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 I197 R1 189 12.7 697584 97.1% 677354 86.2

Breseq alignment

N/A

GATK/CNVnator alignment

BRESEQ :: bam2aln output
TAGTAATTACGTTCAACAATACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATGCCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGATTGCTTACGAGTAATCGCATTTGGCCGGGTTCGCCCGGCC  >  NZ_CP009273/3179194‑3179350
                                                                             |                                                                               
TAGTAATTACGTTCAACAATACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATGCCACCCCGGGCAACGTTTACGC                                                           <  SRR3722076.116509/100‑1 (MQ=60)
                             GATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGATTGCTTACGAGT                              <  SRR3722076.322421/100‑1 (MQ=60)
                              ATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGATTGCTTACGAGTA                             >  SRR3722076.344838/1‑100 (MQ=60)
                                    AACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGATTGCTTACGAGTAATCGCA                       <  SRR3722076.216122/100‑1 (MQ=60)
                                                      GTATGGAATCCCCAAGCAAAGATACCCCCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGATTGCTTACGAGTAATCGCATTTGGCCGGGTTCGCCCG     <  SRR3722076.325147/100‑1 (MQ=60)
                                                         TGGAAACCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGATTGCTTACGAGTAATCGCATTTGGCCGGGTTCGCCCGGCC  <  SRR3722076.265585/100‑1 (MQ=60)
                                                                             |                                                                               
TAGTAATTACGTTCAACAATACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATGCCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGATTGCTTACGAGTAATCGCATTTGGCCGGGTTCGCCCGGCC  >  NZ_CP009273/3179194‑3179350

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑