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
TGATCCCGAACCCATTGGCAGATACAACGTCGCGCCGGGAACCAAAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTTCTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGCCCGCGTAGAAACTGCGGCAACCAGTCGTATGTTTAAACCGCTCTGGCAA  >  NZ_CP009273/2003385‑2003577
                                                                                               |                                                                                                 
TGATCCCGAACCCATTGGCAGATACAACGTCGCGCCGGGAACCAAAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTTCTGG                                                                                               <  SRR3722077.394537/100‑1 (MQ=60)
  ATCCCGAACCCATTGGCAGATACAACGTCGCGCCGGGAACCAAAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTCCTGGGG                                                                                             <  SRR3722077.909802/100‑1 (MQ=60)
        gtataagagaCAGATACAACGTCGCGCCGGGAACCAAAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTCCTGGGGATATGC                                                                                       <  SRR3722077.663789/90‑1 (MQ=60)
        AACCCATTGGCAGATACAACGTCGCGCCGGGAACCAAAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTTCTGGGGATATGC                                                                                       <  SRR3722077.370079/100‑1 (MQ=60)
          CCCATTGGCAGATACAACGTCGCGCCGGGAACCAAAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTTCTGGGGATATGCTC                                                                                     >  SRR3722077.816966/1‑100 (MQ=60)
                GGCAGATACAACGTCGCGCCGGGAACCAAAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTCCTGGGGATATGCTCCCGGAT                                                                               >  SRR3722077.529599/1‑100 (MQ=60)
                GGCAGATACAACGTCGCGCCGGGAACCAAAGTCCTACTGCTCAGTGAACGGGATGAACACCTTCATCTGGATCCGGTTTTCTGGGGATATGCTCCCGGAT                                                                               >  SRR3722077.210379/1‑100 (MQ=60)
                          ACGTCGCGCCGGGAACCAAAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTCCTGGGGATATGCTCCCGGATGGTGGGATAA                                                                     <  SRR3722077.791547/100‑1 (MQ=60)
                                                         CAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTCCTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGCCCtgtctcttata                                      >  SRR3722077.971809/1‑89 (MQ=60)
                                                                         CACCTTCATCTGGATCCGGTTTTCTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGCCCGCGTAGAAACTGCGGCAACCAGTCGTA                      <  SRR3722077.664335/100‑1 (MQ=60)
                                                                           CCTTCATCTGGATCCGGTTTTCTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGCCCGCGTAGAAACTGCGGCAACCAGTCGTATG                    >  SRR3722077.89177/1‑100 (MQ=60)
                                                                           CCTTCATCTGGACCCGGTTTTCTGGGGATATGCTCCCGGATGGTGGGATAAACCtgtctcttatacacatctccgagcccacgagacccacggccatctc                    >  SRR3722077.822990/1‑54 (MQ=60)
                                                                                  CTGGATCCGGTTTCCTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGCCCGCGTAGAAACTGCGGCAACCAGTCGTATGTTTAAAC             <  SRR3722077.700849/100‑1 (MQ=60)
                                                                                   TGGATCCGGTTTCCTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGCCCGCGTAGAAACTGCGGCAACCAGTCGTATGTTTAAACC            <  SRR3722077.758269/100‑1 (MQ=60)
                                                                                     GATCCGGTTTCCTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGCCCGCGTAGAAACTGCGGCAACCAGTCGTATGTTTAAACCGC          >  SRR3722077.216986/1‑100 (MQ=60)
                                                                                           GTTTCCTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGCCCGCGTAGAAACTGCGGCAACCAGTCGTATGTTTAAACCGCTCTGGC    >  SRR3722077.539527/1‑100 (MQ=60)
                                                                                            TTTTCTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGCCCGCGTAGAAACTGCGGCAACCAGTCGTATGTTTAAACCGCTCTGGCA   <  SRR3722077.308139/100‑1 (MQ=60)
                                                                                            TTTCCTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGCCCGCGTAGAAACTGCGGCAACCAGTCGTATGTTTAAACCGCTCTGGCA   <  SRR3722077.1166907/100‑1 (MQ=60)
                                                                                             TTCCTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGCCCGCGTAGAAACTGCGGCAACCAGTCGTATGTTTAAACCGCTCTGGCAA  >  SRR3722077.275955/1‑100 (MQ=60)
                                                                                               |                                                                                                 
TGATCCCGAACCCATTGGCAGATACAACGTCGCGCCGGGAACCAAAGTCCTACTGCTCAGTGAACGTGATGAACACCTTCATCTGGATCCGGTTTTCTGGGGATATGCTCCCGGATGGTGGGATAAACCGCCGCTGATTAACGCCCGCGTAGAAACTGCGGCAACCAGTCGTATGTTTAAACCGCTCTGGCAA  >  NZ_CP009273/2003385‑2003577

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑