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
GTTGATAAGCCCGGGGATAGGCTCAGCAGTATCAATACCAACATCAATTACGTGGACGTTAGCGCCCGCTTGTTCTGCCAGCACACACACGCCGGTTGTTCCACGGGTCATATTTTCAGCCTGTATGGCTGTCACTTCTTTTGGAGAAATAGCGACCCCTTCCTCCCAGACGCCGTGATCGGCACACATAACC  >  NZ_CP009273/2057565‑2057757
                                                                                                   |                                                                                             
GTTGATAAGCCCGGGGATAGGCTCAGCAGTATCAATACCAACATCAATTACGTGGACGTTAGCGCCCGCTTGTTCTGCCAGCACACACACGCCGGTTGTT                                                                                               >  SRR3722077.873000/1‑100 (MQ=60)
  TGATAAGCCCGGGGATAGGCTCAGCAGTATCAATACCAACATCAATTACGTGGACGTTAGCGCCCGCTTGTTCTGCCAGCACACACACGCCGGTTGTCCC                                                                                             >  SRR3722077.253690/1‑100 (MQ=60)
  TGATAAGCCCGGGGATAGGCTCAGCAGTATCAATACCAACATCAATTACGTGGACGTTAGCGCCCGCTTGTTCTGCCAGCACACACACGCCGGTTGTCCC                                                                                             >  SRR3722077.397105/1‑100 (MQ=60)
   GATAAGCCCGGGGATAGGCTCAGCAGTATCAATACCAACATCAATTACGTGGACGTTAGCGCCCGCTTGTTCTGCCAGCACACACACGCCGGTTGTCCCA                                                                                            >  SRR3722077.708535/1‑100 (MQ=60)
      AAGCCCGGGGATAGGCTCAGCAGTATCAATACCAACATCAATTACGTGGACGTTAGCGCCCGCTTGTTCTGCCAGCACACACACGCCGGTTGTCCCACGG                                                                                         <  SRR3722077.302382/100‑1 (MQ=60)
             GGGATAGGCTCAGCAGTATCAATACCAACATCAATTACGTGGACGTTAGCGCCCGCTTGTTCTGCCAGCACACACACGCCGGTTGTCCCACGGGTCATAT                                                                                  >  SRR3722077.992617/1‑100 (MQ=60)
             GGGATAGGCTCAGCAGTATCAATACCAACATCAATTACGTGGACGTTAGCGCCCGCTTGTTCTGCCAGCACACACACGCCGGTTGTCCCACGGGTCATAT                                                                                  >  SRR3722077.878521/1‑100 (MQ=60)
                  AGGCTCAGCAGTATCAATACCAACATCAATTACGTGGACGTTAGCGCCCGCTTGTTCTGCCAGCACACACACGCCGGTTGTTCCACGGGTCATATTTTCA                                                                             >  SRR3722077.843345/1‑100 (MQ=60)
                  AGGCTCAGCAGTATCAATACCAACATCAATTACGTGGACGTTAGCGCCCGCTTGTTCTGCCAGCACACACACGCCGGTTGTCCCACGGGTCATATTTTCA                                                                             >  SRR3722077.561196/1‑100 (MQ=60)
                  AGGCTCAGCAGTATCAATACCAACATCAATTACGTGGACGTTAGCGCCCGCTTGTTCTGCCAGCACACACACGCCGGTTGTCCCACGGGTCATATTTTCA                                                                             >  SRR3722077.540194/1‑100 (MQ=60)
                         GCAGTATCAATACCAACATCAATTACGTGGACGTTAGCGCCCGCTTGTTCTGCCAGCACACACACGCCGGTTGTTCCACGGGTCATATTTTCAGCCTGTA                                                                      >  SRR3722077.56439/1‑100 (MQ=60)
                             TATCAATACCAACATCAATTACGTGGACGTTAGCGCCCGCTTGTTCTGCCAGCACACACACGCCGGTTGTCCCACGGGTCATATTTTCAGCCTGTATGGC                                                                  >  SRR3722077.708877/1‑100 (MQ=60)
                                   TACCAACATCAATTACGTGGACGTTAGCGCCCGCTTGTTCTGCCAGCACACACACGCCGGTTGTCCCACGGGTCATATTTTCAGCCTGTATGGCTGTCAC                                                            >  SRR3722077.701473/1‑100 (MQ=60)
                                   TACCAACATCAATTACGTGGACGTTAGCGCCCGCTTGTTCTGCCAGCACACACACGCCGGTTGTCCCACGGGTCATATTTTCAGCCTGTATGGCTGTCAC                                                            >  SRR3722077.316211/1‑100 (MQ=60)
                                           TCAATTACGTGGACGTTAGCGCCCGCTTGTTCTGCCAGCACACACACGCCGGTTGTCCCACGGGTCATATTTTCAGCCTGTATGGCTGTCACTTCTTTTG                                                    >  SRR3722077.546626/1‑100 (MQ=60)
                                            CAATTACGTGGACGTTAGCGCCCGCTTGTTCTGCCAGCACACACACGCCGGTTGTTCCACGGGTCATATTTTCAGCCTGTATGGCTGTCACTTCTTTTGG                                                   >  SRR3722077.926849/1‑100 (MQ=60)
                                                TACGTGGACGTTAGCGCCCGCTTGTTCTGCCAGCACACACACGCCGGTTGTTCCACGGGTCATATTTTCAGCCTGTATGGCTGTCACTTCTTTTGGAGAA                                               >  SRR3722077.200248/1‑100 (MQ=60)
                                                      GACGTTAGCGCCCGCTTGTTCTGCCAGCACACACACGCCGGTTGTTCCACGGGTCATATTTTCAGCCTGTATGGCTGTCACTTCTTTTGGAGAAATAGCG                                         >  SRR3722077.728661/1‑100 (MQ=60)
                                                      GACGTTAGCGCCCGCTTGTTCTGCCAGCACACACACGCCGGTTGTTCCACGGGTCATATTTTCAGCCTGTATGGCTGTCACTTCTTTTGGAGAAATAGCG                                         >  SRR3722077.742342/1‑100 (MQ=60)
                                                                 CCGCTTGTTCTGCCAGCACACACACGCCGGTTGTCCCACGGGTCATATTTTCAGCCTGTATGGCTGTCACTTCTTTTGGAGAAATAGCGACCCCTTCCTC                              <  SRR3722077.325391/100‑1 (MQ=60)
                                                                       GTTCTGCCAGCACACACACGCCGGTTGTTCCACGGGTCATATTTTCAGCCTGTATGGCTGTCACTTCTTTTGGAGAAATAGCGACCCCTTCCTCCCAGAC                        <  SRR3722077.340220/100‑1 (MQ=60)
                                                                                             GGTTGTTCCACGGGTCATATTTTCAGCCTGTATGGCTGTCACTTCTTTTGGAGAAATAGCGACCCCTTCCTCCCAGACGCCGTGATCGGCACACATAACC  <  SRR3722077.1064180/100‑1 (MQ=60)
                                                                                             GGTTGTTCCACGGGTCATATTTTCAGCCTGTATGGCTGTCACTTCTTTTGGAGAAATAGCGACCCCTTCCTCCCAGACGCCGTGATCGGCACACATAACC  <  SRR3722077.402684/100‑1 (MQ=60)
                                                                                                   |                                                                                             
GTTGATAAGCCCGGGGATAGGCTCAGCAGTATCAATACCAACATCAATTACGTGGACGTTAGCGCCCGCTTGTTCTGCCAGCACACACACGCCGGTTGTTCCACGGGTCATATTTTCAGCCTGTATGGCTGTCACTTCTTTTGGAGAAATAGCGACCCCTTCCTCCCAGACGCCGTGATCGGCACACATAACC  >  NZ_CP009273/2057565‑2057757

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑