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 I211 R1 223 18.0 1007644 96.3% 970361 85.7

Breseq alignment

N/A

GATK/CNVnator alignment

BRESEQ :: bam2aln output
CCATCAGCATATTGATTATCTGGTGTGAATTTCAGGCTTACGGTGAGTCTGGCTACGCTGCCACACAGATTAGCTAATTGAAACGCCTTTCACCCCTGCCATACCTTTTAATAATCGCAACAGGTCTTCTATCGACGTTGTGGCATGAAGCTGGATATCAATGGCGACCACTTCATGAT  >  NZ_CP009273/3648546‑3648724
                                                                                           |                                                                                       
CCATCAGCATATTGATTATCTGGTGTGAATTTCAGGCTTACGGTGAGTCTGGCTACGCTGCCACACAGATTAGCTAATTGAAACGCCTTTCACCCCTGCC                                                                                 >  SRR3722094.272773/1‑100 (MQ=60)
               gagatctacactaagatggtcgccggcagcgtcagatgtgtataagagacagGATTAGCTAATTGAAACGCCTTTCCCCCCTGCCATACCTTTTAATAAT                                                                  <  SRR3722094.74799/48‑1 (MQ=60)
                                CAGGCTTACGGTGAGTCTGGCTCCGCTCCCACACAGATTAGCTAATTGAAACGCCTTCCCCCCCTGCCATACCTTTTAATAATCGCAACAGGTCTTCTAT                                                 <  SRR3722094.337033/100‑1 (MQ=60)
                                                        ataagagacagGATTAGCTAATTGAAACGCCTTTCCCCCCTGCCATACCTTTTAATAATCGCAACAGGTCTTCTATCGACGTTGTGGCATGAAGCTGGAT                         <  SRR3722094.443804/89‑1 (MQ=60)
                                                         CTGCCACACAGATTAGCTAATTGAAACGCCTTTCCCCCCTGCCATACC‑TTTAATAATCGCAACAGGTCTTCTATCGACGTTGTGGCATGAAGCTGGATAT                       <  SRR3722094.97641/100‑1 (MQ=60)
                                                             CACACAGATTAGCTAATTGAAACGCCTTTCCCCCCTGCCATACCTTTTAATAATCGCAACAGGTCTTCTATCGACGTTGTGGCATGAAGCTGGATATCAA                    <  SRR3722094.421047/100‑1 (MQ=60)
                                                                ACAGATTAGCTAATTGAACCCCCTTTCCCCCCTGCCATACCTTTTAATAATCGCAACAGGTCTTCTATCGACGTTGTGGCATGAAGCTGGATATCAATGG                 <  SRR3722094.216638/100‑1 (MQ=60)
                                                                       AGCTAATTGAAACGCCTTTCCCCCCTGCCATACCTTTTAATAATCGCAACAGGTCTTCTATCGACGTTGTGGCATGAAGCTGGATATCAATGGCGACCAC          <  SRR3722094.105605/100‑1 (MQ=60)
                                                                              TGAAACGCCTTTCACCCCTGCCATACCTTTTAATAATCGCAACAGGTCTTCTATCGACGTTGTGGCATGAAGCTGGATATCAATGGCGACCACTTCATGA   <  SRR3722094.361631/100‑1 (MQ=60)
                                                                               GAAACGCCTTTCCCCCCTGCCATACCTTTTAATAATCGCAACAGGTCTTCTATCGACGTTGTGGCATGAAGCTGGATATCAATGGCGACCACTTCATGAT  <  SRR3722094.150716/100‑1 (MQ=60)
                                                                                           |                                                                                       
CCATCAGCATATTGATTATCTGGTGTGAATTTCAGGCTTACGGTGAGTCTGGCTACGCTGCCACACAGATTAGCTAATTGAAACGCCTTTCACCCCTGCCATACCTTTTAATAATCGCAACAGGTCTTCTATCGACGTTGTGGCATGAAGCTGGATATCAATGGCGACCACTTCATGAT  >  NZ_CP009273/3648546‑3648724

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 19 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑