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 I216 R1 8 28.7 1753078 96.2% 1686461 85.5

Breseq alignment

N/A

GATK/CNVnator alignment

BRESEQ :: bam2aln output
CCGTCTGGTCACTGGGAAATTGCCGGTGTCCCGGTTCTGTTTGAGTGGGGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATAAACTGGTCGAACGCGCTAATCTGCCGGGTTACCTCGGTAAC  >  NZ_CP009273/4609714‑4609851
                                                                                                |                                         
CCGTCTGGTCACTGGGAAATTGCCGGTGTCCCGGTTCTGTTTGAGTGGGGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAAC                                        <  SRR3722099.604774/100‑1 (MQ=60)
CCGTCTGGTCACTGGGAAATTGCCGGTGTCCCGGTTCTGTTTGAGTGGGGATATTTCTCCGAACACGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAAC                                        <  SRR3722099.116627/100‑1 (MQ=60)
  GTCTGGTCACTGGGAAATTGCCGGTGTCCCGGTTCTGTTTGAGTGGGGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAACTG                                      <  SRR3722099.518161/100‑1 (MQ=60)
             GGGAAATTGCCGGTGTCCCGGTTCTGTTTGAGTGGGGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAACTGGgcgaagagca                           >  SRR3722099.809372/1‑90 (MQ=60)
                      CCGGTGTCCCGGTTCTGTTTGAGTGGGGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAACTGGgcgaagagcacatgaaaac                  <  SRR3722099.513248/100‑20 (MQ=60)
                           GTCCCGGTTCTGTTTGAGTGGGGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAACTGGgcgaagagcacatgaaaaccggca             >  SRR3722099.578283/1‑76 (MQ=60)
                           GTCCCGGTTCTGTTTGAGTGGGGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAACTGGgcgaagagcacatgaaaaccggca             >  SRR3722099.165592/1‑76 (MQ=60)
                                    CTGTTTGAGTGGGGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAACTGGgcgaagagcacatgaaaaccggcaagccgattt    >  SRR3722099.402477/1‑67 (MQ=60)
                                    CTGTTTGAGTGGGGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAACTGGgcgaagagcacatgaaaaccggcaagccgattt    >  SRR3722099.441124/1‑67 (MQ=60)
                                      GTTTGAGTGGGGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAACTGGgcgaagagcacatgaaaaccggcaagccgattttc  >  SRR3722099.775833/1‑65 (MQ=60)
                                            GTGGGGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAACTGG                                     <  SRR3722099.181156/59‑1 (MQ=60)
                                              GGGGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAACTGG                                     <  SRR3722099.329404/57‑1 (MQ=60)
                                                GGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAACTGG                                     >  SRR3722099.107403/1‑55 (MQ=60)
                                                 GATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAACTGG                                     <  SRR3722099.531868/54‑1 (MQ=60)
                                                  ATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAACTGG                                     >  SRR3722099.37452/1‑53 (MQ=60)
                                                  ATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAACTGG                                     >  SRR3722099.535233/1‑53 (MQ=60)
                                                       TCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAACTGG                                     <  SRR3722099.107716/48‑1 (MQ=60)
                                                                 CGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAACTGG                                     >  SRR3722099.787554/1‑38 (MQ=60)
                                                                                                |                                         
CCGTCTGGTCACTGGGAAATTGCCGGTGTCCCGGTTCTGTTTGAGTGGGGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATAAACTGGTCGAACGCGCTAATCTGCCGGGTTACCTCGGTAAC  >  NZ_CP009273/4609714‑4609851

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑