Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.
ALE, Flask, Isolate Predicted Mutations Mean Coverage Total Reads Percent Mapped Mapped Reads Average Read Length
A0 F0 I1 R1 146 27.9 2327082 89.7% 2087392 107.8

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA AM260479 1,112,158 Δ1 bp coding (2295/2469 nt) xdhB1 ← xanthine dehydrogenase, subunit B

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*AM2604791,112,1560C.100.0% 24.8 / NA 7coding (2297/2469 nt)xdhB1xanthine dehydrogenase, subunit B
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base . (4/3);  total (4/3)

CGCGGCCAAGGGGGGAAAGTCCGGGGGCGCCCGCAGGCGCGCGCTTCCTGCGATCGTTCCGCCAGCTCAGGCTGGCTGCGCCGCGGCTTCGCGCACGGCGTCGACGGCGTCCAGGATCGCCCTCGCTGGTGGCCGGGGCCTTCAGCGGCGGGTTGATGCGGTAGTCGCCAACGGCAGCCACGGCGTCGCGGATCGCGAAGAACACCGAGAACGGCAGCAGCAGCGGCGGCTCGCCCACGGCCTTG  >  AM260479/1112037‑1112281
                                                                                                                       |                                                                                                                             
gacgGGCATGGGGGGAAAGTCCGGGGGCGCCCGCAGGCGCGCGCTTCCTGCGATCGTTCCGCCAGCTCAGGCTGGCTGCGCCGCGGCTTCGCGCACGGCGTCGACGGCGTCCAGGATCG‑CCTCGCTGGTGGCCg                                                                                                                >  2:172125/3‑134 (MQ=255)
                        gggCGCCCGCAGGCGCGCGCTTCCTGCGATCGTTCCGCCAGCTCAGGCTGGCTGCGCCGCGGCTTCGCGCACGGCGTCGACGGCGTCCAGGATCG‑CCTCGCTGGTGGCCGGGGCCTTCAGCGGCGGGTTGATGc                                                                                        >  1:1029558/1‑134 (MQ=255)
                        gggCGCCCGCAGGCGCGCGCTTCCTGCGATCGTTCCGCCAGCTCAGGCTGGCTGCGCCGCGGCTTCGCGCACGGCGTCGACGGCGTCCAGGATCG‑CCTCGCTGGTGGCCGGGGCCTTCAGCGGCGGGTTGATGc                                                                                        <  2:305643/134‑1 (MQ=255)
                                 cAGGCGCGCGCTTCCTGCGATCGTTCCGCCAGCTCAGGCTGGCTGCGCCGCGGCTTCGCGCACGGCGTCGACGGCGTCCAGGATCG‑CCTCGCTGGTGGCCGGGGCCTTCAGCGGCGGGTTGATGCGGTAGTCGc                                                                               >  1:837314/1‑134 (MQ=255)
                                                                                                              ccAGGATCG‑CCTCGCTGGTGGCCGGGGCCTTCAGCGGCGGGTTGATGCg                                                                                       <  1:762325/49‑1 (MQ=38)
                                                                                                              ccAGGATCG‑CCTCGCTGGTGGCCGGGGCCTTCAGCGGCGGGTTGATGCg                                                                                       >  2:762325/1‑49 (MQ=38)
                                                                                                               cAGGATCG‑CCTCGCTGGTGGCCGGGGCCTTCAGCGGCGGGTTGATGCGGTAGTCGCCAACGGCAGCCACGGCGTCGCGGATCGCGAAGAACACCGAGAACGGCAGCAGCAGCGGCGGCTCGCCCACGGCCTTg  <  1:316351/133‑1 (MQ=255)
                                                                                                                       |                                                                                                                             
CGCGGCCAAGGGGGGAAAGTCCGGGGGCGCCCGCAGGCGCGCGCTTCCTGCGATCGTTCCGCCAGCTCAGGCTGGCTGCGCCGCGGCTTCGCGCACGGCGTCGACGGCGTCCAGGATCGCCCTCGCTGGTGGCCGGGGCCTTCAGCGGCGGGTTGATGCGGTAGTCGCCAACGGCAGCCACGGCGTCGCGGATCGCGAAGAACACCGAGAACGGCAGCAGCAGCGGCGGCTCGCCCACGGCCTTG  >  AM260479/1112037‑1112281

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

BRESEQ :: bam2aln output
GGGGGGAAAGTCCGGGGGCGCCCGCAGGCGCGCGCTTCCTGCGATCGTTCCGCCAGCTCAGGCTGGCTGCGCCGCGGCTTCGCGCACGGCGTCGACGGCGTCCAGGATCGCCCTCGCTGGTGGCCGGGGCCTTCAGCGGCGGGTTGATGCGGTAGTCGCCAACGGCAGCCACGGCGTCGCGGATCGCGAAGAACACCGAGAACGGCAGCAGCAGCGGCGGCTCGCCCACGGCCTTGGAGCGGTGGATGCTG  >  AM260479/1112046‑1112296
                                                                                                                |                                                                                                                                          
GGGGGGAAAGTCCGGGGGCGCCCGCAGGCGCGCGCTTCCTGCGATCGTTCCGCCAGCTCAGGCTGGCTGCGCCGCGGCTTCGCGCACGGCGTCGACGGCGTCCAGGATCG‑CCTCGCTGGTGGCCGGGGCCTTCAGCGGCGGGTTGATGCG                                                                                                      >  GWNJ‑0478:712:GW2002102894th:2:2211:7676:40828/1‑150 (MQ=60)
         GTCCGGGGGCGCCCGCAGGCGCGCGCTTCCTGCGATCGTTCCGCCAGCTCAGGCTGGCTGCGCCGCGGCTTCGCGCACGGCGTCGACGGCGTCCAGGATCG‑CCTCGCTGGTGGCCGGGGCCTTCAGCGGCGGGTTGATGCGGTAGTCGCC                                                                                             >  GWNJ‑0478:712:GW2002102894th:2:2114:17488:38008/1‑150 (MQ=60)
                ttttcaagcagaagacggcatacgagattagcgagtgtctcgtgggctcggagatgtgtataagagacagCGGCGTCGACGGCGTCCAGGATCG‑CCTCGCTGGTGGCCGGGGCCTTCAGCGGCGGGTTGATGCGGTAGTCGCCAACGGC                                                                                       <  GWNJ‑0478:712:GW2002102894th:2:2110:6385:57483/79‑1 (MQ=60)
                                                              ccgtcgacgccgtgcgcgaagccgCGGCGTCGACGGCGTCAAGGATCG‑CCTCGCTGGTGGCCGGGGCCTTCAGCGGCGGGTTGATGCGGTAGTCGCCAACGGCAGCCACGGCGTCGCGGATCGCGAAGAACACCGAGAACctgtctctt                                         >  GWNJ‑0478:712:GW2002102894th:2:1205:10529:70597/25‑140 (MQ=60)
                                                                                                     CCAGGATCG‑CCTCGCTGGTGGCCGGGGCCTTCAGCGGCGGGTTGATGCGGTAGTCGCCAACGGCAGCCACGGCGTCGCGGATCGCGAAGAACACCGAGAACGGCAGCAGCAGCGGCGGCTCGCCCACGGCCTTGGAGCGGTGGATGCTG  <  GWNJ‑0478:712:GW2002102894th:2:1203:9593:85876/149‑1 (MQ=60)
                                                                                                                |                                                                                                                                          
GGGGGGAAAGTCCGGGGGCGCCCGCAGGCGCGCGCTTCCTGCGATCGTTCCGCCAGCTCAGGCTGGCTGCGCCGCGGCTTCGCGCACGGCGTCGACGGCGTCCAGGATCGCCCTCGCTGGTGGCCGGGGCCTTCAGCGGCGGGTTGATGCGGTAGTCGCCAACGGCAGCCACGGCGTCGCGGATCGCGAAGAACACCGAGAACGGCAGCAGCAGCGGCGGCTCGCCCACGGCCTTGGAGCGGTGGATGCTG  >  AM260479/1112046‑1112296

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑