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 F2 I213 R1 8 41.3 2526560 96.1% 2428024 85.4

Breseq alignment

N/A

GATK/CNVnator alignment

BRESEQ :: bam2aln output
CCCGTCTGGTCACTGGGAAATTGCCGGTGTCCCGGTTCTGTTTGAGTGGGGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATAAACTGGTCGAACGCGCTAATCTGCCGGGTTACCTCGGTAACTGCCACTCTTCCG  >  NZ_CP009273/4609713‑4609864
                                                                                                 |                                                      
CCCGTCTGGTCACTGGGAAATTGCCGGTGTCCCGGTTCTGTTTGAGT‑GGGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAAC                                                     <  SRR3722096.442629/100‑1 (MQ=60)
 CCGTCTGGTCACTGGGAAATTGCCGGTGTCCCGGTTCTGTTTGAGTGGGGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAAC                                                     <  SRR3722096.187214/100‑1 (MQ=60)
 CCGTCTGGTCACTGGGAAATTGCCGGTGTCCCGGTTCTGTTTGAGTGGGGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAAC                                                     <  SRR3722096.225660/100‑1 (MQ=60)
  CGTCTGGTCACTGGGAAATTGCCGGTGTCCCGGTTCTGTTTGAGTGGGGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAACT                                                    >  SRR3722096.1063927/1‑100 (MQ=60)
  CGTCTGGTCACTGGGAAATTGCCGGTGTCCCGGTTCTGTTTGAGTGGGGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAACT                                                    >  SRR3722096.1199272/1‑100 (MQ=60)
        agatggtcgtcggcagcgtcagatgtgtataagagacagGGGGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAACTGGGCGA                                              <  SRR3722096.744154/61‑1 (MQ=60)
            tgtgtataagagacagGTCCCGGTTCTGTTTGAGTGGGGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAACTGGgcgaagag                                          <  SRR3722096.1277492/84‑9 (MQ=60)
            CTGGGAAATTGCCGGTGTCCCGGTTCTGTTTGAGTGGGGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAACTGGgcgaagag                                          <  SRR3722096.97701/100‑9 (MQ=60)
            CTGGGAAATTGCCGGTGTCCCGGTTCTGTTTGAGTGGGGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAACTGGgcgaagag                                          <  SRR3722096.899466/100‑9 (MQ=60)
            CTGGGAAATTGCCGGTGTCCCGGTTCTGTTTGAGTGGGGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAACTGGgcgaagag                                          <  SRR3722096.449204/100‑9 (MQ=60)
              GGGAAATTGCCGGTGTCCCGGTTCTGTTTGAGTGGGGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAACTGGgcgaagagca                                        >  SRR3722096.1246802/1‑90 (MQ=60)
                  AATTGCCGGTGTCCCGGTTCTGTTTGAGTGGGGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAACTGGgcgaagagcacatg                                    <  SRR3722096.131328/100‑15 (MQ=60)
                    TTGCCGGTGTCCCGGTTCTGTTTGAGTGGGGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAACTGGgcgaagagcacatgaa                                  <  SRR3722096.450691/100‑17 (MQ=60)
                       CCGGTGTCCCGGTTCTGTTTGAGTGGGGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAACTGGgcgaagagcacatgaaaac                               <  SRR3722096.1052368/100‑20 (MQ=60)
                       CCGGTGTCCCGGTTCTGTTTGAGTGGGGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAACTGGgcgaagagcacatgaaaac                               <  SRR3722096.676316/100‑20 (MQ=60)
                          GTGTCCCGGTTCTGTTTGAGTGGGGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAACTGGgcgaagagcacatgaaaaccgg                            >  SRR3722096.184/1‑78 (MQ=60)
                            GTCCCGGTTCTGTTTGAGTGGGGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAACTGGgcgaagagcacatgaaaaccggca                          >  SRR3722096.713664/1‑76 (MQ=60)
                            GTCCCGGTTCTGTTTGAGTGGGGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAACTGGgcgaagagcacatgaaaaccggca                          >  SRR3722096.855101/1‑76 (MQ=60)
                                 GGTTCTGTTTGAGTGGGGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAACTGGgcgaagagcacatgaaaaccggcaagccg                     >  SRR3722096.763622/1‑71 (MQ=60)
                                     CTGTTTGAGTGGGGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAACTGGgcgaagagcacatgaaaaccggcaagccgattt                 >  SRR3722096.143339/1‑67 (MQ=60)
                                      TGTTTGAGTGGGGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATAAACTGGTCGAACGCGCTAATCTGCCGGGTTACCTCGGTAA                <  SRR3722096.268563/100‑1 (MQ=60)
                                             GTGGGGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAACTGG                                                  <  SRR3722096.306415/59‑1 (MQ=60)
                                             GTGGGGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAACTGG                                                  <  SRR3722096.648488/59‑1 (MQ=60)
                                                GGGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAACTGG                                                  >  SRR3722096.530798/1‑56 (MQ=60)
                                                    TATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATAAACTGGTCGAACGCGCTAATCTGCCGGGTTACCTCGGTAACTGCCACTCTTCCG  >  SRR3722096.398849/1‑100 (MQ=60)
                                                      TTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAACTGG                                                  >  SRR3722096.405737/1‑50 (MQ=60)
                                                               TCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAACTGG                                                  <  SRR3722096.667851/41‑1 (MQ=60)
                                                                CACGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAACTGG                                                  >  SRR3722096.1042287/1‑40 (MQ=60)
                                                                  CGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAACTGG                                                  <  SRR3722096.770056/38‑1 (MQ=60)
                                                                                                 |                                                      
CCCGTCTGGTCACTGGGAAATTGCCGGTGTCCCGGTTCTGTTTGAGTGGGGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATAAACTGGTCGAACGCGCTAATCTGCCGGGTTACCTCGGTAACTGCCACTCTTCCG  >  NZ_CP009273/4609713‑4609864

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑