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 I217 R1 10 20.8 1414158 96.8% 1368904 86.5

Breseq alignment

N/A

GATK/CNVnator alignment

BRESEQ :: bam2aln output
CTTCTTCCCAGGGCTGGATAAACCGTGGCCGCATACGCATCAATGTATGCGCATGAACTACGTACCAGAGCCGGAGAAAATTGAGGCGGGGGTGAAGATTCTGGCGGAAGAGATAGAAAGAGCCTGGGCTGAAAGTCACTAAAAATTGC  >  NZ_CP009273/3734177‑3734325
                                                                                            |                                                        
CTTCTTCCCAGGGCTGGATAAACCGTGGCCGCATACGCATCAATGTATGCGCATGAACTACGTACCAGAGCCGGAGAAAATTGAGGCGGGGGGGAAGATT                                                   >  SRR3722100.415551/1‑100 (MQ=60)
            GCTGGATAAACCGTGGCCGCATACGCATCAATGTATGCGCATGAACTACGTACCAGAGCCGGAGAAAATTGAGGCGGGGGGGAAGTTTTTGGCGGAAGga                                       >  SRR3722100.390700/1‑98 (MQ=60)
               GGATAAACCGTGGCCGCATACGCATCAATGTATGCGCATGAACTACGTACCAGAGCCGGAGAAAATTGAGGCGGGGGGGAAGATctgtctcttatacaca                                    >  SRR3722100.657739/1‑84 (MQ=60)
               GGATAAACCGTGGCCGCATACGCATCAATGTATGCGCATGAACTACGTACCAGAGCCGGAGAAAATTGAGGCGGGGGGGAAGATTCTGGCGGGAGAGATA                                    >  SRR3722100.326059/1‑100 (MQ=60)
               GGATAAACCGTGGCCGCATACGCATCAATGTATGCGCATGAACTACGTACCAGAGCCGGAGAAAATTGAGGCGGGGGGGAAGATTCTGGCGGAAGAGATA                                    >  SRR3722100.117334/1‑100 (MQ=60)
                        GTGGCCGCATACGCATCAATGTATGCGCATGAACTACGTACCAGAGCCGGAGAAAATTGAGGCGGGGGTGAAGATTCTGGCGGAAGAGATAGAAAGAGCC                           <  SRR3722100.377237/100‑1 (MQ=60)
                                     CATCAATGTATGCGCATGAACTACGTACCAGAGCCGGAGAAAATTGAGGCGGGGGGGAAGATTCTGGCGGAAGAGATAGAAAGAGCCTGGGCTGAAAGTC              >  SRR3722100.41343/1‑100 (MQ=60)
                                                 CGCATGAACTACGTACCAGAGCCGGAGAAAATTGAGGCGGGGGGGAAGATTCTGGCGGAAGAGATAGAAAAAGCCTGGGCTGAAAGTCACTAAAAAattc  >  SRR3722100.459002/1‑96 (MQ=60)
                                                                                            |                                                        
CTTCTTCCCAGGGCTGGATAAACCGTGGCCGCATACGCATCAATGTATGCGCATGAACTACGTACCAGAGCCGGAGAAAATTGAGGCGGGGGTGAAGATTCTGGCGGAAGAGATAGAAAGAGCCTGGGCTGAAAGTCACTAAAAATTGC  >  NZ_CP009273/3734177‑3734325

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: ‑