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 I200 R1 216 30.8 1683622 97.2% 1636480 87.0

Breseq alignment

N/A

GATK/CNVnator alignment

BRESEQ :: bam2aln output
GTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGCCCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCA‑GGG‑GGGTATTATTGTAGAGTTTCCCCATATGTTTCTATGGGATCCAGGAAATGACAATCAGGAGTTACAAAAACTTAAATCTGGTCAGGGCAAATATCGAGACTG  >  NZ_CP009273/2759139‑2759331
                                                                                               |                                                                                                   
GTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGCCCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCA‑GGG‑GGGTATTAT                                                                                               <  SRR3722079.242973/100‑1 (MQ=60)
      gatcctctctggtctcgtgggctcggagatgtgtataagagacagATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGG‑GGGTATTATTGTAG                                                                                          <  SRR3722079.348888/55‑1 (MQ=60)
        CCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGCCCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGG‑GGGTATTATTGTAGAG                                                                                        <  SRR3722079.830352/100‑1 (MQ=60)
        CCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGCCCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCA‑GGGCGGGTATTATTGTAGAG                                                                                        <  SRR3722079.648753/100‑1 (MQ=60)
                    ACGATCCTGCCCTATAGTTGGAGTGCCCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGG‑GGGTATTATTGTAGAGTTTCCCCATATG                                                                            <  SRR3722079.236853/100‑1 (MQ=60)
                    ACGATCCTGCCCTATAGTTGGAGTGCCCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGG‑GGGTATTATTGTAGAGTTTCCCCATATG                                                                            <  SRR3722079.556468/100‑1 (MQ=60)
                       ATCCTGCCCTATAGTTGGAGTGCCCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGG‑GGGTATTATTGTAGAGTTTCCCCATATGTTT                                                                         >  SRR3722079.839805/1‑100 (MQ=60)
                        cggagatgtgtataagagacagCCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGG‑GGGTATTATTGTAGAGTTTCCCCATATGTTTC                                                                        <  SRR3722079.350808/78‑1 (MQ=60)
                               CTATAGTTGGAGTGCCCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGG‑GGGTATTATTGTAGAGTTTCCCCATATGTTTCctgtctc                                                                 >  SRR3722079.594813/1‑93 (MQ=60)
                                         cggagatgtgtataagagacagAAATTTAGCAAATCAATACACTTCAGGGG‑GGGTATTATTGTAGAGTTTCCCCATATGTTTCTATGGGATCCAGGAAAT                                                       <  SRR3722079.488785/78‑1 (MQ=60)
                                                 CTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCAGGGG‑GGGTATTATTGTAGAGTTTCCCCATATGTTTCTATGGGATCCAGGAAATGACAATCA                                               >  SRR3722079.322793/1‑100 (MQ=60)
                                                                              ATACACTTCA‑GGG‑GGGTATTATTGTAGAGTTTCCCCATATGTTTCTATGGGATCCAGGAAATGACAATCAGGAGTTACAAAAACTTAAATCTGGTCAGGG                 >  SRR3722079.847776/1‑100 (MQ=60)
                                                                                   CTTCAGGGG‑GGGTATTATTGTAGAGTTTCCCCATATGTTTCTATGGGATCCAGGAAATGACAATCAGGAGTTACAAAAACTTAAATCTGGTCAGGGCAAA             >  SRR3722079.320820/1‑100 (MQ=60)
                                                                                             GGGTATTATTGTAGAGTTTCCCCATATGTTTCTATGGGATCCAGGAAATGACAATCAGGAGTTACAAAAACTTAAATCTGGTCAGGGCAAATATCGAGAC    <  SRR3722079.340568/100‑1 (MQ=60)
                                                                                              GGTATTATTGTAGAGTTTCCCCATATGTTTCTATGGGATCCAGGAAATGACAATCAGGAGTTACAAAAACTTAAATCTGGTCGGGGCAAATATCGAGACT   >  SRR3722079.527553/1‑100 (MQ=60)
                                                                                               GTATTATTGTAGAGTTTCCCCATATGTTTCTATGGGATCCAGGAAATGACAATCAGGAGTTACAAAAACTTAAATCTGGTCAGGGCAAATATCGAGACTG  >  SRR3722079.103221/1‑100 (MQ=60)
                                                                                               GTATTATTGTAGAGTTTCCCCATATGTTTCTATGGGATCCAGGAAATGACAATCAGGAGTTACAAAAACTTAAATCTGGTCAGGGCAAATATCGAGACTG  >  SRR3722079.671630/1‑100 (MQ=60)
                                                                                               |                                                                                                   
GTGGACTGCCCCCCCGGTAGACGATCCTGCCCTATAGTTGGAGTGCCCCCTATTCAGGTGGCTAAATTTAGCAAATCAATACACTTCA‑GGG‑GGGTATTATTGTAGAGTTTCCCCATATGTTTCTATGGGATCCAGGAAATGACAATCAGGAGTTACAAAAACTTAAATCTGGTCAGGGCAAATATCGAGACTG  >  NZ_CP009273/2759139‑2759331

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑