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
A1 F1 I1 R1 154 26.6 2069536 90.2% 1866721 108.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA AM260479 1,042,407 T→G K131N (AAA→AAC)  h16_A0947 ← Coproporphyrinogen III oxidase, Fe‑S oxidoreductase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*AM2604791,042,4070TG100.0% 51.0 / NA 14K131N (AAA→AAC) h16_A0947Coproporphyrinogen III oxidase, Fe‑S oxidoreductase
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base G (7/7);  total (7/7)

CTTCGGCACCGCCGTGGATGCGCCCGAGCGCCTGGAGGTGCCGGTCGTTGAAGCTCTGGATGCCGATCGACAGCCGGTTGATGCCGCTGGCGCGGTAGCTGGCGAACTTGTCGGCCTCGAAGGTGCCGGGTTTGGCCTCCATCGTGATCTCGGCGTCGGCATCCAGCGGCAGCAGCGCGCGGATATCCGACAGCAGCCGGTCCATGCCTGCCGCCGACAGCAGGCTGGGCGTGCCGCCGCCGATAAAGACCGTATGCACC  >  AM260479/1042277‑1042536
                                                                                                                                  |                                                                                                                                 
cTTCGGCACCGCCGTGGATGCGCCCGAGCGCCTGGAGGTGCCGGTCGTTGAAGCTCTGGATGCCGATCGACAGCCGGTTGATGCCGCTGGCGCGGTAGCTGGCGAACTTGTCGGCCTCGAAGGTGCCGGGGTTg                                                                                                                                <  1:625461/134‑1 (MQ=255)
     gCACCGCCGTGGATGCGCCCGAGCGCCTGGAGGTGCCGGTCGTTGAAGCTCTGGATGCCGATCGACAGCCGGTTGATGCCGCTGGCGCGGTAGCTGGCGAACTTGTCGGCCTCGAAGGTGCCGGGGTTGGCCTc                                                                                                                           >  1:434116/1‑134 (MQ=255)
               ggATGCGCCCGAGCGCCTGGAGGTGCCGGTCGTTGAAGCTCTGGATGCCGATCGACAGCCGGTTGATGCCGCTGGCGCGGTAGCTGGCGAACTTGTCGGCCTCGAAGGTGCCGGGGTTGGCCTCCATCGTGAtc                                                                                                                 >  2:995554/1‑134 (MQ=255)
                          aGCGCCTGGAGGTGCCGGTCGTTGAAGCTCTGGATGCCGATCGACAGCCGGTTGATGCCGCTGGCGCGGTAGCTGGCGAACTTGTCGGCCTCGAAGGTGCCGGGGTTGGCCTCCATCGTGATCTCGGCGTCgg                                                                                                       >  1:57557/1‑133 (MQ=255)
                                  gAGGTGCCGGTCGTTGAAGCTCTGGATGCCGATCGACAGCCGGTTGATGCCGCTGGCGCGGTAGCTGGCGAACTTGTCGGCCTCGAAGGTGCCGGGGTTGGCCTCCATCGTGATCTCGGCGTCGGCATCCAGc                                                                                               <  2:800679/133‑1 (MQ=255)
                                                           aTGCCGATCGACAGCCGGTTGATGCCGCTGGCGCGGTAGCTGGCGAACTTGTCGGCCTCGAAGGTGCCGGGGTTGGCCTCCATCGTGATCTCGGCGTCGGCATCCAGCGGCAGCAGCGCGCGGATATCCGAcag                                                                     <  2:434116/134‑1 (MQ=255)
                                                                      cAGCCGGTTGATGCCGCTGGCGCGGTAGCTGGCGAACTTGTCGGCCTCGAAGGTGCCGGGGTTGGCCTCCATCGTGATCTCGGCGTCGGCATCCAGCGGCAGCAGCGCGCGGATATCCGACAGCAGCCGGTCCa                                                          >  1:595320/1‑134 (MQ=255)
                                                                                aTGCCGCTGGCGCGGTAGCTGGCGAACTTGTCGGCCTCGAAGGTGCCGGGGTTGGCCTCCATCGTGATCTCGGCGTCGGCATCCAGCGGCAGCAGCGCGCGGATATCCGAcag                                                                     >  1:606715/1‑113 (MQ=255)
                                                                                aTGCCGCTGGCGCGGTAGCTGGCGAACTTGTCGGCCTCGAAGGTGCCGGGGTTGGCCTCCATCGTGATCTCGGCGTCGGCATCCAGCGGCAGCAGCGCGCGGATATCCGAcag                                                                     <  2:606715/113‑1 (MQ=255)
                                                                                                  cTGGCGAACTTGTCGGCCTCGAAGGTGCCGGGGTTGGCCTCCATCGTGATCTCGGCGTCGGCATCCAGCGGCAGCAGCGCGCGGATATCCGACAGCAGCCGGTCCATGCCTGccgccg                                              >  1:364980/1‑118 (MQ=255)
                                                                                                  cTGGCGAACTTGTCGGCCTCGAAGGTGCCGGGGTTGGCCTCCATCGTGATCTCGGCGTCGGCATCCAGCGGCAGCAGCGCGCGGATATCCGACAGCAGCCGGTCCATGCCTGccgccg                                              <  2:364980/118‑1 (MQ=255)
                                                                                                                         ggTGCCGGGGTTGGCCTCCATCGTGATCTCGGCGTCGGCATCCAGCGGCagcagc                                                                                      <  1:420502/55‑1 (MQ=255)
                                                                                                                         ggTGCCGGGGTTGGCCTCCATCGTGATCTCGGCGTCGGCATCCAGCGGCagcagc                                                                                      >  2:420502/1‑55 (MQ=255)
                                                                                                                              cGGGGTTGGCCTCCATCGTGATCTCGGCGTCGGCATCCAGCGGCAGCAGCGCGCGGATATCCGACAGCAGCCGGTCCATGCCTGCCGCCGACAGCAGGCTGGGCGTGCCGCCGCCGATAAAGACCGTATGCAcc  <  1:398823/134‑1 (MQ=255)
                                                                                                                                  |                                                                                                                                 
CTTCGGCACCGCCGTGGATGCGCCCGAGCGCCTGGAGGTGCCGGTCGTTGAAGCTCTGGATGCCGATCGACAGCCGGTTGATGCCGCTGGCGCGGTAGCTGGCGAACTTGTCGGCCTCGAAGGTGCCGGGTTTGGCCTCCATCGTGATCTCGGCGTCGGCATCCAGCGGCAGCAGCGCGCGGATATCCGACAGCAGCCGGTCCATGCCTGCCGCCGACAGCAGGCTGGGCGTGCCGCCGCCGATAAAGACCGTATGCACC  >  AM260479/1042277‑1042536

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ 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
GCCTTGCGCGCTTCGGCACCGCCGTGGATGCGCCCGAGCGCCTGGAGGTGCCGGTCGTTGAAGCTCTGGATGCCGATCGACAGCCGGTTGATGCCGCTGGCGCGGTAGCTGGCGAACTTGTCGGCCTCGAAGGTGCCGGGTTTGGCCTCCATCGTGATCTCGGCGTCGGCATCCAGCGGCAGCAGCGCGCGGATATCCGACAGCAGCCGGTCCATGCCTGCCGCCGACAGCAGGCTGGGCGTGCCGCCGCCGATAAAGACCGTATGCACCGGCCGGCCCCACACC  >  AM260479/1042267‑1042551
                                                                                                                                            |                                                                                                                                                
GCCTTGCGCGCTTCGGCACCGCCGTGGATGCGCCCGAGCGCCTGGAGGTGCCGGTCGTTGAAGCTCTGGATGCCGATCGACAGCCGGTTGATGCCGCTGGCGCGGTAGCTGGCGAACTTGTCGGCCTCGAAGGTGCCGGGGTTGGCCTCC                                                                                                                                         >  GWNJ‑0478:712:GW2002102894th:2:1213:10280:37403/1‑150 (MQ=60)
        CGCTTCGGCACCGCCGTGGATGCGCCCGAGCGCCTGGAGGTGCCGGTCGTTGAAGCTCTGGATGCCGATCGACAGCCGGTTGATGCCGCTGGCGCGGTAGCTGGCGAACTTGTCGGCCTCGAAGGTGCCGGGGTTGGCCTCCATCGTGAT                                                                                                                                 <  GWNJ‑0478:712:GW2002102894th:2:1203:1566:64956/150‑1 (MQ=60)
         GCTTCGGCACCGCCGTGGATGCGCCCGAGCGCCTGGAGGTGCCGGTCGTTGAAGCTCTGGATGCCGATCGACAGCCGGTTGATGCCGCTGGCGCGGTAGCTGGCGAACTTGTCGGCCTCGAAGGTGCCGGGGTTGGCCTCCATCGTGATC                                                                                                                                <  GWNJ‑0478:712:GW2002102894th:2:2108:5649:35490/150‑1 (MQ=60)
                     CCGTGGATGCGCCCGAGCGCCTGGAGGTGCCGGTCGTTGAAGCTCTGGATGCCGATCGACAGCCGGTTGATGCCGCTGGCGCGGTAGCTGGCGAACTTGTCGGCCTCGAAGGTGCCGGGGTTGGCCTCCATCGTGATCTCGGCGTCGGC                                                                                                                     >  GWNJ‑0478:712:GW2002102894th:2:1102:19182:97693/1‑149 (MQ=60)
                                                   aagcagaagacggcatacgagatgtagctccgtctcgtgggctcggagatgtgtataagagacagCTTGTCGGCCTCGAAGGTGCCGGGGTTGGCCTCCATCGTGATCTCGGCGTCGGCATCCAGCGGCAGCAGCGCGCGGATATCCGAC                                                                                      <  GWNJ‑0478:712:GW2002102894th:2:1210:20591:58959/85‑1 (MQ=60)
                                                                 CTGGATGCCGATCGACAGCCGGTTGATGCCGCTGGCGCGGTAGCTGGCGAACTTGTCGGCCTCGAAGGTGCCGGGGTTGGCCTCCATCGTGATCTCGGCGTCGGCATCCAGCGGCAGCAGCGCGCGGATATCCGACAGCAGCCGGTCCAT                                                                        >  GWNJ‑0478:712:GW2002102894th:2:2107:14127:38757/1‑150 (MQ=60)
                                                                           ATCGACAGCCGGTTGATGCCGCTGGCGCGGTAGCTGGCGAACTTGTCGGCCTCGAAGGTGCCGGGGTTGGCCTCCATCGTGATCTCGGCGTCGGCATCCAGCGGCAGCAGCGCGCGGATATCCGACAGCAGCCGGTCCATGCCctgtctc                                                              >  GWNJ‑0478:712:GW2002102894th:2:2106:15699:10458/1‑143 (MQ=60)
                                                                                             CCGCTGGCGCGGTAGCTGGCGAACTTGTCGGCCTCGAAGGTGCCGGGGTTGGCCTCCATCGTGATCTCGGCGTCGGCATCCAGCGGCAGCAGCGCGCGGATATCCGACAGCAGCCGGTCCATGCCTGCCGCCGACAGCAGGCTGGGCGct                                            >  GWNJ‑0478:712:GW2002102894th:2:1208:8979:32944/1‑148 (MQ=60)
                                                                                                                                       CCGGGGTTGGCCTCCATCGTGATCTCGGCGTCGGCATCCAGCGGCAGCAGCGCGCGGATATCCGACAGCAGCCGGTCCATGCCTGCCGCCGACAGCAGGCTGGGCGTGCCGCCGCCGATAAAGACCGTATGCACCGGCCGGCCCCACACC  <  GWNJ‑0478:712:GW2002102894th:2:1211:10533:35577/150‑1 (MQ=60)
                                                                                                                                            |                                                                                                                                                
GCCTTGCGCGCTTCGGCACCGCCGTGGATGCGCCCGAGCGCCTGGAGGTGCCGGTCGTTGAAGCTCTGGATGCCGATCGACAGCCGGTTGATGCCGCTGGCGCGGTAGCTGGCGAACTTGTCGGCCTCGAAGGTGCCGGGTTTGGCCTCCATCGTGATCTCGGCGTCGGCATCCAGCGGCAGCAGCGCGCGGATATCCGACAGCAGCCGGTCCATGCCTGCCGCCGACAGCAGGCTGGGCGTGCCGCCGCCGATAAAGACCGTATGCACCGGCCGGCCCCACACC  >  AM260479/1042267‑1042551

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑