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 I196 R1 3 18.2 1013968 97.0% 983548 86.5

Breseq alignment

N/A

GATK/CNVnator alignment

BRESEQ :: bam2aln output
GTCCTGGATGGGCGCGTTTTCTCTGTCGATGCTCTTCTGGGCCGAACTCCTCTGGATCATTACTCACTGATCCTTGACCCCGCTGCGGCGGGGTTGTCATTTGCTTTGCCACAAGGTTTCTCCTCTTTTATCAATTTGGGTTGTTATCAAATCGTTACGCGATG  >  NZ_CP009273/1329855‑1330018
                                                                                             |                                                                      
GTCCTGGATGGGCGCGTTTTCTCTGTCGATGCTCTTCTGGGCCGAACTCCTCTGGATCATTACTCACTGATCCTTGACCCCGCTGCGGCGGGGGTGTCAT                                                                  >  SRR3722074.330702/1‑100 (MQ=60)
              CGTTTTCTCTGTCGATGCTCTTCTGGGCCGAACTCCTCTGGATCATTACTCACTGATCCTTGACCCCGCTGCGGCGGGGGTGTCATTTGCTTTGCCACAA                                                    >  SRR3722074.119562/1‑100 (MQ=60)
                                 CTTCTGGGCCGAACTCCTCTGGATCATTACTCACTGATCCTTGACCCCGCTGCGGCGGGGGTGTCATTTTCTTTGCCACAAGGTTTTTCCTCTTTTTTCA                                 >  SRR3722074.342655/1‑100 (MQ=60)
                                 CTTCTGGGCCGAACTCCTCTGGATCATTACTCACTGATCCTTGACCCCGCTGCGGCGGGGGTGTCATTTGCTTTTCCACAAGGTTTCTCCTCTTTTTTCA                                 >  SRR3722074.331444/1‑100 (MQ=60)
                                                CCTCTGGATCATTACTCACTGATCCTTGACCCCGCTGCGGCGGGGTTGTCATTctgtctcttatacacatctccgagcccacgagactcctgagcatctc                  >  SRR3722074.116734/1‑53 (MQ=60)
                                                                CACTGATCCTTGACCCCGCTGCGGCGGGGGTGTCATTTGCTTTGCCACAAGGTTTCTCCTCTTTTATCAATTTGGGTTGTTATCAAATCGTTACGCGATG  >  SRR3722074.165300/1‑100 (MQ=60)
                                                                                             |                                                                      
GTCCTGGATGGGCGCGTTTTCTCTGTCGATGCTCTTCTGGGCCGAACTCCTCTGGATCATTACTCACTGATCCTTGACCCCGCTGCGGCGGGGTTGTCATTTGCTTTGCCACAAGGTTTCTCCTCTTTTATCAATTTGGGTTGTTATCAAATCGTTACGCGATG  >  NZ_CP009273/1329855‑1330018

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑