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 I194 R1 197 32.2 1845014 95.2% 1756453 85.4

Breseq alignment

N/A

GATK/CNVnator alignment

BRESEQ :: bam2aln output
TGGTCATAATAGTGGCGATCTGTTTCTCATTCAGGTTGGCGAGCGCCTTAATACGCTCCAGCAAAATGGCGAAGTTATTGGTCGTCTCGGCGGTGATGAGTTTTTAGTTGTTTCACTAAACAACGAGAATGCGGATATTTCGTCGCTGCGAGAACGCATTCAGCAGCAAATACGTGGAGAATATCACTT  >  NZ_CP009273/1872640‑1872828
                                                                                          |                                                                                                  
TGGTCATAATAGTGGCGATCTGTTTCTCATTCAGGTTGGCGAGCGCCTTAATACGCTCCAGCAAAATGGCGAAGTTATTGGTCGTCTCGGGGGTGATGAG                                                                                           <  SRR3722072.153791/100‑1 (MQ=60)
 GGTCATAATAGTGGCGATCTGTTTCTCATTCAGGTTGGCGAGCGCCTTAATACGCTCCAGCAAAATGGCGAAGTTATTGGTCGTCTCGGGGGTGATGAGT                                                                                          >  SRR3722072.834037/1‑100 (MQ=60)
 GGTCATAATAGTGGCGATCTGTTTCTCATTCAGGTTGGCGAGCGCCTTAATACGCTCCAGCAAAATGGCGAAGTTATTGGTCGTCTCGGGGGTGATGAGT                                                                                          >  SRR3722072.487754/1‑100 (MQ=60)
   TCATAATAGTGGGGATCTGTTTCTCATTCAGGTTGGCGAGCGCCTTAATACGCTCCAGCAAAATGGCGAAGTTATTGGTCGTCTCGGGGGTGATGAGTTT                                                                                        >  SRR3722072.162219/1‑100 (MQ=60)
      TAATAGTGGCGATCTGTTTCTCATTCAGGTTGGCGAGCGCCTTAATACGCTCCAGCAAAATGGCGAAGTTATTGGTCGTCTCGGGGGTGATGAGTTTTTA                                                                                     >  SRR3722072.316020/1‑100 (MQ=60)
      TAATAGTGGCGATCTGTTTCTCATTCAGGTTGGCGAGCGCCTTAATACGCTCCAGCAAAATGGCGAAGTTATTGGTCGTCTCGGGGGTGATGAGTTTTTA                                                                                     >  SRR3722072.457694/1‑100 (MQ=60)
      TAATAGTGGCGATCTGTTTCTCATTCAGGTTGGCGAGCGCCTTAATACGCTCCAGCAAAATGGCGAAGTTATTGGTCGTCTCGGCGGGGATGAGGTTTTA                                                                                     >  SRR3722072.270755/1‑100 (MQ=60)
                   CTGTTTCTCATTCAGGTTGGCGAGCGCCTTAATACGCTCCAGCAAAATGGCGAAGTTATTGGTCGTCTCGGCGGTGATGAGTTTTTAGTTGTTTCACTAA                                                                        >  SRR3722072.455223/1‑100 (MQ=60)
                     GTTTCTCATTCAGGTTGGCGAGCGCCTTAATACGCTCCAGCAAAATGGCGAAGTTATTGGTCGTCTCGGGGGTGATGAGTTTTTAGTTGTTTCACTAAAC                                                                      <  SRR3722072.407308/100‑1 (MQ=60)
                       TTCTCATTCAGGTTGGCGAGCGCCTTAATACGCTCCAGCAAAATGGCGAAGTTATTGGTCGTCTCGGCGGGGATGAGGTTTTTGTTGTTTCACCAAACAA                                                                    >  SRR3722072.699807/1‑100 (MQ=60)
                              TCAGGTTGGCGAGCGCCTTAATACGCTCCAGCAAAATGGCGAAGTTATTGGTCGTCTCGGGGGTGATGAGTTTTTAGTTGTTTCACTAAACAACGAGAAT                                                             <  SRR3722072.106399/100‑1 (MQ=60)
                                          GCGCCTTAATACGCTCCAGCAAAATGGCGAAGTTATTGGTCGTCTCGGGGGTGATGAGTTTTTAGTTGTTTCACTAAACAACGAGAATGCGGATATTTCG                                                 <  SRR3722072.767141/100‑1 (MQ=60)
                                             CCTTAATACGCTCCAGCAAAATGGCGAAGTTATTGGTCGTCTCGGCGGTGATGAGTTTTTAGTTGTTTTACTAAACAACGAGAATGCGGATATTTTGTCG                                              >  SRR3722072.206367/1‑100 (MQ=60)
                                             CCTTAATACGCTCCAGCAAAATGGCGAAGTTATTGGTCGTCTCGGCGGGGGTGAGCTTTTAGTTGTTTtgcctaataaacagaattccgagatttcgtcg                                              >  SRR3722072.377232/1‑68 (MQ=60)
                                                                     CGAAGTTATTGGTCGTCTCGGCGGTGATGAGTTTTTAGTTGTTTCACTAAACAACGAGAATGCGGATATTTCGTCGCTGCGAGAACGCATTCAGCAGCAA                      <  SRR3722072.94789/100‑1 (MQ=60)
                                                                        AGTTATTGGTCGTCTCGGGGGTGATGAGTTTTTAGTTGTTTCACTAAACAACGAGAATGCGGATATTTCGTCGCTGCGAGAACGCATTCAGCAGCAAATA                   >  SRR3722072.4009/1‑100 (MQ=60)
                                                                                    TCTCGGGGGTGATGAGTTTTTAGTTGTTTCACTAAACAACGAGAATGCGGATATTTCGTCGCTGCGAGAACGCATTCAGCAGCAAATACGTGGAGAATAT       >  SRR3722072.445895/1‑100 (MQ=60)
                                                                                         GGGGTGATGAGTTTTTAGTTGTTTCACTAAACAACGAGAATGCGGATATTTCGTCGCTGCGAGAACGCATTCAGCAGCAAATACGTGGAGAATATCACTT  <  SRR3722072.500968/100‑1 (MQ=60)
                                                                                          |                                                                                                  
TGGTCATAATAGTGGCGATCTGTTTCTCATTCAGGTTGGCGAGCGCCTTAATACGCTCCAGCAAAATGGCGAAGTTATTGGTCGTCTCGGCGGTGATGAGTTTTTAGTTGTTTCACTAAACAACGAGAATGCGGATATTTCGTCGCTGCGAGAACGCATTCAGCAGCAAATACGTGGAGAATATCACTT  >  NZ_CP009273/1872640‑1872828

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑