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 F3 I103 R1 7 22.4 1331362 95.8% 1275444 85.7

Breseq alignment

N/A

GATK/CNVnator alignment

BRESEQ :: bam2aln output
TTAATGATCCCAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAACGGGGAAAACGAAATTCAATACCGTCGGTAAT  >  NZ_CP009273/4558224‑4558399
                                                                                                 |                                                                              
TTAATGATCCCAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAA                                                                              >  SRR3721968.679020/1‑100 (MQ=60)
TTAATGATCCCAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAA                                                                              >  SRR3721968.246640/1‑100 (MQ=60)
  AATGATCCCAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAA                                                                            >  SRR3721968.254793/1‑100 (MQ=60)
        CCCAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAAaag                                                                      >  SRR3721968.325108/1‑97 (MQ=60)
            GGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAAAGGGGCA                                                                  >  SRR3721968.522649/1‑100 (MQ=60)
                   TCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAAaaagggaaaaaaaa                                                           >  SRR3721968.631565/1‑86 (MQ=60)
                        TCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAAaaggggctaaaaaaaaaaa                                                      >  SRR3721968.412084/1‑81 (MQ=60)
                           GTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTCCT                                                   <  SRR3721968.275331/100‑1 (MQ=60)
                              GACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAAaaggannnnnnnnnnnnnnnnnnnn                                                >  SRR3721968.222603/1‑75 (MQ=60)
                                                  ATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAAaaaggcataaaaaaaaacaccctttccggggaacccccacgggga                            >  SRR3721968.622495/1‑55 (MQ=60)
                                                   TACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAAagagggataaaaaaaaaaacctttttcggggaaaccccacggggga                           >  SRR3721968.325101/1‑54 (MQ=60)
                                                   TACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAAaatgggataaaaaaaaacaccttttcccggggaaccccaccgctgt                           >  SRR3721968.223485/1‑54 (MQ=60)
                                                   TACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAAaaaggcataaaaaaaaaacccttttccggggaacccccacggggga                           >  SRR3721968.82367/1‑54 (MQ=60)
                                                       AAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAAaaagggaaaaaaaaaaaaaccctttcccgggaaaccccacggggaaaaag                       >  SRR3721968.264199/1‑50 (MQ=60)
                                                        AATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAAaaggggataaaaaaaaaaaccctgtccggggaaccccaacgggggaaaaga                      >  SRR3721968.538535/1‑49 (MQ=60)
                                                                    CGGGAAAAACAGCGTGGCGGCATGGCGGGGAAAAAAAaaggggaaaacaaaaaactccctttccggaggaacccaacgggggaaaagaaaatcaaaaccg          >  SRR3721968.437189/1‑37 (MQ=60)
                                                                          AAACAGCGTGGCGGCATGGCGGGTAAAAAAAAATGGGATAACAAAAAAACCCCTTTCCGGGGAACCCCAACGGGGGAAAAGAAAATAAATACCGTCGGGA    >  SRR3721968.69096/1‑100 (MQ=20)
                                                                          AAACAGCGTGGCGGCATGGCGGGGAAAAAAAAGGGGGATAAAAAAAAACCCCTTTTCCGGGGAACCCCCACGGGGAAAAAGAAATTCAAAACCGTCGGGA    >  SRR3721968.195973/1‑100 (MQ=29)
                                                                            ACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAACGGGGAAAACGAAATTCAATACCGTCGGTAAT  <  SRR3721968.652085/100‑1 (MQ=60)
                                                                                                 |                                                                              
TTAATGATCCCAGGCTGGATCAGATCCGTCGACAGATACGCAGCAAAGTCATACAAAATCAACGCCATCGGGAAAAACAGCGTGGCGGCATGGCGGGTAAAAAAACGTGGCATAACAAACAACTCCTTGTCCGGAGAACCCCAACGGGGAAAACGAAATTCAATACCGTCGGTAAT  >  NZ_CP009273/4558224‑4558399

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑