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 I227 R1 223 21.3 1167702 97.0% 1132670 86.4

Breseq alignment

N/A

GATK/CNVnator alignment

BRESEQ :: bam2aln output
GCGTTACACCTTGAGTGCCCGCCGGGCCGACAACAAAGTCAGGTTGCGCAGGCAGGGTAATCGGGGAAGGATTCCACGCTGCAGCACCTGGTGTCAGGGATGCAAAATAGTGTTGAGCATCGAAATTCTGCGCTTCTTTTGCCGACAGAATCGGGCGAGAAGAGGTACCAGGCGCGGTTTGATCA  >  NZ_CP009273/802458‑802642
                                                                                           |                                                                                             
GCGTTACACCTTGAGTGCCCGCCGGGCCGACAACAAAGTCAGGTTGCGCAGGCAGGGTAATCGGGGAAGGATTCCACGCTGCAGCACCTGGGGTCAGGGA                                                                                       >  SRR3722111.278937/1‑100 (MQ=60)
                         GCCGACAACAAAGTCAGGTTGCGCAGGCAGGGTAATCGGGGAAGGATTCCACGCTGCAGCACCTGGGGTCAGGGATGCAAAATAGTGTTGAGCATCGAAA                                                              >  SRR3722111.104182/1‑100 (MQ=60)
                                            TGCGCAGGCAGGGTAATCGGGGAAGGATTCCACGCTGCAGCACCTGGGGTCAGGGATGCAAAATAGTGTTGctgtctcttatacacatctgacgctgccg                                           >  SRR3722111.118941/1‑71 (MQ=60)
                                                                 GAAGGATTCCACGCTGCAGCACCTGGTGTCAGGGATGCAAAATAGTGTTGAGCATCGAAATTCTGCGCTTCTTTTGCCGACAGAATCGGGCGctgtctct                      >  SRR3722111.368253/1‑92 (MQ=60)
                                                                                     ACCTGGGGTCAGGGATGCAAAATAGTGTTGAGCATCGAAATTCTGCGCTTCTTTTGCCGACAGAATCGGGCGAGAAGAGGGACCAGGCGCGGTTTGATCA  >  SRR3722111.473699/1‑100 (MQ=60)
                                                                                           |                                                                                             
GCGTTACACCTTGAGTGCCCGCCGGGCCGACAACAAAGTCAGGTTGCGCAGGCAGGGTAATCGGGGAAGGATTCCACGCTGCAGCACCTGGTGTCAGGGATGCAAAATAGTGTTGAGCATCGAAATTCTGCGCTTCTTTTGCCGACAGAATCGGGCGAGAAGAGGTACCAGGCGCGGTTTGATCA  >  NZ_CP009273/802458‑802642

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑