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
TGATCTTCAACACCTTCCCGCAAGAAGCGCGCCTGGCGACTCATCCGGGCACCGGAATCCTGCAACGCCAGTCCGACAAAAATCAGGATGAAAATCACCCAGAACATAACGTTCACGCCACCATTAAAATTGGGCGTCGGGGAGTTATACCAGAATAGATTCAAAAAAGGCGTA  >  NZ_CP009273/1803126‑1803299
                                                                           |                                                                                                  
TGATCTTCAACACCTTCCCGCAAGAAGCGCGCCTGGCGACTCATCCGGGCACCGGAATCCTGCAACGCCAGTCCGGCAAAAATCAGGATGAAAATCACCC                                                                            <  SRR3722077.908900/100‑1 (MQ=60)
   TCTTCAACACCTTCCCGCAAGAAGCGCGCCTGGCGACTCATCCGGGCACCGGAATCCTGCAACGCCAGTCCGGCAAAAATCAGGATGAAAATCACCCAGA                                                                         >  SRR3722077.12216/1‑100 (MQ=60)
   TCTTCAACACCTTCCCGCAAGAAGCGCGCCTGGCGACTCATCCGGGCACCGGAATCCTGCAACGCCAGTCCGGCAAAAATCAGGATGAAAATCACCCAGA                                                                         >  SRR3722077.390065/1‑100 (MQ=60)
    CTTCAACACCTTCCCGCAAGAAGCGCGCCTGGCGACTCATCCGGGCACCGGAATCCTGCAACGCCAGTCCGACAAAAATCAGGATGAAAATCACCCAGAA                                                                        >  SRR3722077.768691/1‑100 (MQ=60)
          CACCTTCCCGCAAGAAGCGCGCCTGGCGACTCATCCGGGCACCGGAATCCTGCAACGCCAGTCCGACAAAAATCAGGATGAAAATCACCCAGAACATAAC                                                                  <  SRR3722077.38010/100‑1 (MQ=60)
                    CAAGAAGCGCGCCTGGCGACTCATCCGGGCACCGGAATCCTGCAACGCCAGTCCGGCAAAAATCAGGATGAAAATCACCCAGAACATAACGTTCACGCCA                                                        >  SRR3722077.602606/1‑100 (MQ=60)
                    CAAGAAGCGCGCCTGGCGACTCATCCGGGCACCGGAATCCTGCAACGCCAGTCCGACAAAAATCAGGATGAAAATCACCCAGAACATAACGTTCACGCCA                                                        >  SRR3722077.735133/1‑100 (MQ=60)
                              GCCTGGCGACTCATCCGGGCACCGGAATCCTGCAACGCCAGTCCGGCAAAAATCAGGATGAAAATCACCCAGAACATAACGTTCACGCCACCATTAAAAT                                              <  SRR3722077.505218/100‑1 (MQ=60)
                              GCCTGGCGACTCATCCGGGCACCGGAATCCTGCAACGCCAGTCCGACAAAAATCAGGATGAAAATCACCCAGAACATAACGTTCACGCCACCATTAAAAT                                              <  SRR3722077.409479/100‑1 (MQ=60)
                                  GGCGACTCATCCGGGCACCGGAATCCTGCAACGCCAGTCCGGCAAAAATCAGGATGAAAATCACCCAGAACATAACGTTCACGCCACCATTAAAATTGGG                                          <  SRR3722077.881186/100‑1 (MQ=60)
                                      ACTCATCCGGGCACCGGAATCCTGCAACGCCAGTCCGACAAAAATCAGGATGAAAATCACCCAGAACATAACGTTCACGCCACCATTAAAATTGGGCGTC                                      >  SRR3722077.757239/1‑100 (MQ=60)
                                         CATCCGGGCACCGGAATCCTGCAACGCCAGTCCGGCAAAAATCAGGATGAAAATCACCCAGAACATAACGTTCACGCCACCATTAAAATTGGGCGTCGGG                                   >  SRR3722077.87784/1‑100 (MQ=60)
                                                  ACCGGAATCCTGCAACGCCAGTCCGACAAAAATCAGGATGAAAATCACCCAGAACATAACGTTCACGCCACCATTAAAATTGGGCGTCGGGGAGTTATAC                          <  SRR3722077.337326/100‑1 (MQ=60)
                                                    CGGAATCCTGCAACGCCAGTCCGACAAAAATCAGGATGAAAATCACCCAGAACATAACGTTCACGCCACCATTAAAATTGGGCGTCGGGGAGTTATACCA                        <  SRR3722077.323414/100‑1 (MQ=60)
                                                        ATCCTGCAACGCCAGTCCGGCAAAAATCAGGATGAAAATCACCCAGAACATAACGTTCACGCCACCATTAAAATTGGGCGTCGGGGAGTTATACCtgtct                    >  SRR3722077.1154943/1‑95 (MQ=60)
                                                        ATCCTGCAACGCCAGTCCGGCAAAAATCAGGATGAAAATCACCCAGAACATAACGTTCACGCCACCATTAAAATTGGGCGTCGGGGAGTTATACCAGAAT                    <  SRR3722077.436016/100‑1 (MQ=60)
                                                        ATCCTGCAACGCCAGTCCGGCAAAAATCAGGATGAAAATCACCCAGAACATAACGTTCACGCCACCATTAAAATTGGGCGTCGGGGAGTTATACCAGAAT                    <  SRR3722077.878297/100‑1 (MQ=60)
                                                                  GCCAGTCCGACAAAAATCAGGATGAAAATCACCCAGAACATAACGTTCACGCCACCATTAAAATTGGGCGTCGGGGAGTTATACCAGAATAGATTCAAAA          <  SRR3722077.1028772/100‑1 (MQ=60)
                                                                    CAGTCCGGCAAAAATCAGGATGAAAATCACCCAGAACATAACGTTCACGCCACCATTAAAATTGGGCGTCGGGGAGTTATACCAGAATAGATTCAAAAAA        <  SRR3722077.110405/100‑1 (MQ=60)
                                                                          GGCAAAAATCAGGATGAAAATCACCCAGAACATAACGTTCACGCCACCATTAAAATctgtctcttatacacatctccgagcccacgagacccacggccat  >  SRR3722077.557084/1‑56 (MQ=60)
                                                                           |                                                                                                  
TGATCTTCAACACCTTCCCGCAAGAAGCGCGCCTGGCGACTCATCCGGGCACCGGAATCCTGCAACGCCAGTCCGACAAAAATCAGGATGAAAATCACCCAGAACATAACGTTCACGCCACCATTAAAATTGGGCGTCGGGGAGTTATACCAGAATAGATTCAAAAAAGGCGTA  >  NZ_CP009273/1803126‑1803299

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: ‑