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 F1 I168 R2 5 0.0 0 0.0% 0 0.0

Breseq alignment

N/A

GATK/CNVnator alignment

BRESEQ :: bam2aln output
TAATTACCTTATGTAATCTATCGTAATACTTCGATTGGTAAAATTCATCGATCGACGCAGGAATTTTTTCATGTTCGATATGAATTTCACCTGCTATATATTTATTTAGAAGAGTTACAAA  >  NZ_CP009273/3796444‑3796564
                                                               |                                                         
TAATTACCTTATGTAATCTATCGTAATACTTCGATTGGTAAAATTCATCGATCGACGCAGGAAATTTTTCATGTTCGATATGAATTTCACCTGCTATATA                       >  SRR3722039.84771/1‑100 (MQ=60)
TAAGTACCTTATGTAATCTATCGTAATACTTCGATTGGTAAAATTCATCGATCGACGCAGGAAATTTTTCATGTTCGATATGAATTTCACCTGCTATATA                       >  SRR3722039.84772/1‑100 (MQ=60)
                     CGTAATACTTCGATTGGTAAAATTCATCGATCGACGCAGGAATTTTTTCATGTTCGATATGAATTTCACCTGCTATATATTTATTTAGAAGAGTTACAAA  >  SRR3722039.48314/1‑100 (MQ=60)
                                                               |                                                         
TAATTACCTTATGTAATCTATCGTAATACTTCGATTGGTAAAATTCATCGATCGACGCAGGAATTTTTTCATGTTCGATATGAATTTCACCTGCTATATATTTATTTAGAAGAGTTACAAA  >  NZ_CP009273/3796444‑3796564

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑