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
TAACGCGATAATGATTATTTCTGGCGACGTCGTGGATAATCACGGAAGCCACGCGAATCGCGCGATCCAGCCATTTTTTGTCGTGAGTGACGTCATAAACAATCAAGAAAGCTTCCACCGCGTGCATATTGGCATTGCCGCCGCGGTACTCTTCGGTTTTGCTGAAGGCTTCGTCCCAGGATTCCAGGCA  >  NZ_CP009273/4064468‑4064657
                                                                                                |                                                                                             
tgggctcggagatgtgtataagagacagGTCGTGGATAATCACGGAAGCCACGCGAATCGCGCGATCCAGCCATTTTTTGTCGTGAGTGACGTCATGAAC                                                                                            <  SRR3722077.630156/72‑1 (MQ=60)
TAACGCGATAATGATTATTTCTGGCGACGTCGTGGATAATCACGGAAGCCACGCGAATCGCGCGATCCAGCCATTTTTTGTCGTGAGTGACGTCATGAAC                                                                                            <  SRR3722077.1026295/100‑1 (MQ=60)
TAACGCGATAATGATTATTTCTGGCGACGTCGTGGATAATCACGGAAGCCACGCGAATCGCGCGATCCAGCCATTTTTTGTCGTGAGTGACGTCATAAAC                                                                                            <  SRR3722077.397112/100‑1 (MQ=60)
                      GGCGACGTCGTGGATAATCACGGAAGCCACGCGAATCGCGCGATCCAGCCATTTTTTGTCGTGAGTGACGTCATGAACAATCAAGAAAGCTTCCACCGCG                                                                      >  SRR3722077.230982/1‑100 (MQ=60)
                           CGTCGTGGATAATCACGGAAGCCACGCGAATCGCGCGATCCAGCCATTTTTTGTCGTGAGTGACGTCATGAACAATCAAGAAAGCTTCCACCGCGTGCAT                                                                 >  SRR3722077.995701/1‑100 (MQ=60)
                            GTCGTGGATAATCACGGAAGCCACGCGAATCGCGCGATCCAGCCATTTTTTGTCGTGAGTGACGTCATAAACAATCAAGAAAGCTTCCACCGCGTGCATA                                                                >  SRR3722077.598387/1‑100 (MQ=60)
                                 GGATAATCACGGAAGCCACGCGAATCGCGCGATCCAGCCATTTTTTGTCGTGAGTGACGTCATAAACAATCAAGAAAGCTTCCACCGCGTGCATATTGGC                                                           <  SRR3722077.122622/100‑1 (MQ=60)
                                      ATCACGGAAGCCACGCGAATCGCGCGATCCAGCCATTTTTTGTCGTGAGTGACGTCATGAACAATCAAGAAAGCTTCCACCGCGTGCATATTGGCATTGC                                                      >  SRR3722077.303878/1‑100 (MQ=60)
                                      ATCACGGAAGCCACGCGAATCGCGCGATCCAGCCATTTTTTGTCGTGAGTGACGTCATGAACAATCAAGAAAGCTTCCACCGCGTGCATATTGGCATTGC                                                      >  SRR3722077.711336/1‑100 (MQ=60)
                                      ATCACGGAAGCCACGCGAATCGCGCGATCCAGCCATTTTTTGTCGTGAGTGACGTCATAAACAATCAAGAAAGCTTCCACCGCGTGCATATTGGCATTGC                                                      >  SRR3722077.138004/1‑100 (MQ=60)
                                       TCACGGAAGCCACGCGAATCGCGCGATCCAGCCATTTTTTGTCGTGAGTGACGTCATAAACAATCAAGAAAGCTTCCACCGCGTGCATATTGGCATTGCC                                                     >  SRR3722077.1127487/1‑100 (MQ=60)
                                                   CGCGAATCGCGCGATCCAGCCATTTTTTGTCGTGAGTGACGTCATGAACAATCAAGAAAGCTTCCACCGCGTGCATATTGGCATTGCCGCCGCGGTACTC                                         <  SRR3722077.327935/100‑1 (MQ=60)
                                                           GCGCGATCCAGCCATTTTTTGTCGTGAGTGACGTCATGAACAATCAAGAAAGCTTCCACCGCGTGCATATTGGCATTGCCGCCGCGGTACTCTTCGGTTT                                 <  SRR3722077.316011/100‑1 (MQ=60)
                                                                ATCCAGCCATTTTTTGTCGTGAGTGACGTCATGAACAATCAAGAAAGCTTCCACCGCGTGCATATTGGCATTGCCGCCGCGGTACTCTTCGGTTTTGCTG                            >  SRR3722077.294583/1‑100 (MQ=60)
                                                                ATCCAGCCATTTTTTGTCGTGAGAGACGTCATGAACAATCAAGAAAGCTTCCACCGCGGGCATATTGGCATTGCCGCCGCGGCACTCTTCGGTTTTGCTG                            >  SRR3722077.389782/1‑100 (MQ=60)
                                                                               GTCGTGAGTGACGTCATGAACAATCAAGAAAGCTTCCACCGCGTGCATATTGGCATTGCCGCCGCGGTACTCTTCGGTTTTGCTGAAGGCTTCGTCCCAG             >  SRR3722077.991048/1‑100 (MQ=60)
                                                                                          CGTCATAAACAATCAAGAAAGCTTCCACCGCGTGCATATTGGCATTGCCGCCGCGGTACTCTTCGGTTTTGCTGAAGGCTTCGTCCCAGGATTCCAGGCA  >  SRR3722077.781862/1‑100 (MQ=60)
                                                                                                |                                                                                             
TAACGCGATAATGATTATTTCTGGCGACGTCGTGGATAATCACGGAAGCCACGCGAATCGCGCGATCCAGCCATTTTTTGTCGTGAGTGACGTCATAAACAATCAAGAAAGCTTCCACCGCGTGCATATTGGCATTGCCGCCGCGGTACTCTTCGGTTTTGCTGAAGGCTTCGTCCCAGGATTCCAGGCA  >  NZ_CP009273/4064468‑4064657

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑