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
GGGAATTATGAGCCAGTTTTTTTATATTCATCCTGATAACCCACAGCAACGTCTGATCAACCAGGCGGTGGAGATCGTGCGTAAAGGCGGGGTGATTGTTTATCCAACTGATTCCGGCTATGCGCTCGGCTGTAAAATTG  >  NZ_CP009273/1318348‑1318487
                                                                                            |                                               
GGGAATTATGAGCCAGTTTTTTTATATTCATCCTGATAACCCACAGCAACGTCTGATCAACCAGGCGGTGGAGATCGTGCGTAAAGGCGGGGTGGTTGTT                                          >  SRR3722099.419383/1‑100 (MQ=60)
                            CATCCTGATAACCCACAGCAACGTCTGATCAACCAGGCGGTGGAGATCGTGCGTAAAGGCGGGGGGATTGTTTATCCAACTGATTCCGGCTATTCGCTTG              >  SRR3722099.800429/1‑100 (MQ=60)
                                      ACCCACAGCAACGTCTGATCAACCAGGCGGTGGAGATCGTGCGTAAAGGCGGGGGGATTGTTTATCCAACTGATTCCGGCTATGCGCTCGGCTGTAAAAT    >  SRR3722099.679249/1‑100 (MQ=60)
                                        CCACAGCAACGTCTGATCAACCAGGCGGTGGAGATCGTGCGTAAAGGCGGGGGGATTGTTTATCCAACTGATTCCGGCTATGCGCTCGGCTGTAAAATTG  >  SRR3722099.883882/1‑100 (MQ=60)
                                                                                            |                                               
GGGAATTATGAGCCAGTTTTTTTATATTCATCCTGATAACCCACAGCAACGTCTGATCAACCAGGCGGTGGAGATCGTGCGTAAAGGCGGGGTGATTGTTTATCCAACTGATTCCGGCTATGCGCTCGGCTGTAAAATTG  >  NZ_CP009273/1318348‑1318487

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑