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
GTCATATTTGCGATCACCAGTGCCAATACAACTGTACCCGCCTGGATTACGACAGTGCGCTGAATATCCGCGAACTGAAAAAAGTCGCGCTGGAAAAAGGTTGGGATGAATATAAGCAACGCTGGCACAAACCAGCCGGTTCTGGTTCACGCCATCCGGTTGCCGTGATTGGTGC  >  NZ_CP009273/3010917‑3011091
                                                                                             |                                                                                 
gatggccgtgggtctcgtgggctcggagatgtgtataagagacaGATTACGACAGTGCGCTGAATATCCGCGAACTGAAAAAAGTCGCGCTGGGAAAAGG                                                                             <  SRR3722077.940260/56‑1 (MQ=60)
GTCATATTTGCGATCACCAGTGCCAATACAACTGTACCCGCCTGGATTACGACAGTGCGCTGAATATCCGCGAACTGAAAAAAGTCGCGCTGGAAAAAGG                                                                             >  SRR3722077.61807/1‑100 (MQ=60)
      ttggcgacccCCAGTGCAAAAACAACTGTACCCGCCTGGATTACGACAGTGCGCTGAATATCCGCGAACTGAAAAAAGTCGCGCTGGAAAAAGGTTGGGA                                                                       <  SRR3722077.562249/90‑1 (MQ=60)
              CACCAGTGCCAATACAACTGTACCCGCCTGGATTACGACAGTGCGCTGAATATCCGCGAACTGAAAAAAGTCGCGCTGGGAAAAGGTTGGGATGAATATA                                                               >  SRR3722077.570107/1‑100 (MQ=60)
              CACCAGTGCCAATACAACTGTACCCGCCTGGATTACGACAGTGCGCTGAATATCCGCGAACTGAAAAAAGTCGCGCTGGAAAAAGGTTGGGATGAATATA                                                               >  SRR3722077.513059/1‑100 (MQ=60)
              CACCAGTGCCAATACAACTGTACCCGCCTGGATTACGACAGTGCGCTGAATATCCGCGAACTGAAAAAAGTCGCGCTGGAAAAAGGTTGGGATGAATATA                                                               >  SRR3722077.50478/1‑100 (MQ=60)
                 ccgtgcaaataaaactttcCCCGCCTGGATTACGACAGTGCGCTGAATATCCGCGAACTGAAAAAAGTCGCGCTGGAAAAAGGTTGGGATGAATATAAGC                                                            <  SRR3722077.224197/81‑1 (MQ=60)
                 cagtccaaaaACAACTGTCCCCGCCTGGATTACGACAGTGCGCTGAATATCCGCGAACTGAAAAAAGTCGCGCTGGGAAAAGGTTGGGATGAATATAAGC                                                            <  SRR3722077.726332/90‑1 (MQ=60)
                 cagcccaAATACAACTTTCCCCGCCTGGATTACGACAGTGCGCTGAATATCCGCGAACTGAAAAAAGTCGCGCTGGGAAAAGGTTGGGATGAATATAAGC                                                            <  SRR3722077.80812/93‑1 (MQ=60)
                 CAGTCCCAATACAACTGTCCCCGCCTGGATTACGACAGTGCGCTGAATATCCGCGAACTGAAAAAAGTCGCGCTGGGAAAAGGTTGGGATGAATATAAGC                                                            <  SRR3722077.177026/100‑1 (MQ=60)
                   GTGCCAATACAACTGTACCCGCCTGGATTACGACAGTGCGCTGAATATCCGCGAACTGAAAAAAGTCGCGCTGGGAAAAGGTTGGGATGAATATAAGCAA                                                          >  SRR3722077.694806/1‑100 (MQ=60)
                   GTGCCAATACAACTGTACCCGCCTGGATTACGACAGTGCGCTGAATATCCGCGAACTG‑AAAAAGTCGCGCTGGAAAAAGGTTGGGATGAATATAAGCAAC                                                         >  SRR3722077.353236/1‑100 (MQ=60)
                           AAAACTGCACCCGCCTGGATTACGACAGTGCGCTGAATATCCGCGAACTGAAAAAAGTCGCGCTGGAAAAAGGTTGGGATGAATATAAGCAACGCTGGCA                                                  <  SRR3722077.225148/100‑1 (MQ=60)
                            AAACTGTACCCGCCTGGATTACGACAGTGCGCTGAATATCCGCGAACTGAAAAAAGTCGCGCTGGAAAAAGGTTGGGATGAATATAAGCAACGCTGGCAC                                                 <  SRR3722077.587562/100‑1 (MQ=60)
                                            GATTACGACAGTGCGCTGAATATCCGCGAACTGAAAAAAGTCGCGCTGGGAAAAGGTTGGGATGAATATAAGCAACGCTGGCACAAACCAGCCGGTTCTG                                 >  SRR3722077.412823/1‑100 (MQ=60)
                                            GATTACGACAGTGCGCTGAATATCCGCGAACTGAAAAAAGTCGCGCTGGGAAAAGGTTGGGATGAATATAAGCAACGCTGGCACAAACCAGCCGGTTCTG                                 >  SRR3722077.68278/1‑100 (MQ=60)
                                            GATTACGACAGTGCGCTGAATATCCGCGAACTGAAAAAAGTCGCGCTGGGAAAAGGTTGGGATGAATATAAGCAACGCTGGCACAAACCAGCCGGTTCTG                                 >  SRR3722077.995485/1‑100 (MQ=60)
                                                        GCGCTGAATATCCGCGAACTGAAAAAAGTCGCGCTGGAAAAAGGTTGGGATGAATATAAGCAACGCTGGCACAAACCAGCCGGTTCTGGTTCACGCCATC                     <  SRR3722077.288452/100‑1 (MQ=60)
                                                            TGAATATCCGCGAACTGAAAAAAGTCGCGCTGGGAAAAGGTTGGGATGAATATAAGCAACGCTGGCACAAACCAGCCGGTTCTGGTTCACGCCATCCGGT                 <  SRR3722077.752150/100‑1 (MQ=60)
                                                               ATATCCGCGAACTGAAAAAAGTCGCGCTGGGAAAAGGTTGGGATGAATATAAGCAACGCTGGCACAAACCAGCCGGTTCTGGTTCACGCCATCCGGTTGC              <  SRR3722077.648970/100‑1 (MQ=60)
                                                               ATATCCGCGAACTGAAAAAAGTCGCGCTGGGAAAAGGTTGGGATGAATATAAGCAACGCTGGCACAAACCAGCCGGTTCTGGTTCACGCCATCCGGTTGC              <  SRR3722077.1052639/100‑1 (MQ=60)
                                                                 ATCCGCGAACTGAAAAAAGTCGCGCTGGGAAAAGGTTGGGATGAATATAAGCctgtctcttatacacatctccgagcccacgagacccacggccatctcg            >  SRR3722077.31259/1‑52 (MQ=60)
                                                                  TCCGCGAACTGAAAAAAGTCGCGCTGGAAAAAGGTTGGGATGAATATAAGCctgtctcttatacacatctccgagcccacgagacccacggccatctcgt           >  SRR3722077.187896/1‑51 (MQ=60)
                                                                           TGAAAAAAGTCGCGCTGGAAAAAGGTTGGGATGAATATAAGCAACGCTGGCACAAACCAGCCGGTTCTGGTTCACGCCATCCGGTTGCCGTGATTGGTGC  <  SRR3722077.870771/100‑1 (MQ=60)
                                                                                             |                                                                                 
GTCATATTTGCGATCACCAGTGCCAATACAACTGTACCCGCCTGGATTACGACAGTGCGCTGAATATCCGCGAACTGAAAAAAGTCGCGCTGGAAAAAGGTTGGGATGAATATAAGCAACGCTGGCACAAACCAGCCGGTTCTGGTTCACGCCATCCGGTTGCCGTGATTGGTGC  >  NZ_CP009273/3010917‑3011091

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 10 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑