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 I193 R1 5 20.3 1169676 96.1% 1124058 86.2

Breseq alignment

N/A

GATK/CNVnator alignment

BRESEQ :: bam2aln output
GAACTGTGCAGGATGCGAGCTGATTTTTGAAGACAAGATAAGCGGCACAAAGTCCGAAAGGCCGGGACTGAAAAAACTGCTCAGGACATTATCGGCAGGTGACACTCTGGTTGTCTGGAAGCTGGATCGGCTGGGGCGTAGTATGCGGCATCTTGTCGTGCTGGTGGA  >  NZ_CP009273/1205206‑1205373
                                                                                                   |                                                                    
GAACTGTGCAGGATGCGAGCTGATTTTTGAAGACAAGATAAGCGGCACAAAGTCCGAAAGGCCGGGACTGAAAAAACTGCTCAGGACATTATCGGCAGGG                                                                      >  SRR3722071.287236/1‑100 (MQ=60)
     GTGCAGGATGCGAGCTGATTTTTGAAGACAAGATAAGCGGCACAAAGTCCGAAAGGCCGGGACTGAAAAAACTGCTCAGGACATTATCGGCAGGGGAGAC                                                                 >  SRR3722071.192069/1‑100 (MQ=60)
     GTGCAGGATGCGAGCTGATTTTTGAAGACAAGATAAGCGGCACAAAGTCCGAAAGGCCGGGACTGAAAAAACTGCTCAGGACATTATCGGCAGGGGACAC                                                                 >  SRR3722071.227084/1‑100 (MQ=60)
     GTGCAGGATGCGAGCTGATTTTTGAAGACAAGATAAGCGGCACAAAGTCCGAAAGGCCGGGACTGAAAAAACTGCTCAGGACATTATCGGCAGGGGACAC                                                                 >  SRR3722071.350616/1‑100 (MQ=60)
                                                     CCGAAAGGCCGGGACTGAAAAAACTGCTCAGGACATTATCGGCAGGGGACACTCTGGTTGTCTGGAAGCTGGGTCGGCTGGGGGGGAGGATGCGGGATCT                 >  SRR3722071.311787/1‑100 (MQ=60)
                                                                    TGAAAAAACTGCTCAGGACATTATCGGCAGGTGACACTCTGGTTGTCTGGAAGCTGGATCGGCTGGGGCGTAGTATGCGGCATCTTGTCGTGCTGGTGGA  <  SRR3722071.121336/100‑1 (MQ=60)
                                                                                                   |                                                                    
GAACTGTGCAGGATGCGAGCTGATTTTTGAAGACAAGATAAGCGGCACAAAGTCCGAAAGGCCGGGACTGAAAAAACTGCTCAGGACATTATCGGCAGGTGACACTCTGGTTGTCTGGAAGCTGGATCGGCTGGGGCGTAGTATGCGGCATCTTGTCGTGCTGGTGGA  >  NZ_CP009273/1205206‑1205373

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑