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 I198 R1 96 36.2 2313912 84.6% 1957569 85.2

Breseq alignment

N/A

GATK/CNVnator alignment

BRESEQ :: bam2aln output
CAAAGCAGCAAGCAAGCCAACACCACGACAACCAGAACGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTAGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGATATTCGTGCTTTTTCGGAATGAGTCGCTTGCTTCAGCGCATATTGCCGCTACGATTAAG  >  NZ_CP009273/1902965‑1903155
                                                                                                |                                                                                              
cggagatgtgtataagagacagCCACGACAACCAGAACGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTAGCA                                                                                             <  SRR3722077.502202/78‑1 (MQ=60)
              AGCCAACACCACGACAACCAGAACGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTAGCATGCGTTAGTTAAAC                                                                               >  SRR3722077.1167675/1‑100 (MQ=60)
               GCCAAAACCACGACAACCAGAACGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTTGCATGCGTTAGTTAAACA                                                                              >  SRR3722077.916860/1‑100 (MQ=60)
                         ggcatacgagatggccgtgggtctcgtgggttcggagatgtgtataagagacagCCTTATGTCATTAAACTAGCATGCGTTAGTTAAACAGCGCCTAACT                                                                    <  SRR3722077.1090751/46‑1 (MQ=60)
                          GACAACCAGAACGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTTGCATGCGTTAGTTAAACAGCGCCTAACTA                                                                   <  SRR3722077.1131727/100‑1 (MQ=60)
                          GACAACCAGAACGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTTGCATGCGTTAGTTAAACAGCGCCTAACTA                                                                   <  SRR3722077.18306/100‑1 (MQ=60)
                          GACAACCAGAACGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTTGCATGCGTTAGTTAAACAGCGCCTAACTA                                                                   <  SRR3722077.273013/100‑1 (MQ=60)
                             AACCAGAACGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTTGCATGCGTTAGTTAAACAGCGCCTAACTATGT                                                                <  SRR3722077.825802/100‑1 (MQ=60)
                             AACCAGAACGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTAGCATGCGTTAGTTAAACAGCGCCTAACTATGT                                                                >  SRR3722077.597676/1‑100 (MQ=60)
                                      ccgtgggtctcgtgggctcggagatgtgtataagagacagACCTTATGTCATTAAACTTGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGATATTCG                                                       <  SRR3722077.806794/60‑1 (MQ=60)
                                                                  TCCGTTTCACCTACCTTATGTCATTAAACTAGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGATATTCGTGCTTTTTCGGAATGAGTCGCTTGCTTC                           <  SRR3722077.948376/100‑1 (MQ=60)
                                                                       gagatgtgtataagagacagAAACTTGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGATATTCGTGCTTTTTCGGAATGAGTCGCTTGCTTCAGCGC                      <  SRR3722077.501739/80‑1 (MQ=60)
                                                                        TCACCTACCTTATGTCATTAAACTTGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGATATTCGTGCTTTTTCGGAATGAGTCGCTTGCTTCAGCGCA                     >  SRR3722077.890238/1‑100 (MQ=60)
                                                                            CTACCTTATGTCATTAAACTTGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGATATTCGTGCTTTTTCGGAATGAGTCGCTTGCTTCAGCGCATATT                 <  SRR3722077.46130/100‑1 (MQ=60)
                                                                              ACCTTATGTCATTAAACTAGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGATATTCGTGCTTTTTCGGAATGAGTCGCTTGCTTCAGCGCATATTGC               >  SRR3722077.135075/1‑100 (MQ=60)
                                                                               CCTTATGTCATTAAACTTGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGATATTCGTGCTTTTTCGGAATGAGTCGCTTGCTTCAGCGCATATTGCC              >  SRR3722077.784844/1‑100 (MQ=60)
                                                                                       CATTAAACTAGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGATATTCGTGCTTTTTCGAAATGAGTCGCTTGCTTCAGCGCATATTGCCGCTACGAT      >  SRR3722077.221596/1‑100 (MQ=60)
                                                                                           AAACTAGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGATATTCGTGCTTTTTCGGAATGAGTCGCTTGCTTCAGCGCATATTGCCGCTACGATTAAG  >  SRR3722077.105451/1‑100 (MQ=60)
                                                                                                |                                                                                              
CAAAGCAGCAAGCAAGCCAACACCACGACAACCAGAACGACCCATCGAAACTTTTTCACTCCAATCTCCGTTTCACCTACCTTATGTCATTAAACTAGCATGCGTTAGTTAAACAGCGCCTAACTATGTCGATATTCGTGCTTTTTCGGAATGAGTCGCTTGCTTCAGCGCATATTGCCGCTACGATTAAG  >  NZ_CP009273/1902965‑1903155

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑