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
ACCAAAATATTACCCAATGAAATATCCACGCACCTCACTGCGCTATTCTGGGTTGAACTGTGGATTCGCCAACATAAAGCCGCCATCCACTATCAACGACTGCCCGGTGGTGTAATTTGCGCCCTCCGAACAAAGCCACACCACCAGGCTGGCAATCTCATGCGTTGCGCCAAAACGCCGCAAGGGAATCGAA  >  NZ_CP009273/2219946‑2220138
                                                                                                  |                                                                                              
ACCAAAATATTACCCAATGAAATATCCACGCACCTCACTGCGCTATTCTGGGTTGAACTGTGGATTCGCCAACATAAAGCCGCCATCCACTATCAACGGC                                                                                               <  SRR3722077.356955/100‑1 (MQ=60)
      ATATTACCCAATGAAATATCCACGCACCTCACTGCGCTATTCTGGGTTGAACTGTGGATTCGCCAACATAAAGCCGCCATCCACTATCAACGGCTGCCCG                                                                                         >  SRR3722077.545060/1‑100 (MQ=60)
       TATTACCCAATGAAATATCCACGCACCTCACTGCGCTATTCTGGGTTGAACTGTGGATTCGCCAACATAAAGCCGCCATCCACTATCAACGGCTGCCCGG                                                                                        <  SRR3722077.803906/100‑1 (MQ=60)
               AATGAAATATCCACGCACCTCACTGCGCTATTCTGGGTTGAACTGTGGATTCGCCAACATAAAGCCGCCATCCACTATCAACGGCTGCCCGGTGGTGTAA                                                                                <  SRR3722077.1067331/100‑1 (MQ=60)
                 TGAAATATCCACGCACCTCACTGCGCTATTCTGGGTTGAACTGTGGATTCGCCAACATAAAGCCGCCATCCACTATCAACGGCTGCCCGGTGGTGTAATT                                                                              <  SRR3722077.486414/100‑1 (MQ=60)
                     ATATCCACGCACCTCACTGCGCTATTCTGGGTTGAACTGTGGATTCGCCAACATAAAGCCGCCATCCACTATCAACGACTGCCCGGTGGTGTAATTTGCG                                                                          >  SRR3722077.1017654/1‑100 (MQ=60)
                            CGCACCTCACTGCGCTATTCTGGGTTGAACTGTGGATTCGCCAACATAAAGCCGCCATCCACTATCAACGGCTGCCCGGTGGTGTctgtctcttatacac                                                                   >  SRR3722077.862986/1‑85 (MQ=60)
                            CGCACCTCACTGCGCTATTCTGGGTTGAACTGTGGATTCGCCAACATAAAGCCGCCATCCACTATCAACGGCTGCCCGGTGGTGTctgtctcttatacac                                                                   >  SRR3722077.608343/1‑85 (MQ=60)
                               ACCTCACTGCGCTATTCTGGGTTGAACTGTGGATTCGCCAACATAAAGCCGCCATCCACTATCAACGGCTGCCCGGTGGTGTAATTTGCGCCCTCCGAAC                                                                <  SRR3722077.4318/100‑1 (MQ=60)
                                  TCACTGCGCTATTCTGGGTTGAACTGTGGATTCGCCAACATAAAGCCGCCATCCACTATCAACGGCTGCCCGGTGGTGTAATTTGCGCCCTCCGAACAAA                                                             >  SRR3722077.1135739/1‑100 (MQ=60)
                                       GCGCTATTCTGGGTTGAACTGTGGATTCGCCAACATAAAGCCGCCATCCACTATCAACGACTGCCCGGTGGTGTAATTTGCGCCCTCCGAACAAAGCCAC                                                        >  SRR3722077.1044532/1‑100 (MQ=60)
                                            ATTCTGGGTTGAACTGTGGATTCGCCAACATAAAGCCGCCATCCACTATCAACGGCTGCCCGGTGGTGTAATTTGCGCCCTCCGAACAAAGCCACACCAC                                                   >  SRR3722077.11798/1‑100 (MQ=60)
                                            ATTCTGGGTTGAACTGTGGATTCGCCAACATAAAGCCGCCATCCACTATCAACGGCTGCCCGGTGGTGTAATTTGCGCCCTCCGAACAAAGCCACACCAC                                                   >  SRR3722077.904988/1‑100 (MQ=60)
                                            ATTCTGGGTTGAACTGTGGATTCGCCAACATAAAGCCGCCATCCACTATCAACGACTGCCCGGTGGTGTAATTTGCGCCCTCCGAACctgtctcttatac                                                   >  SRR3722077.325249/1‑87 (MQ=60)
                                                 ggccgtgggtctcgtgggctcggagatgtgtataagagacagATCAACGGCTGCCCGGTGGTGTAATTTGCGCCCTCCGAACAAAGCCACACCACCAGGC                                              <  SRR3722077.790398/58‑1 (MQ=60)
                                                 GGGTTGAACTGTGGATTCGCCAACATAAAGCCGCCATCCACTATCAACGGCTGCCCGGTGGTGTAATTTGCGCCCTCCGAACAAAGCCACACCACCAGGC                                              <  SRR3722077.5958/100‑1 (MQ=60)
                                                 GGGTTGAACTGTGGATTCGCCAACATAAAGCCGCCATCCACTATCAACGGCTGCCCGGTGGTGTAATTTGCGCCCTCCGAACAAAGCCACACCACCAGGC                                              >  SRR3722077.959346/1‑100 (MQ=60)
                                                 GGGTTGAACTGTGGATTCGCCAACATAAAGCCGCCATCCACTATCAACGACTGCCCGGTGGTGTAATTTGCGCCCTCCGAACAAAGCCACACCACCAGGC                                              >  SRR3722077.555641/1‑100 (MQ=60)
                                                        ACTGTGGATTCGCCAACATAAAGCCGCCATCCACTATCAACGACTGCCCGGTGGTGTAATTTGCGCCCTCCGAACAAAGCCACACCACCAGGCTGGCAAT                                       >  SRR3722077.90305/1‑100 (MQ=60)
                                                                 ctcggagatgtgtataagagacagCTATCAACGGCTGCCCGGTGGTGTAATTTGCGCCCTCCGAACAAAGCCACACCACCAGGCTGGCAATCTCATGCGT                              <  SRR3722077.23595/76‑1 (MQ=60)
                                                                      AACATAAAGCCGCCATCCACTATCAACGACTGCCCGGTGGTGTAATTTGCGCCCTCCGAACAAAGCCACACCACCAGGCTGGCAATCTCATGCGTTGCGC                         <  SRR3722077.686405/100‑1 (MQ=60)
                                                                                           ATCAACGACTGCCCGGTGGTGTAATTTGCGCCCTCCGAACAAAGCCACACCACCAGGCTGGCAATCTCATGCGTTGCGCCAAAACGCCGCAAGGGAATCG    >  SRR3722077.1046793/1‑100 (MQ=60)
                                                                                             CAACGACTGCCCGGTGGTGTAATTTGCGCCCTCCGAACAAAGCCACACCACCAGGCTGGCAATCTCATGCGTTGCGCCAAAACGCCGCAAGGGAATCGAA  <  SRR3722077.195728/100‑1 (MQ=60)
                                                                                                  |                                                                                              
ACCAAAATATTACCCAATGAAATATCCACGCACCTCACTGCGCTATTCTGGGTTGAACTGTGGATTCGCCAACATAAAGCCGCCATCCACTATCAACGACTGCCCGGTGGTGTAATTTGCGCCCTCCGAACAAAGCCACACCACCAGGCTGGCAATCTCATGCGTTGCGCCAAAACGCCGCAAGGGAATCGAA  >  NZ_CP009273/2219946‑2220138

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑