 +457,15 @@ def testSecondSourceAminoReport(self):
 
         expected_text = """\
 seed,region,q-cutoff,query.nuc.pos,refseq.aa.pos,\
-A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y,*,X,partial,del,ins,clip,g2p_overlap
-R2-seed,R2,15,1,1,0,0,0,0,0,0,0,0,8,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
-R2-seed,R2,15,4,2,0,0,0,0,8,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
-R2-seed,R2,15,,3,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
-R2-seed,R2,15,,4,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
-R2-seed,R2,15,,5,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
-R1-seed,R1,15,1,1,0,0,0,0,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
-R1-seed,R1,15,4,2,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
-R1-seed,R1,15,,3,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y,*,X,partial,del,ins,clip,g2p_overlap,coverage
+R2-seed,R2,15,1,1,0,0,0,0,0,0,0,0,8,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,8
+R2-seed,R2,15,4,2,0,0,0,0,8,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,8
+R2-seed,R2,15,,3,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+R2-seed,R2,15,,4,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+R2-seed,R2,15,,5,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+R1-seed,R1,15,1,1,0,0,0,0,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,9
+R1-seed,R1,15,4,2,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,9
+R1-seed,R1,15,,3,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
 """
 
         self.report.write_amino_header(self.report_file)
@@ -487,10 +487,10 @@ def testAminoReportWithG2pOverlap(self):
 
         expected_text = """\
 seed,region,q-cutoff,query.nuc.pos,refseq.aa.pos,\
-A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y,*,X,partial,del,ins,clip,g2p_overlap
-R6a-seed,R6,15,1,1,0,0,0,0,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,8
-R6a-seed,R6,15,4,2,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,8
-R6a-seed,R6,15,,3,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y,*,X,partial,del,ins,clip,g2p_overlap,coverage
+R6a-seed,R6,15,1,1,0,0,0,0,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,8,9
+R6a-seed,R6,15,4,2,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,8,9
+R6a-seed,R6,15,,3,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
 """
 
         self.report.write_amino_header(self.report_file)
@@ -512,10 +512,10 @@ def testAminoReportWithoutG2pOverlap(self):
 
         expected_text = """\
 seed,region,q-cutoff,query.nuc.pos,refseq.aa.pos,\
-A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y,*,X,partial,del,ins,clip,g2p_overlap
-R6a-seed,R6,15,1,1,0,0,0,0,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
-R6a-seed,R6,15,4,2,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
-R6a-seed,R6,15,,3,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y,*,X,partial,del,ins,clip,g2p_overlap,coverage
+R6a-seed,R6,15,1,1,0,0,0,0,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,9
+R6a-seed,R6,15,4,2,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,9
+R6a-seed,R6,15,,3,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
 """
 
         self.report.write_amino_header(self.report_file)
@@ -537,10 +537,10 @@ def testAminoReportWithIndirectG2pOverlap(self):
 
         expected_text = """\
 seed,region,q-cutoff,query.nuc.pos,refseq.aa.pos,\
-A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y,*,X,partial,del,ins,clip,g2p_overlap
-R6a-seed,R6,15,1,1,0,0,0,0,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
-R6a-seed,R6,15,4,2,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
-R6a-seed,R6,15,,3,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,8
+A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y,*,X,partial,del,ins,clip,g2p_overlap,coverage
+R6a-seed,R6,15,1,1,0,0,0,0,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,9
+R6a-seed,R6,15,4,2,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,9
+R6a-seed,R6,15,,3,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,8,0
 """
 
         self.report.write_amino_header(self.report_file)
@@ -614,12 +614,12 @@ def testAminoReportWithDifferingConsensus(self):
 
         expected_text = """\
 seed,region,q-cutoff,query.nuc.pos,refseq.aa.pos,\
-A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y,*,X,partial,del,ins,clip,g2p_overlap
-HIV1-C-BR-JX140663-seed,R1,15,2,1,0,0,0,0,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,8
-HIV1-C-BR-JX140663-seed,R1,15,5,2,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,6
-HIV1-C-BR-JX140663-seed,R1,15,8,3,0,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,8
-HIV1-C-BR-JX140663-seed,R1,15,,4,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,8
-HIV1-C-BR-JX140663-seed,R1,15,,5,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y,*,X,partial,del,ins,clip,g2p_overlap,coverage
+HIV1-C-BR-JX140663-seed,R1,15,2,1,0,0,0,0,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,8,9
+HIV1-C-BR-JX140663-seed,R1,15,5,2,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,6,9
+HIV1-C-BR-JX140663-seed,R1,15,8,3,0,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,8,9
+HIV1-C-BR-JX140663-seed,R1,15,,4,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,8,0
+HIV1-C-BR-JX140663-seed,R1,15,,5,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
 """
 
         self.report.write_amino_header(self.report_file)
@@ -677,12 +677,12 @@ def testAminoReportOverlapWithDifferentSeed(self):
 
         expected_text = """\
 seed,region,q-cutoff,query.nuc.pos,refseq.aa.pos,\
-A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y,*,X,partial,del,ins,clip,g2p_overlap
-HIV1-C-BR-JX140663-seed,R1,15,2,1,0,0,0,0,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,8
-HIV1-C-BR-JX140663-seed,R1,15,5,2,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,8
-HIV1-C-BR-JX140663-seed,R1,15,8,3,0,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,8
-HIV1-C-BR-JX140663-seed,R1,15,,4,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,8
-HIV1-C-BR-JX140663-seed,R1,15,,5,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y,*,X,partial,del,ins,clip,g2p_overlap,coverage
+HIV1-C-BR-JX140663-seed,R1,15,2,1,0,0,0,0,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,8,9
+HIV1-C-BR-JX140663-seed,R1,15,5,2,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,8,9
+HIV1-C-BR-JX140663-seed,R1,15,8,3,0,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,8,9
+HIV1-C-BR-JX140663-seed,R1,15,,4,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,8,0
+HIV1-C-BR-JX140663-seed,R1,15,,5,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
 """
 
         self.report.write_amino_header(self.report_file)
@@ -706,31 +706,31 @@ def testSecondSourceNucleotideReport(self):
 """)
 
         expected_text = """\
-seed,region,q-cutoff,query.nuc.pos,refseq.nuc.pos,A,C,G,T,N,del,ins,clip,g2p_overlap
-R2-seed,R2,15,1,1,8,0,0,0,0,0,0,0,0
-R2-seed,R2,15,2,2,8,0,0,0,0,0,0,0,0
-R2-seed,R2,15,3,3,8,0,0,0,0,0,0,0,0
-R2-seed,R2,15,4,4,0,0,0,8,0,0,0,0,0
-R2-seed,R2,15,5,5,0,0,0,8,0,0,0,0,0
-R2-seed,R2,15,6,6,0,0,0,8,0,0,0,0,0
-R2-seed,R2,15,,7,0,0,0,0,0,0,0,0,0
-R2-seed,R2,15,,8,0,0,0,0,0,0,0,0,0
-R2-seed,R2,15,,9,0,0,0,0,0,0,0,0,0
-R2-seed,R2,15,,10,0,0,0,0,0,0,0,0,0
-R2-seed,R2,15,,11,0,0,0,0,0,0,0,0,0
-R2-seed,R2,15,,12,0,0,0,0,0,0,0,0,0
-R2-seed,R2,15,,13,0,0,0,0,0,0,0,0,0
-R2-seed,R2,15,,14,0,0,0,0,0,0,0,0,0
-R2-seed,R2,15,,15,0,0,0,0,0,0,0,0,0
-R1-seed,R1,15,1,1,9,0,0,0,0,0,0,0,0
-R1-seed,R1,15,2,2,9,0,0,0,0,0,0,0,0
-R1-seed,R1,15,3,3,9,0,0,0,0,0,0,0,0
-R1-seed,R1,15,4,4,0,0,0,9,0,0,0,0,0
-R1-seed,R1,15,5,5,0,0,0,9,0,0,0,0,0
-R1-seed,R1,15,6,6,0,0,0,9,0,0,0,0,0
-R1-seed,R1,15,,7,0,0,0,0,0,0,0,0,0
-R1-seed,R1,15,,8,0,0,0,0,0,0,0,0,0
-R1-seed,R1,15,,9,0,0,0,0,0,0,0,0,0
+seed,region,q-cutoff,query.nuc.pos,refseq.nuc.pos,A,C,G,T,N,del,ins,clip,g2p_overlap,coverage
+R2-seed,R2,15,1,1,8,0,0,0,0,0,0,0,0,8
+R2-seed,R2,15,2,2,8,0,0,0,0,0,0,0,0,8
+R2-seed,R2,15,3,3,8,0,0,0,0,0,0,0,0,8
+R2-seed,R2,15,4,4,0,0,0,8,0,0,0,0,0,8
+R2-seed,R2,15,5,5,0,0,0,8,0,0,0,0,0,8
+R2-seed,R2,15,6,6,0,0,0,8,0,0,0,0,0,8
+R2-seed,R2,15,,7,0,0,0,0,0,0,0,0,0,0
+R2-seed,R2,15,,8,0,0,0,0,0,0,0,0,0,0
+R2-seed,R2,15,,9,0,0,0,0,0,0,0,0,0,0
+R2-seed,R2,15,,10,0,0,0,0,0,0,0,0,0,0
+R2-seed,R2,15,,11,0,0,0,0,0,0,0,0,0,0
+R2-seed,R2,15,,12,0,0,0,0,0,0,0,0,0,0
+R2-seed,R2,15,,13,0,0,0,0,0,0,0,0,0,0
+R2-seed,R2,15,,14,0,0,0,0,0,0,0,0,0,0
+R2-seed,R2,15,,15,0,0,0,0,0,0,0,0,0,0
+R1-seed,R1,15,1,1,9,0,0,0,0,0,0,0,0,9
+R1-seed,R1,15,2,2,9,0,0,0,0,0,0,0,0,9
+R1-seed,R1,15,3,3,9,0,0,0,0,0,0,0,0,9
+R1-seed,R1,15,4,4,0,0,0,9,0,0,0,0,0,9
+R1-seed,R1,15,5,5,0,0,0,9,0,0,0,0,0,9
+R1-seed,R1,15,6,6,0,0,0,9,0,0,0,0,0,9
+R1-seed,R1,15,,7,0,0,0,0,0,0,0,0,0,0
+R1-seed,R1,15,,8,0,0,0,0,0,0,0,0,0,0
+R1-seed,R1,15,,9,0,0,0,0,0,0,0,0,0,0
 """
 
         self.report.write_nuc_header(self.report_file)
@@ -749,16 +749,16 @@ def testNucleotideReportWithG2pOverlap(self):
 """)
 
         expected_text = """\
-seed,region,q-cutoff,query.nuc.pos,refseq.nuc.pos,A,C,G,T,N,del,ins,clip,g2p_overlap
-R1-seed,R1,15,1,1,9,0,0,0,0,0,0,0,8
-R1-seed,R1,15,2,2,9,0,0,0,0,0,0,0,8
-R1-seed,R1,15,3,3,9,0,0,0,0,0,0,0,8
-R1-seed,R1,15,4,4,0,0,0,9,0,0,0,0,8
-R1-seed,R1,15,5,5,0,0,0,9,0,0,0,0,8
-R1-seed,R1,15,6,6,0,0,0,9,0,0,0,0,8
-R1-seed,R1,15,,7,0,0,0,0,0,0,0,0,0
-R1-seed,R1,15,,8,0,0,0,0,0,0,0,0,0
-R1-seed,R1,15,,9,0,0,0,0,0,0,0,0,0
+seed,region,q-cutoff,query.nuc.pos,refseq.nuc.pos,A,C,G,T,N,del,ins,clip,g2p_overlap,coverage
+R1-seed,R1,15,1,1,9,0,0,0,0,0,0,0,8,9
+R1-seed,R1,15,2,2,9,0,0,0,0,0,0,0,8,9
+R1-seed,R1,15,3,3,9,0,0,0,0,0,0,0,8,9
+R1-seed,R1,15,4,4,0,0,0,9,0,0,0,0,8,9
+R1-seed,R1,15,5,5,0,0,0,9,0,0,0,0,8,9
+R1-seed,R1,15,6,6,0,0,0,9,0,0,0,0,8,9
+R1-seed,R1,15,,7,0,0,0,0,0,0,0,0,0,0
+R1-seed,R1,15,,8,0,0,0,0,0,0,0,0,0,0
+R1-seed,R1,15,,9,0,0,0,0,0,0,0,0,0,0
 """
 
         self.report.write_nuc_header(self.report_file)
@@ -781,16 +781,16 @@ def testSoftClippingNucleotideReport(self):
 """)
 
         expected_text = """\
-seed,region,q-cutoff,query.nuc.pos,refseq.nuc.pos,A,C,G,T,N,del,ins,clip,g2p_overlap
-R1-seed,R1,15,1,1,0,0,0,0,0,0,0,9,0
-R1-seed,R1,15,2,2,0,0,0,0,0,0,0,9,0
-R1-seed,R1,15,3,3,9,0,0,0,0,0,0,0,0
-R1-seed,R1,15,4,4,0,0,0,9,0,0,0,0,0
-R1-seed,R1,15,5,5,0,0,0,9,0,0,0,0,0
-R1-seed,R1,15,6,6,0,0,0,9,0,0,0,0,0
-R1-seed,R1,15,7,7,9,0,0,0,0,0,0,0,0
-R1-seed,R1,15,8,8,0,0,0,0,0,0,0,9,0
-R1-seed,R1,15,9,9,0,0,0,0,0,0,0,0,0
+seed,region,q-cutoff,query.nuc.pos,refseq.nuc.pos,A,C,G,T,N,del,ins,clip,g2p_overlap,coverage
+R1-seed,R1,15,1,1,0,0,0,0,0,0,0,9,0,0
+R1-seed,R1,15,2,2,0,0,0,0,0,0,0,9,0,0
+R1-seed,R1,15,3,3,9,0,0,0,0,0,0,0,0,9
+R1-seed,R1,15,4,4,0,0,0,9,0,0,0,0,0,9
+R1-seed,R1,15,5,5,0,0,0,9,0,0,0,0,0,9
+R1-seed,R1,15,6,6,0,0,0,9,0,0,0,0,0,9
+R1-seed,R1,15,7,7,9,0,0,0,0,0,0,0,0,9
+R1-seed,R1,15,8,8,0,0,0,0,0,0,0,9,0,0
+R1-seed,R1,15,9,9,0,0,0,0,0,0,0,0,0,0
 """
 
         self.report.read_clipping(clipping)
@@ -816,10 +816,10 @@ def testSoftClippingAminoReport(self):
 
         expected_text = """\
 seed,region,q-cutoff,query.nuc.pos,refseq.aa.pos,\
-A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y,*,X,partial,del,ins,clip,g2p_overlap
-R1-seed,R1,15,1,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,9,0
-R1-seed,R1,15,4,2,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
-R1-seed,R1,15,7,3,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,9,0
+A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y,*,X,partial,del,ins,clip,g2p_overlap,coverage
+R1-seed,R1,15,1,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,9,0,0
+R1-seed,R1,15,4,2,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,9
+R1-seed,R1,15,7,3,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,9,0,0
 """
 
         self.report.read_clipping(clipping)
@@ -847,16 +847,16 @@ def testInsertionBetweenReadAndConsensusNucleotideReport(self):
 """)
 
         expected_text = """\
-seed,region,q-cutoff,query.nuc.pos,refseq.nuc.pos,A,C,G,T,N,del,ins,clip,g2p_overlap
-R1-seed,R1,15,1,1,9,0,0,0,0,0,0,0,0
-R1-seed,R1,15,2,2,9,0,0,0,0,0,0,0,0
-R1-seed,R1,15,3,3,9,0,0,0,0,0,2,0,0
-R1-seed,R1,15,4,4,0,0,0,9,0,0,0,0,0
-R1-seed,R1,15,5,5,0,0,0,9,0,0,0,0,0
-R1-seed,R1,15,6,6,0,0,0,9,0,0,0,0,0
-R1-seed,R1,15,,7,0,0,0,0,0,0,0,0,0
-R1-seed,R1,15,,8,0,0,0,0,0,0,0,0,0
-R1-seed,R1,15,,9,0,0,0,0,0,0,0,0,0
+seed,region,q-cutoff,query.nuc.pos,refseq.nuc.pos,A,C,G,T,N,del,ins,clip,g2p_overlap,coverage
+R1-seed,R1,15,1,1,9,0,0,0,0,0,0,0,0,9
+R1-seed,R1,15,2,2,9,0,0,0,0,0,0,0,0,9
+R1-seed,R1,15,3,3,9,0,0,0,0,0,2,0,0,9
+R1-seed,R1,15,4,4,0,0,0,9,0,0,0,0,0,9
+R1-seed,R1,15,5,5,0,0,0,9,0,0,0,0,0,9
+R1-seed,R1,15,6,6,0,0,0,9,0,0,0,0,0,9
+R1-seed,R1,15,,7,0,0,0,0,0,0,0,0,0,0
+R1-seed,R1,15,,8,0,0,0,0,0,0,0,0,0,0
+R1-seed,R1,15,,9,0,0,0,0,0,0,0,0,0,0
 """
 
         self.report.read_insertions(conseq_ins_csv)
@@ -881,10 +881,10 @@ def testInsertionBetweenReadAndConsensusAminoReport(self):
 
         expected_text = """\
 seed,region,q-cutoff,query.nuc.pos,refseq.aa.pos,\
-A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y,*,X,partial,del,ins,clip,g2p_overlap
-R1-seed,R1,15,1,1,0,0,0,0,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,0,0
-R1-seed,R1,15,4,2,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
-R1-seed,R1,15,,3,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y,*,X,partial,del,ins,clip,g2p_overlap,coverage
+R1-seed,R1,15,1,1,0,0,0,0,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,0,0,9
+R1-seed,R1,15,4,2,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,9
+R1-seed,R1,15,,3,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
 """
 
         self.report.read_insertions(conseq_ins_csv)
@@ -915,10 +915,10 @@ def testSubstitutionAtBoundary(self):
 
         expected_text = """\
 seed,region,q-cutoff,query.nuc.pos,refseq.aa.pos,\
-A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y,*,X,partial,del,ins,clip,g2p_overlap
-R4-seed,R4,15,10,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,9,0,0,0,0,0,0,0,0
-R4-seed,R4,15,13,2,0,0,0,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
-R4-seed,R4,15,16,3,0,0,0,0,0,0,0,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y,*,X,partial,del,ins,clip,g2p_overlap,coverage
+R4-seed,R4,15,10,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,9,0,0,0,0,0,0,0,0,9
+R4-seed,R4,15,13,2,0,0,0,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,9
+R4-seed,R4,15,16,3,0,0,0,0,0,0,0,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,9
 """
 
         self.report.write_amino_header(self.report_file)
@@ -990,16 +990,16 @@ def testOffsetNucleotideReport(self):
 """)
 
         expected_text = """\
-seed,region,q-cutoff,query.nuc.pos,refseq.nuc.pos,A,C,G,T,N,del,ins,clip,g2p_overlap
-R1-seed,R1,15,1,1,0,0,0,0,0,0,0,0,0
-R1-seed,R1,15,2,2,0,0,0,0,0,0,0,0,0
-R1-seed,R1,15,3,3,0,0,0,0,0,0,0,0,0
-R1-seed,R1,15,4,4,0,0,0,1,0,0,0,0,0
-R1-seed,R1,15,5,5,0,0,0,1,0,0,0,0,0
-R1-seed,R1,15,6,6,0,0,0,9,0,0,0,0,0
-R1-seed,R1,15,7,7,0,8,0,0,0,0,0,0,0
-R1-seed,R1,15,8,8,0,0,8,0,0,0,0,0,0
-R1-seed,R1,15,9,9,8,0,0,0,0,0,0,0,0
+seed,region,q-cutoff,query.nuc.pos,refseq.nuc.pos,A,C,G,T,N,del,ins,clip,g2p_overlap,coverage
+R1-seed,R1,15,1,1,0,0,0,0,0,0,0,0,0,0
+R1-seed,R1,15,2,2,0,0,0,0,0,0,0,0,0,0
+R1-seed,R1,15,3,3,0,0,0,0,0,0,0,0,0,0
+R1-seed,R1,15,4,4,0,0,0,1,0,0,0,0,0,1
+R1-seed,R1,15,5,5,0,0,0,1,0,0,0,0,0,1
+R1-seed,R1,15,6,6,0,0,0,9,0,0,0,0,0,9
+R1-seed,R1,15,7,7,0,8,0,0,0,0,0,0,0,8
+R1-seed,R1,15,8,8,0,0,8,0,0,0,0,0,0,8
+R1-seed,R1,15,9,9,8,0,0,0,0,0,0,0,0,8
 """
 
         self.report.read(aligned_reads)
@@ -1015,16 +1015,16 @@ def testPartialCodonNucleotideReport(self):
 """)
 
         expected_text = """\
-seed,region,q-cutoff,query.nuc.pos,refseq.nuc.pos,A,C,G,T,N,del,ins,clip,g2p_overlap
-R1-seed,R1,15,1,1,9,0,0,0,0,0,0,0,0
-R1-seed,R1,15,2,2,9,0,0,0,0,0,0,0,0
-R1-seed,R1,15,3,3,9,0,0,0,0,0,0,0,0
-R1-seed,R1,15,4,4,0,0,0,9,0,0,0,0,0
-R1-seed,R1,15,5,5,0,0,0,9,0,0,0,0,0
-R1-seed,R1,15,6,6,0,0,0,0,0,0,0,0,0
-R1-seed,R1,15,,7,0,0,0,0,0,0,0,0,0
-R1-seed,R1,15,,8,0,0,0,0,0,0,0,0,0
-R1-seed,R1,15,,9,0,0,0,0,0,0,0,0,0
+seed,region,q-cutoff,query.nuc.pos,refseq.nuc.pos,A,C,G,T,N,del,ins,clip,g2p_overlap,coverage
+R1-seed,R1,15,1,1,9,0,0,0,0,0,0,0,0,9
+R1-seed,R1,15,2,2,9,0,0,0,0,0,0,0,0,9
+R1-seed,R1,15,3,3,9,0,0,0,0,0,0,0,0,9
+R1-seed,R1,15,4,4,0,0,0,9,0,0,0,0,0,9
+R1-seed,R1,15,5,5,0,0,0,9,0,0,0,0,0,9
+R1-seed,R1,15,6,6,0,0,0,0,0,0,0,0,0,0
+R1-seed,R1,15,,7,0,0,0,0,0,0,0,0,0,0
+R1-seed,R1,15,,8,0,0,0,0,0,0,0,0,0,0
+R1-seed,R1,15,,9,0,0,0,0,0,0,0,0,0,0
 """
 
         self.report.read(aligned_reads)
@@ -1040,16 +1040,16 @@ def testLowQualityNucleotideReport(self):
 """)
 
         expected_text = """\
-seed,region,q-cutoff,query.nuc.pos,refseq.nuc.pos,A,C,G,T,N,del,ins,clip,g2p_overlap
-R1-seed,R1,15,1,1,9,0,0,0,0,0,0,0,0
-R1-seed,R1,15,2,2,9,0,0,0,0,0,0,0,0
-R1-seed,R1,15,3,3,9,0,0,0,0,0,0,0,0
-R1-seed,R1,15,4,4,0,0,0,9,0,0,0,0,0
-R1-seed,R1,15,5,5,0,0,0,0,9,0,0,0,0
-R1-seed,R1,15,6,6,0,0,0,9,0,0,0,0,0
-R1-seed,R1,15,,7,0,0,0,0,0,0,0,0,0
-R1-seed,R1,15,,8,0,0,0,0,0,0,0,0,0
-R1-seed,R1,15,,9,0,0,0,0,0,0,0,0,0
+seed,region,q-cutoff,query.nuc.pos,refseq.nuc.pos,A,C,G,T,N,del,ins,clip,g2p_overlap,coverage
+R1-seed,R1,15,1,1,9,0,0,0,0,0,0,0,0,9
+R1-seed,R1,15,2,2,9,0,0,0,0,0,0,0,0,9
+R1-seed,R1,15,3,3,9,0,0,0,0,0,0,0,0,9
+R1-seed,R1,15,4,4,0,0,0,9,0,0,0,0,0,9
+R1-seed,R1,15,5,5,0,0,0,0,9,0,0,0,0,0
+R1-seed,R1,15,6,6,0,0,0,9,0,0,0,0,0,9
+R1-seed,R1,15,,7,0,0,0,0,0,0,0,0,0,0
+R1-seed,R1,15,,8,0,0,0,0,0,0,0,0,0,0
+R1-seed,R1,15,,9,0,0,0,0,0,0,0,0,0,0
 """
 
         self.report.read(aligned_reads)
@@ -1066,10 +1066,10 @@ def testLowQualityAminoReport(self):
 
         expected_text = """\
 seed,region,q-cutoff,query.nuc.pos,refseq.aa.pos,\
-A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y,*,X,partial,del,ins,clip,g2p_overlap
-R1-seed,R1,15,1,1,0,0,0,0,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
-R1-seed,R1,15,4,2,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,9,0,0,0,0,0
-R1-seed,R1,15,,3,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y,*,X,partial,del,ins,clip,g2p_overlap,coverage
+R1-seed,R1,15,1,1,0,0,0,0,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,9
+R1-seed,R1,15,4,2,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,9,0,0,0,0,0,0
+R1-seed,R1,15,,3,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
 """
 
         self.report.read(aligned_reads)
@@ -1086,10 +1086,10 @@ def testPartialDeletionAminoReport(self):
 
         expected_text = """\
 seed,region,q-cutoff,query.nuc.pos,refseq.aa.pos,\
-A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y,*,X,partial,del,ins,clip,g2p_overlap
-R1-seed,R1,15,1,1,0,0,0,0,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
-R1-seed,R1,15,4,2,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,9,0,0,0,0
-R1-seed,R1,15,,3,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y,*,X,partial,del,ins,clip,g2p_overlap,coverage
+R1-seed,R1,15,1,1,0,0,0,0,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,9
+R1-seed,R1,15,4,2,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,9,0,0,0,0,0
+R1-seed,R1,15,,3,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
 """
 
         self.report.read(aligned_reads)
@@ -1112,10 +1112,10 @@ def testShiftedReadingFrameAminoReport(self):
 
         expected_text = """\
 seed,region,q-cutoff,query.nuc.pos,refseq.aa.pos,\
-A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y,*,X,partial,del,ins,clip,g2p_overlap
-R1-seed,R1,15,2,1,0,0,0,0,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
-R1-seed,R1,15,5,2,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
-R1-seed,R1,15,8,3,0,0,0,0,0,0,0,0,0,0,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0
+A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y,*,X,partial,del,ins,clip,g2p_overlap,coverage
+R1-seed,R1,15,2,1,0,0,0,0,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,9
+R1-seed,R1,15,5,2,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,9
+R1-seed,R1,15,8,3,0,0,0,0,0,0,0,0,0,0,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,9
 """
 
         self.report.read(aligned_reads)
@@ -1137,16 +1137,16 @@ def testShiftedReadingFrameNucleotideReport(self):
 """)
 
         expected_text = """\
-seed,region,q-cutoff,query.nuc.pos,refseq.nuc.pos,A,C,G,T,N,del,ins,clip,g2p_overlap
-R1-seed,R1,15,2,1,9,0,0,0,0,0,0,0,0
-R1-seed,R1,15,3,2,9,0,0,0,0,0,0,0,0
-R1-seed,R1,15,4,3,9,0,0,0,0,0,0,0,0
-R1-seed,R1,15,5,4,0,0,0,9,0,0,0,0,0
-R1-seed,R1,15,6,5,0,0,0,9,0,0,0,0,0
-R1-seed,R1,15,7,6,0,0,0,9,0,0,0,0,0
-R1-seed,R1,15,8,7,0,9,0,0,0,0,0,0,0
-R1-seed,R1,15,9,8,0,0,9,0,0,0,0,0,0
-R1-seed,R1,15,10,9,9,0,0,0,0,0,0,0,0
+seed,region,q-cutoff,query.nuc.pos,refseq.nuc.pos,A,C,G,T,N,del,ins,clip,g2p_overlap,coverage
+R1-seed,R1,15,2,1,9,0,0,0,0,0,0,0,0,9
+R1-seed,R1,15,3,2,9,0,0,0,0,0,0,0,0,9
+R1-seed,R1,15,4,3,9,0,0,0,0,0,0,0,0,9
+R1-seed,R1,15,5,4,0,0,0,9,0,0,0,0,0,9
+R1-seed,R1,15,6,5,0,0,0,9,0,0,0,0,0,9
+R1-seed,R1,15,7,6,0,0,0,9,0,0,0,0,0,9
+R1-seed,R1,15,8,7,0,9,0,0,0,0,0,0,0,9
+R1-seed,R1,15,9,8,0,0,9,0,0,0,0,0,0,9
+R1-seed,R1,15,10,9,9,0,0,0,0,0,0,0,0,9
 """
 
         self.report.read(aligned_reads)
@@ -1167,16 +1167,16 @@ def testDeletionNucleotideReport(self):
 """)
 
         expected_text = """\
-seed,region,q-cutoff,query.nuc.pos,refseq.nuc.pos,A,C,G,T,N,del,ins,clip,g2p_overlap
-R1-seed,R1,15,1,1,9,0,0,0,0,0,0,0,0
-R1-seed,R1,15,2,2,9,0,0,0,0,0,0,0,0
-R1-seed,R1,15,3,3,9,0,0,0,0,0,0,0,0
-R1-seed,R1,15,4,4,0,0,0,0,0,9,0,0,0
-R1-seed,R1,15,5,5,0,0,0,0,0,9,0,0,0
-R1-seed,R1,15,6,6,0,0,0,0,0,9,0,0,0
-R1-seed,R1,15,7,7,9,0,0,0,0,0,0,0,0
-R1-seed,R1,15,8,8,0,0,9,0,0,0,0,0,0
-R1-seed,R1,15,9,9,0,0,9,0,0,0,0,0,0
+seed,region,q-cutoff,query.nuc.pos,refseq.nuc.pos,A,C,G,T,N,del,ins,clip,g2p_overlap,coverage
+R1-seed,R1,15,1,1,9,0,0,0,0,0,0,0,0,9
+R1-seed,R1,15,2,2,9,0,0,0,0,0,0,0,0,9
+R1-seed,R1,15,3,3,9,0,0,0,0,0,0,0,0,9
+R1-seed,R1,15,4,4,0,0,0,0,0,9,0,0,0,9
+R1-seed,R1,15,5,5,0,0,0,0,0,9,0,0,0,9
+R1-seed,R1,15,6,6,0,0,0,0,0,9,0,0,0,9
+R1-seed,R1,15,7,7,9,0,0,0,0,0,0,0,0,9
+R1-seed,R1,15,8,8,0,0,9,0,0,0,0,0,0,9
+R1-seed,R1,15,9,9,0,0,9,0,0,0,0,0,0,9
 """
 
         self.report.read(aligned_reads)
@@ -1197,22 +1197,22 @@ def testDeletionBetweenSeedAndCoordinateNucleotideReport(self):
 """)
 
         expected_text = """\
-seed,region,q-cutoff,query.nuc.pos,refseq.nuc.pos,A,C,G,T,N,del,ins,clip,g2p_overlap
-R2-seed,R2,15,1,1,9,0,0,0,0,0,0,0,0
-R2-seed,R2,15,2,2,9,0,0,0,0,0,0,0,0
-R2-seed,R2,15,3,3,9,0,0,0,0,0,0,0,0
-R2-seed,R2,15,4,4,0,0,0,9,0,0,0,0,0
-R2-seed,R2,15,5,5,0,0,0,9,0,0,0,0,0
-R2-seed,R2,15,6,6,0,0,0,9,0,0,0,0,0
-R2-seed,R2,15,,7,0,0,0,0,0,9,0,0,0
-R2-seed,R2,15,,8,0,0,0,0,0,9,0,0,0
-R2-seed,R2,15,,9,0,0,0,0,0,9,0,0,0
-R2-seed,R2,15,7,10,0,9,0,0,0,0,0,0,0
-R2-seed,R2,15,8,11,0,9,0,0,0,0,0,0,0
-R2-seed,R2,15,9,12,0,9,0,0,0,0,0,0,0
-R2-seed,R2,15,10,13,0,9,0,0,0,0,0,0,0
-R2-seed,R2,15,11,14,0,0,9,0,0,0,0,0,0
-R2-seed,R2,15,12,15,9,0,0,0,0,0,0,0,0
+seed,region,q-cutoff,query.nuc.pos,refseq.nuc.pos,A,C,G,T,N,del,ins,clip,g2p_overlap,coverage
+R2-seed,R2,15,1,1,9,0,0,0,0,0,0,0,0,9
+R2-seed,R2,15,2,2,9,0,0,0,0,0,0,0,0,9
+R2-seed,R2,15,3,3,9,0,0,0,0,0,0,0,0,9
+R2-seed,R2,15,4,4,0,0,0,9,0,0,0,0,0,9
+R2-seed,R2,15,5,5,0,0,0,9,0,0,0,0,0,9
+R2-seed,R2,15,6,6,0,0,0,9,0,0,0,0,0,9
+R2-seed,R2,15,,7,0,0,0,0,0,9,0,0,0,9
+R2-seed,R2,15,,8,0,0,0,0,0,9,0,0,0,9
+R2-seed,R2,15,,9,0,0,0,0,0,9,0,0,0,9
+R2-seed,R2,15,7,10,0,9,0,0,0,0,0,0,0,9
+R2-seed,R2,15,8,11,0,9,0,0,0,0,0,0,0,9
+R2-seed,R2,15,9,12,0,9,0,0,0,0,0,0,0,9
+R2-seed,R2,15,10,13,0,9,0,0,0,0,0,0,0,9
+R2-seed,R2,15,11,14,0,0,9,0,0,0,0,0,0,9
+R2-seed,R2,15,12,15,9,0,0,0,0,0,0,0,0,9
 """
 
         self.report.read(aligned_reads)
@@ -1234,12 +1234,12 @@ def testDeletionBetweenSeedAndCoordinateAminoReport(self):
 
         expected_text = """\
 seed,region,q-cutoff,query.nuc.pos,refseq.aa.pos,\
-A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y,*,X,partial,del,ins,clip,g2p_overlap
-R2-seed,R2,15,1,1,0,0,0,0,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
-R2-seed,R2,15,4,2,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
-R2-seed,R2,15,,3,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,9,0,0,0
-R2-seed,R2,15,7,4,0,0,0,0,0,0,0,0,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0
-R2-seed,R2,15,10,5,0,0,0,0,0,0,0,0,0,0,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0
+A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y,*,X,partial,del,ins,clip,g2p_overlap,coverage
+R2-seed,R2,15,1,1,0,0,0,0,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,9
+R2-seed,R2,15,4,2,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,9
+R2-seed,R2,15,,3,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,9,0,0,0,9
+R2-seed,R2,15,7,4,0,0,0,0,0,0,0,0,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,9
+R2-seed,R2,15,10,5,0,0,0,0,0,0,0,0,0,0,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,9
 """
 
         self.report.read(aligned_reads)
@@ -1260,12 +1260,12 @@ def testDeletionBetweenSeedAndConsensusAminoReport(self):
         #         A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y,*,X,partial,del,ins,clip
         expected_text = """\
 seed,region,q-cutoff,query.nuc.pos,refseq.aa.pos,\
-A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y,*,X,partial,del,ins,clip,g2p_overlap
-R5-seed,R5,15,1,1,0,0,0,0,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
-R5-seed,R5,15,4,2,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
-R5-seed,R5,15,7,3,0,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
-R5-seed,R5,15,10,4,0,0,0,0,0,0,0,0,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0
-R5-seed,R5,15,13,5,0,0,0,0,0,0,0,0,0,0,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0
+A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y,*,X,partial,del,ins,clip,g2p_overlap,coverage
+R5-seed,R5,15,1,1,0,0,0,0,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,9
+R5-seed,R5,15,4,2,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,9
+R5-seed,R5,15,7,3,0,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,9
+R5-seed,R5,15,10,4,0,0,0,0,0,0,0,0,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,9
+R5-seed,R5,15,13,5,0,0,0,0,0,0,0,0,0,0,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,9
 """
 
         self.report.write_amino_header(self.report_file)
@@ -1288,10 +1288,10 @@ def testDeletionWithMinorityVariant(self):
 
         expected_text = """\
 seed,region,q-cutoff,query.nuc.pos,refseq.aa.pos,\
-A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y,*,X,partial,del,ins,clip,g2p_overlap
-R1-seed,R1,15,1,1,0,0,0,0,0,0,0,0,7,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
-R1-seed,R1,15,4,2,0,0,0,0,2,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,5,0,0,0
-R1-seed,R1,15,7,3,0,0,0,0,0,0,0,0,0,0,0,0,0,0,7,0,0,0,0,0,0,0,0,0,0,0,0
+A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y,*,X,partial,del,ins,clip,g2p_overlap,coverage
+R1-seed,R1,15,1,1,0,0,0,0,0,0,0,0,7,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,7
+R1-seed,R1,15,4,2,0,0,0,0,2,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,5,0,0,0,7
+R1-seed,R1,15,7,3,0,0,0,0,0,0,0,0,0,0,0,0,0,0,7,0,0,0,0,0,0,0,0,0,0,0,0,7
 """
 
         self.report.read(aligned_reads)
@@ -1308,10 +1308,10 @@ def testDeletionNotAlignedToCodons(self):
 
         expected_text = """\
 seed,region,q-cutoff,query.nuc.pos,refseq.aa.pos,\
-A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y,*,X,partial,del,ins,clip,g2p_overlap
-R1-seed,R1,15,1,1,0,0,0,0,0,0,0,0,5,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
-R1-seed,R1,15,4,2,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,5,0,0,0
-R1-seed,R1,15,7,3,0,0,0,0,0,0,0,0,0,0,0,0,0,0,5,0,0,0,0,0,0,0,0,0,0,0,0
+A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y,*,X,partial,del,ins,clip,g2p_overlap,coverage
+R1-seed,R1,15,1,1,0,0,0,0,0,0,0,0,5,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,5
+R1-seed,R1,15,4,2,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,5,0,0,0,5
+R1-seed,R1,15,7,3,0,0,0,0,0,0,0,0,0,0,0,0,0,0,5,0,0,0,0,0,0,0,0,0,0,0,0,5
 """
         self.report.remap_conseqs = {'R1-seed': 'AAATTTAGG'}
 
@@ -1334,15 +1334,15 @@ def testInsertionBetweenSeedAndCoordinateAminoReport(self):
 
         expected_text = """\
 seed,region,q-cutoff,query.nuc.pos,refseq.aa.pos,\
-A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y,*,X,partial,del,ins,clip,g2p_overlap
-R3-seed,R3,15,10,1,0,0,0,0,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
-R3-seed,R3,15,13,2,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
-R3-seed,R3,15,16,3,0,0,0,0,0,0,0,0,0,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0
-R3-seed,R3,15,19,4,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,9,0,0,0,0,0,0,0,9,0,0
-R3-seed,R3,15,25,5,0,0,0,0,0,0,0,0,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0
-R3-seed,R3,15,28,6,0,0,0,0,0,0,0,0,0,0,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0
-R3-seed,R3,15,31,7,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
-R3-seed,R3,15,34,8,0,0,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y,*,X,partial,del,ins,clip,g2p_overlap,coverage
+R3-seed,R3,15,10,1,0,0,0,0,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,9
+R3-seed,R3,15,13,2,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,9
+R3-seed,R3,15,16,3,0,0,0,0,0,0,0,0,0,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,9
+R3-seed,R3,15,19,4,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,9,0,0,0,0,0,0,0,9,0,0,9
+R3-seed,R3,15,25,5,0,0,0,0,0,0,0,0,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,9
+R3-seed,R3,15,28,6,0,0,0,0,0,0,0,0,0,0,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,9
+R3-seed,R3,15,31,7,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,9
+R3-seed,R3,15,34,8,0,0,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,9
 """
         expected_insertions = """\
 seed,region,qcut,left,insert,count,before
@@ -1371,31 +1371,31 @@ def testInsertionBetweenSeedAndCoordinateNucleotideReport(self):
 R3-seed,15,0,9,0,CATGAGCGAAAATTTCAGACTGGGCCCCGAGAGCATCAGTTTAAA
 """)
         expected_text = """\
-seed,region,q-cutoff,query.nuc.pos,refseq.nuc.pos,A,C,G,T,N,del,ins,clip,g2p_overlap
-R3-seed,R3,15,10,1,9,0,0,0,0,0,0,0,0
-R3-seed,R3,15,11,2,9,0,0,0,0,0,0,0,0
-R3-seed,R3,15,12,3,9,0,0,0,0,0,0,0,0
-R3-seed,R3,15,13,4,0,0,0,9,0,0,0,0,0
-R3-seed,R3,15,14,5,0,0,0,9,0,0,0,0,0
-R3-seed,R3,15,15,6,0,0,0,9,0,0,0,0,0
-R3-seed,R3,15,16,7,0,9,0,0,0,0,0,0,0
-R3-seed,R3,15,17,8,9,0,0,0,0,0,0,0,0
-R3-seed,R3,15,18,9,0,0,9,0,0,0,0,0,0
-R3-seed,R3,15,19,10,9,0,0,0,0,0,0,0,0
-R3-seed,R3,15,20,11,0,9,0,0,0,0,0,0,0
-R3-seed,R3,15,21,12,0,0,0,9,0,0,9,0,0
-R3-seed,R3,15,25,13,0,9,0,0,0,0,0,0,0
-R3-seed,R3,15,26,14,0,9,0,0,0,0,0,0,0
-R3-seed,R3,15,27,15,0,9,0,0,0,0,0,0,0
-R3-seed,R3,15,28,16,0,9,0,0,0,0,0,0,0
-R3-seed,R3,15,29,17,0,0,9,0,0,0,0,0,0
-R3-seed,R3,15,30,18,9,0,0,0,0,0,0,0,0
-R3-seed,R3,15,31,19,0,0,9,0,0,0,0,0,0
-R3-seed,R3,15,32,20,9,0,0,0,0,0,0,0,0
-R3-seed,R3,15,33,21,0,0,9,0,0,0,0,0,0
-R3-seed,R3,15,34,22,0,9,0,0,0,0,0,0,0
-R3-seed,R3,15,35,23,9,0,0,0,0,0,0,0,0
-R3-seed,R3,15,36,24,0,0,0,9,0,0,0,0,0
+seed,region,q-cutoff,query.nuc.pos,refseq.nuc.pos,A,C,G,T,N,del,ins,clip,g2p_overlap,coverage
+R3-seed,R3,15,10,1,9,0,0,0,0,0,0,0,0,9
+R3-seed,R3,15,11,2,9,0,0,0,0,0,0,0,0,9
+R3-seed,R3,15,12,3,9,0,0,0,0,0,0,0,0,9
+R3-seed,R3,15,13,4,0,0,0,9,0,0,0,0,0,9
+R3-seed,R3,15,14,5,0,0,0,9,0,0,0,0,0,9
+R3-seed,R3,15,15,6,0,0,0,9,0,0,0,0,0,9
+R3-seed,R3,15,16,7,0,9,0,0,0,0,0,0,0,9
+R3-seed,R3,15,17,8,9,0,0,0,0,0,0,0,0,9
+R3-seed,R3,15,18,9,0,0,9,0,0,0,0,0,0,9
+R3-seed,R3,15,19,10,9,0,0,0,0,0,0,0,0,9
+R3-seed,R3,15,20,11,0,9,0,0,0,0,0,0,0,9
+R3-seed,R3,15,21,12,0,0,0,9,0,0,9,0,0,9
+R3-seed,R3,15,25,13,0,9,0,0,0,0,0,0,0,9
+R3-seed,R3,15,26,14,0,9,0,0,0,0,0,0,0,9
+R3-seed,R3,15,27,15,0,9,0,0,0,0,0,0,0,9
+R3-seed,R3,15,28,16,0,9,0,0,0,0,0,0,0,9
+R3-seed,R3,15,29,17,0,0,9,0,0,0,0,0,0,9
+R3-seed,R3,15,30,18,9,0,0,0,0,0,0,0,0,9
+R3-seed,R3,15,31,19,0,0,9,0,0,0,0,0,0,9
+R3-seed,R3,15,32,20,9,0,0,0,0,0,0,0,0,9
+R3-seed,R3,15,33,21,0,0,9,0,0,0,0,0,0,9
+R3-seed,R3,15,34,22,0,9,0,0,0,0,0,0,0,9
+R3-seed,R3,15,35,23,9,0,0,0,0,0,0,0,0,9
+R3-seed,R3,15,36,24,0,0,0,9,0,0,0,0,0,9
 """
 
         self.report.read(aligned_reads)
@@ -1557,12 +1557,12 @@ def testGapBetweenForwardAndReverse(self):
 
         expected_text = """\
 seed,region,q-cutoff,query.nuc.pos,refseq.aa.pos,\
-A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y,*,X,partial,del,ins,clip,g2p_overlap
-R2-seed,R2,15,1,1,0,0,0,0,0,0,0,0,5,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
-R2-seed,R2,15,4,2,0,0,0,0,5,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
-R2-seed,R2,15,7,3,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
-R2-seed,R2,15,10,4,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
-R2-seed,R2,15,13,5,0,0,0,0,0,0,0,0,0,0,0,0,0,0,5,0,0,0,0,0,0,0,0,0,0,0,0
+A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y,*,X,partial,del,ins,clip,g2p_overlap,coverage
+R2-seed,R2,15,1,1,0,0,0,0,0,0,0,0,5,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,5
+R2-seed,R2,15,4,2,0,0,0,0,5,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,5
+R2-seed,R2,15,7,3,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+R2-seed,R2,15,10,4,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+R2-seed,R2,15,13,5,0,0,0,0,0,0,0,0,0,0,0,0,0,0,5,0,0,0,0,0,0,0,0,0,0,0,0,5
 """
 
         self.report.read(aligned_reads)
@@ -1765,16 +1765,16 @@ def testRegionWithoutCoordinateReferenceNucleotideReport(self):
 """)
 
         expected_text = """\
-seed,region,q-cutoff,query.nuc.pos,refseq.nuc.pos,A,C,G,T,N,del,ins,clip,g2p_overlap
-R-NO-COORD,R-NO-COORD,15,1,,9,0,0,0,0,0,0,0,0
-R-NO-COORD,R-NO-COORD,15,2,,9,0,0,0,0,0,0,0,0
-R-NO-COORD,R-NO-COORD,15,3,,9,0,0,0,0,0,0,0,0
-R-NO-COORD,R-NO-COORD,15,4,,0,0,0,9,0,0,0,0,0
-R-NO-COORD,R-NO-COORD,15,5,,0,0,0,9,0,0,0,0,0
-R-NO-COORD,R-NO-COORD,15,6,,0,0,0,9,0,0,0,0,0
-R-NO-COORD,R-NO-COORD,15,7,,0,0,0,0,0,0,0,0,0
-R-NO-COORD,R-NO-COORD,15,8,,0,0,0,0,0,0,0,0,0
-R-NO-COORD,R-NO-COORD,15,9,,0,0,0,0,0,0,0,0,0
+seed,region,q-cutoff,query.nuc.pos,refseq.nuc.pos,A,C,G,T,N,del,ins,clip,g2p_overlap,coverage
+R-NO-COORD,R-NO-COORD,15,1,,9,0,0,0,0,0,0,0,0,9
+R-NO-COORD,R-NO-COORD,15,2,,9,0,0,0,0,0,0,0,0,9
+R-NO-COORD,R-NO-COORD,15,3,,9,0,0,0,0,0,0,0,0,9
+R-NO-COORD,R-NO-COORD,15,4,,0,0,0,9,0,0,0,0,0,9
+R-NO-COORD,R-NO-COORD,15,5,,0,0,0,9,0,0,0,0,0,9
+R-NO-COORD,R-NO-COORD,15,6,,0,0,0,9,0,0,0,0,0,9
+R-NO-COORD,R-NO-COORD,15,7,,0,0,0,0,0,0,0,0,0,0
+R-NO-COORD,R-NO-COORD,15,8,,0,0,0,0,0,0,0,0,0,0
+R-NO-COORD,R-NO-COORD,15,9,,0,0,0,0,0,0,0,0,0,0
 """
 
         self.report.read(aligned_reads)
@@ -1848,14 +1848,14 @@ def testMultipleCoordinateAminoReport(self):
 
         expected_text = """\
 seed,region,q-cutoff,query.nuc.pos,refseq.aa.pos,\
-A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y,*,X,partial,del,ins,clip,g2p_overlap
-R1-seed,R1a,15,1,1,0,0,0,0,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
-R1-seed,R1a,15,4,2,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
-R1-seed,R1a,15,,3,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
-R1-seed,R1b,15,,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
-R1-seed,R1b,15,1,2,0,0,0,0,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
-R1-seed,R1b,15,4,3,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
-R1-seed,R1b,15,,4,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y,*,X,partial,del,ins,clip,g2p_overlap,coverage
+R1-seed,R1a,15,1,1,0,0,0,0,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,9
+R1-seed,R1a,15,4,2,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,9
+R1-seed,R1a,15,,3,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+R1-seed,R1b,15,,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+R1-seed,R1b,15,1,2,0,0,0,0,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,9
+R1-seed,R1b,15,4,3,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,9
+R1-seed,R1b,15,,4,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
 """
 
         self.report.read(aligned_reads)
diff --git a/micall/tests/hivdb_test.py b/micall/tests/hivdb_test.py
index 457e9382a..c4cfeee4d 100644
--- a/micall/tests/hivdb_test.py
+++ b/micall/tests/hivdb_test.py
@@ -138,13 +138,13 @@ class ReadAminosTest(TestCase):
     def test_simple(self):
         amino_csv = StringIO("""\
 seed,region,q-cutoff,query.nuc.pos,refseq.aa.pos,\
-A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y,*,X,partial,del,ins,clip,g2p_overlap
-R1-seed,R1,15,1,1,0,0,0,0,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
-R1-seed,R1,15,4,2,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
-R1-seed,R1,15,7,3,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y,*,X,partial,del,ins,clip,g2p_overlap,coverage
+R1-seed,R1,15,1,1,0,0,0,0,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,9
+R1-seed,R1,15,4,2,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,9
+R1-seed,R1,15,7,3,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,9
 """)
         min_fraction = 0.2
-        expected_aminos = [('R1', [['K'], ['F'], ['A']])]
+        expected_aminos = [('R1', [{'K': 1.0}, {'F': 1.0}, {'A': 1.0}])]
 
         aminos = list(read_aminos(amino_csv, min_fraction))
 
@@ -153,13 +153,13 @@ def test_simple(self):
     def test_mixtures(self):
         amino_csv = StringIO("""\
 seed,region,q-cutoff,query.nuc.pos,refseq.aa.pos,\
-A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y,*,X,partial,del,ins,clip,g2p_overlap
-R1-seed,R1,15,1,1,1,0,0,0,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
-R1-seed,R1,15,4,2,2,0,0,0,8,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
-R1-seed,R1,15,,3,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y,*,X,partial,del,ins,clip,g2p_overlap,coverage
+R1-seed,R1,15,1,1,1,0,0,0,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,10
+R1-seed,R1,15,4,2,2,0,0,0,8,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,10
+R1-seed,R1,15,,3,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
 """)
         min_fraction = 0.2
-        expected_aminos = [('R1', [['K'], ['A', 'F'], []])]
+        expected_aminos = [('R1', [{'K': 0.9}, {'F': 0.8, 'A': 0.2}, {}])]
 
         aminos = list(read_aminos(amino_csv, min_fraction))
 
@@ -168,13 +168,13 @@ def test_mixtures(self):
     def test_no_coverage(self):
         amino_csv = StringIO("""\
 seed,region,q-cutoff,query.nuc.pos,refseq.aa.pos,\
-A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y,*,X,partial,del,ins,clip,g2p_overlap
-R1-seed,R1,15,1,1,0,0,0,0,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
-R1-seed,R1,15,4,2,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
-R1-seed,R1,15,,3,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y,*,X,partial,del,ins,clip,g2p_overlap,coverage
+R1-seed,R1,15,1,1,0,0,0,0,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,9
+R1-seed,R1,15,4,2,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,9
+R1-seed,R1,15,,3,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
 """)
         min_fraction = 0.2
-        expected_aminos = [('R1', [['K'], ['F'], []])]
+        expected_aminos = [('R1', [{'K': 1.0}, {'F': 1.0}, {}])]
 
         aminos = list(read_aminos(amino_csv, min_fraction))
 
@@ -183,17 +183,17 @@ def test_no_coverage(self):
     def test_multiple_regions(self):
         amino_csv = StringIO("""\
 seed,region,q-cutoff,query.nuc.pos,refseq.aa.pos,\
-A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y,*,X,partial,del,ins,clip,g2p_overlap
-R1-seed,R1,15,1,1,0,0,0,0,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
-R1-seed,R1,15,4,2,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
-R1-seed,R1,15,,3,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
-R2-seed,R2,15,1,1,0,0,0,0,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
-R2-seed,R2,15,4,2,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
-R2-seed,R2,15,7,3,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y,*,X,partial,del,ins,clip,g2p_overlap,coverage
+R1-seed,R1,15,1,1,0,0,0,0,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,9
+R1-seed,R1,15,4,2,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,9
+R1-seed,R1,15,,3,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+R2-seed,R2,15,1,1,0,0,0,0,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,9
+R2-seed,R2,15,4,2,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,9
+R2-seed,R2,15,7,3,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,9
 """)
         min_fraction = 0.2
-        expected_aminos = [('R1', [['K'], ['F'], []]),
-                           ('R2', [['K'], ['F'], ['C']])]
+        expected_aminos = [('R1', [{'K': 1.0}, {'F': 1.0}, {}]),
+                           ('R2', [{'K': 1.0}, {'F': 1.0}, {'C': 1.0}])]
 
         aminos = list(read_aminos(amino_csv, min_fraction))
 
@@ -202,22 +202,22 @@ def test_multiple_regions(self):
     def test_reported_regions(self):
         amino_csv = StringIO("""\
 seed,region,q-cutoff,query.nuc.pos,refseq.aa.pos,\
-A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y,*,X,partial,del,ins,clip,g2p_overlap
-R1-seed,R1,15,1,1,0,0,0,0,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
-R1-seed,R1,15,4,2,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
-R1-seed,R1,15,,3,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
-R2-seed,R2,15,1,1,0,0,0,0,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
-R2-seed,R2,15,4,2,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
-R2-seed,R2,15,7,3,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
-R3-seed,R3,15,1,1,0,0,0,0,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
-R3-seed,R3,15,4,2,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
-R3-seed,R3,15,7,3,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y,*,X,partial,del,ins,clip,g2p_overlap,coverage
+R1-seed,R1,15,1,1,0,0,0,0,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,9
+R1-seed,R1,15,4,2,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,9
+R1-seed,R1,15,,3,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+R2-seed,R2,15,1,1,0,0,0,0,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,9
+R2-seed,R2,15,4,2,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,9
+R2-seed,R2,15,7,3,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,9
+R3-seed,R3,15,1,1,0,0,0,0,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,9
+R3-seed,R3,15,4,2,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,9
+R3-seed,R3,15,7,3,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,9
 """)
         min_fraction = 0.2
         reported_regions = {'R1': ['Region1', False],  # No data
                             'R2': ['Region2', True]}   # Others are skipped
         expected_aminos = [('Region1', None),
-                           ('Region2', [['K'], ['F'], ['C']])]
+                           ('Region2', [{'K': 1.0}, {'F': 1.0}, {'C': 1.0}])]
 
         aminos = list(read_aminos(amino_csv,
                                   min_fraction,
@@ -228,15 +228,15 @@ def test_reported_regions(self):
     def test_missing_region(self):
         amino_csv = StringIO("""\
 seed,region,q-cutoff,query.nuc.pos,refseq.aa.pos,\
-A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y,*,X,partial,del,ins,clip,g2p_overlap
-R2-seed,R2,15,1,1,0,0,0,0,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
-R2-seed,R2,15,4,2,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
-R2-seed,R2,15,7,3,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y,*,X,partial,del,ins,clip,g2p_overlap,coverage
+R2-seed,R2,15,1,1,0,0,0,0,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,9
+R2-seed,R2,15,4,2,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,9
+R2-seed,R2,15,7,3,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,9
 """)
         min_fraction = 0.2
         reported_regions = {'R1': ['Region1', False],  # No data
                             'R2': ['Region2', True]}   # Others are skipped
-        expected_aminos = [('Region2', [['K'], ['F'], ['C']]),
+        expected_aminos = [('Region2', [{'K': 1.0}, {'F': 1.0}, {'C': 1.0}]),
                            ('Region1', None)]
 
         aminos = list(read_aminos(amino_csv,
@@ -248,13 +248,13 @@ def test_missing_region(self):
     def test_deletions(self):
         amino_csv = StringIO("""\
 seed,region,q-cutoff,query.nuc.pos,refseq.aa.pos,\
-A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y,*,X,partial,del,ins,clip,g2p_overlap
-R1-seed,R1,15,1,1,0,0,0,0,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0
-R1-seed,R1,15,4,2,0,0,0,0,8,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,0,0,0
-R1-seed,R1,15,,3,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y,*,X,partial,del,ins,clip,g2p_overlap,coverage
+R1-seed,R1,15,1,1,0,0,0,0,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,10
+R1-seed,R1,15,4,2,0,0,0,0,8,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,0,0,0,10
+R1-seed,R1,15,,3,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
 """)
         min_fraction = 0.2
-        expected_aminos = [('R1', [['K'], ['F', 'd'], []])]
+        expected_aminos = [('R1', [{'K': 0.9}, {'F': 0.8, 'd': 0.2}, {}])]
 
         aminos = list(read_aminos(amino_csv, min_fraction))
 
@@ -263,13 +263,13 @@ def test_deletions(self):
     def test_insertions(self):
         amino_csv = StringIO("""\
 seed,region,q-cutoff,query.nuc.pos,refseq.aa.pos,\
-A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y,*,X,partial,del,ins,clip,g2p_overlap
-R1-seed,R1,15,1,1,0,0,0,0,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0
-R1-seed,R1,15,4,2,0,0,0,0,8,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,0,0
-R1-seed,R1,15,,3,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y,*,X,partial,del,ins,clip,g2p_overlap,coverage
+R1-seed,R1,15,1,1,0,0,0,0,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,9
+R1-seed,R1,15,4,2,0,0,0,0,8,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,0,0,8
+R1-seed,R1,15,,3,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
 """)
         min_fraction = 0.2
-        expected_aminos = [('R1', [['K'], ['F', 'i'], []])]
+        expected_aminos = [('R1', [{'K': 1.0}, {'F': 1.0, 'i': 0.25}, {}])]
 
         aminos = list(read_aminos(amino_csv, min_fraction))
 
@@ -278,13 +278,13 @@ def test_insertions(self):
     def test_stop_codons(self):
         amino_csv = StringIO("""\
 seed,region,q-cutoff,query.nuc.pos,refseq.aa.pos,\
-A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y,*,X,partial,del,ins,clip,g2p_overlap
-R1-seed,R1,15,1,1,0,0,0,0,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0
-R1-seed,R1,15,4,2,0,0,0,0,8,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,0,0,0,0,0,0
-R1-seed,R1,15,,3,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
+A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y,*,X,partial,del,ins,clip,g2p_overlap,coverage
+R1-seed,R1,15,1,1,0,0,0,0,0,0,0,0,9,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,10
+R1-seed,R1,15,4,2,0,0,0,0,8,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,0,0,0,0,0,0,10
+R1-seed,R1,15,,3,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
 """)
         min_fraction = 0.2
-        expected_aminos = [('R1', [['K'], ['F'], []])]
+        expected_aminos = [('R1', [{'K': 0.9}, {'F': 0.8}, {}])]
 
         aminos = list(read_aminos(amino_csv, min_fraction))
 
@@ -294,7 +294,7 @@ def test_stop_codons(self):
 class WriteResistanceTest(TestCase):
     def test_simple(self):
         self.maxDiff = None
-        aminos = [('RT', [['A']] * 40 + [['L']])]
+        aminos = [('RT', [{'A': 1.0}] * 40 + [{'L': 1.0}])]
         resistance_csv = StringIO()
         mutations_csv = StringIO()
         expected_resistance = """\
@@ -312,8 +312,8 @@ def test_simple(self):
 RT,NNRTI,RPV,rilpivirine,1,Susceptible,0.0
 """
         expected_mutations = """\
-drug_class,mutation
-NRTI,M41L
+drug_class,mutation,prevalence
+NRTI,M41L,1.0
 """
 
         write_resistance(aminos, resistance_csv, mutations_csv)
@@ -323,7 +323,7 @@ def test_simple(self):
 
     def test_low_coverage(self):
         aminos = [('PR', None),
-                  ('RT', [['A']] * 40 + [['L']])]
+                  ('RT', [{'A': 1.0}] * 40 + [{'L': 1.0}])]
         resistance_csv = StringIO()
         mutations_csv = StringIO()
         expected_resistance = """\
@@ -349,8 +349,37 @@ def test_low_coverage(self):
 RT,NNRTI,RPV,rilpivirine,1,Susceptible,0.0
 """
         expected_mutations = """\
-drug_class,mutation
-NRTI,M41L
+drug_class,mutation,prevalence
+NRTI,M41L,1.0
+"""
+
+        write_resistance(aminos, resistance_csv, mutations_csv)
+
+        self.assertEqual(expected_resistance, resistance_csv.getvalue())
+        self.assertEqual(expected_mutations, mutations_csv.getvalue())
+
+    def test_mixture(self):
+        self.maxDiff = None
+        aminos = [('RT', [{'A': 1.0}] * 40 + [{'L': 0.3}])]
+        resistance_csv = StringIO()
+        mutations_csv = StringIO()
+        expected_resistance = """\
+region,drug_class,drug,drug_name,level,level_name,score
+RT,NRTI,3TC,lamivudine,1,Susceptible,0.0
+RT,NRTI,ABC,abacavir,1,Susceptible,5.0
+RT,NRTI,AZT,zidovudine,3,Low-Level Resistance,15.0
+RT,NRTI,D4T,stavudine,3,Low-Level Resistance,15.0
+RT,NRTI,DDI,didanosine,2,Potential Low-Level Resistance,10.0
+RT,NRTI,FTC,emtricitabine,1,Susceptible,0.0
+RT,NRTI,TDF,tenofovir,1,Susceptible,5.0
+RT,NNRTI,EFV,efavirenz,1,Susceptible,0.0
+RT,NNRTI,ETR,etravirine,1,Susceptible,0.0
+RT,NNRTI,NVP,nevirapine,1,Susceptible,0.0
+RT,NNRTI,RPV,rilpivirine,1,Susceptible,0.0
+"""
+        expected_mutations = """\
+drug_class,mutation,prevalence
+NRTI,M41L,0.3
 """
 
         write_resistance(aminos, resistance_csv, mutations_csv)