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 I224 R1 7 23.0 1302986 97.5% 1270411 87.2

Breseq alignment

N/A

GATK/CNVnator alignment

BRESEQ :: bam2aln output
CTGGCGATTCCGTTCTTTGTGCTGGCGGGTGAAATCATGAATGCGGGCGGCTTGTCAAAACGCATTGTTGACCTGCCGATGAAACTGGTGGGGCATAAACCAGGCGGGCTGGGCTACGTCGGCGTGCTGGCAGCTATGATTATGGCGAGCCTTTCTGGTTC  >  NZ_CP009273/3738332‑3738492
                                                                      |                                                                                          
cgggcgtttccgttttttgtgggggggggtaaaataatgaagggggggggtttgaaaaaccgctTTGTTGCCCTGCCGATGAAACTGGTGGGGCATAAAC                                                               <  SRR3722108.306707/36‑1 (MQ=60)
CGGGCGTTTCCGTTTTTTGTGCTGGCGGGAAAAATCATGAAGGCGGGCGGTTTGTAAAAACGCATTGTTGACCTGCCGATGAAACTGGTGGGGCATAAAC                                                               <  SRR3722108.7254/100‑1 (MQ=60)
      tttccttttTTTGTGCGGGGGGGTAAAATCATGAATGGGGGGGGCTTGTAAAAACGCTTTGTTGCCCTGCCGATGAAACTGGTGGGGCATAAACCAGGCG                                                         <  SRR3722108.166925/91‑1 (MQ=59)
           GTTCTTTGTGCTGGCGGGGAAAATCATGAAGGGGGGGGGCTTGACAAAACGCATTGTTGCCCTGCCGATGAAACTGGTGGGGCATAAACCAGGCGGGCTG                                                    <  SRR3722108.412208/100‑1 (MQ=60)
                   TGCTGGCGGGTGAAATCATGAAGGCGGGGGGCTTGTCAAAACGCATTGTTGCCCTGCCGATGAAACTGGTGGGGCATAAACCAGGCGGGCTGGGCTACGT                                            <  SRR3722108.109645/100‑1 (MQ=60)
                   TGCTGGCGGGAGAAATCATGAATGCGGGGGGTTTGTAAAAACGCTTTGTTGCCCTGCCGATGAAACTGGTGGGGCATAAACCAGGCGGGCTGGGCTACGT                                            <  SRR3722108.514594/100‑1 (MQ=60)
                                             GGGGGCTTGAAAAAACGCTTTGTTGCCCTGCCGATGAAACTGGTGGGGCATAAACCAGGCGGGCTGGGCTACGTCGGCGTGCTGGCAGCTATGATTATGG                  <  SRR3722108.548876/100‑1 (MQ=60)
                                               gggtttgtaaaaccgctTTGTTGCCCTGCCGATGAAACTGGTGGGGCATAAACCAGGCGGGCTGGGCTACGTCGGCGTGCTGGCAGCTATGATTATGGCG                <  SRR3722108.73460/83‑1 (MQ=60)
                                                             GCTTTGTTGCCCTGCCGATGAAACTGGTGGGGCATAAACCAGGCGGGCTGGGCTACGTCGGCGTGCTGGCAGCTATGATTATGGCGAGCCTTTCTGGTTC  <  SRR3722108.32570/100‑1 (MQ=60)
                                                                      |                                                                                          
CTGGCGATTCCGTTCTTTGTGCTGGCGGGTGAAATCATGAATGCGGGCGGCTTGTCAAAACGCATTGTTGACCTGCCGATGAAACTGGTGGGGCATAAACCAGGCGGGCTGGGCTACGTCGGCGTGCTGGCAGCTATGATTATGGCGAGCCTTTCTGGTTC  >  NZ_CP009273/3738332‑3738492

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑