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 F3 I129 R1 10 20.4 1208620 95.3% 1151814 84.1

Breseq alignment

N/A

GATK/CNVnator alignment

BRESEQ :: bam2aln output
GCATGGGAATGACGGAAAAGCAGGGCGGTTCCGATGTTATGAGCAACACCACCCGTGCAGAGCGTCTGGAAGATGGCTCTTATCGGCTGGTGGGGCATAAATGGTTTTTCTCGGTTCCGCAAAGCGATGCGCATCTGGTGCTGGCGCAGACCGCGGGTGGTCTGTCCTGCTTTTTTGT  >  NZ_CP009273/4404633‑4404810
                                                                                          |                                                                                       
GCATGGGAATGACGGAAAAGCAGGGCGGTTCCGATGTTATGAGCAACACCACCCGTGCAGAGCGTCTGGAAGATGGCTCTTATCGGCTGGGGGGGGATAA                                                                                >  SRR3721996.5646/1‑100 (MQ=60)
    GGGAATGACGGAAAAGCAGGGCGGTTCCGATGTTATGAGCAACACCACCCGTGCAGAGCGTCTGGAAGATGGCTCTTATCGGCTGGGGGGGCATAAATGG                                                                            >  SRR3721996.164291/1‑100 (MQ=60)
           ACGGAAAAGCAGGGCGGTTCCGATGTTATGAGCAACACCACCCGTGCAGAGCGTCTGGAAGATGGCTCTTATCGGCTGGGGGGGCATAAAAGGTTTTTCT                                                                     >  SRR3721996.434038/1‑100 (MQ=60)
            CGGAAAAGCAGGGCGGTTCCGATGTTATGAGCAACACCACCCGTGCAGAGAGTCTGGAAGATGGCTCTTATCGGCTGGGGCGGCATAACATGTTTTTCTC                                                                    >  SRR3721996.402123/1‑100 (MQ=60)
                                   GTTATGAGCAACACCACCCGTGCAGAGCGTCTGGAAGATGGCTCTTATCGGCTGGGGGGGCATAAATGGGTTTTCTCGGTTCCCCAAAGGGATACGCATA                                             >  SRR3721996.413895/1‑100 (MQ=60)
                                   GTTATGAGCAACACCACCCGTGCAGAGCGTCTGGAAGATGGCTCTTATCGGCTGGAGGGGCATAAATGGATTTTTTCGGTTCCGCgaaaaggtgcgcatt                                             >  SRR3721996.213000/1‑85 (MQ=60)
                                        GAGCAACACCACCCGTGCAGAGCGTCTGGAAGATGGCTCTTATCGGCTGGGGGGGCATAAATGGTTTTTCTCGGTTCCGCAAAGCGATGCGCATCTGGTG                                        >  SRR3721996.77649/1‑100 (MQ=60)
                                        GAGCAACACCACCCGTGCAGAGCGTCTGGAAGATGGCTCTTATCGGCTGGGGGGGCAAAAATGGTTTTTCTCGGGTCCGCAAAGCGATGCGCATCTGGTG                                        >  SRR3721996.265272/1‑100 (MQ=60)
                                                   CCCGTGCAGAGCGTCTGGAAGATGGCTCTTATCGGCTGGGGGGGCATAAATGGGTTTTCTCGGTTCCGCAAAGCGATGCGCATCTGGTGCTGGCGCAGAC                             >  SRR3721996.579094/1‑100 (MQ=60)
                                                      GTGCAGAGCGTCTGGAAGATGGCTCTTATCGGCTGGGGGGGCATAAATGGTTTTTCTCGGTTCCGCAAAGCGATGCGCATCTGGTGCTGGCGCAGACCGC                          >  SRR3721996.600214/1‑100 (MQ=60)
                                                              CGTCTGGAAGATGGCTCTTATCGGCTGGTGGGGCATAAATGGTTTTTCTCGGTTCCGCAAAGCGATGCGCATCTGGTGCTGGCGCAGACCGCGGGTGGTC                  <  SRR3721996.237100/100‑1 (MQ=60)
                                                                              CTTATCGGCTGGTGGGGCATAAATGGTTTTTCTCGGTTCCGCAAAGCGATGCGCATCTGGTGCTGGCGCAGACCGCGGGctgtctcttatacacatctga  >  SRR3721996.230443/1‑79 (MQ=60)
                                                                                          |                                                                                       
GCATGGGAATGACGGAAAAGCAGGGCGGTTCCGATGTTATGAGCAACACCACCCGTGCAGAGCGTCTGGAAGATGGCTCTTATCGGCTGGTGGGGCATAAATGGTTTTTCTCGGTTCCGCAAAGCGATGCGCATCTGGTGCTGGCGCAGACCGCGGGTGGTCTGTCCTGCTTTTTTGT  >  NZ_CP009273/4404633‑4404810

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑