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 I126 R1 7 27.8 1630878 95.5% 1557488 84.0

Breseq alignment

N/A

GATK/CNVnator alignment

BRESEQ :: bam2aln output
GCCATTGGATTCGGCAATCCACTCCAGTAATTTCAGGCCACGCGTTAAAGACTGAACCTGTCCAGTCGCTGGTGCGGTGGCAACGGCGGGTTTTCTGCCGCGTTTCGCGGGAATGGGTGCGACCATGACAGTCTCTTTTTTCTGTATCGTGGAAATCATTTTCATTTTTATTGTTAGCTAATG  >  NZ_CP009273/4213431‑4213613
                                                                                              |                                                                                        
GCCATTGGATTCGGCAATCCACTCCAGTAATTTCAGGCCACGCGTTAAAGACTGAACCTGTCCAGTCGCTGGTGCGGTGGCAACGGCGGGGTTTTTGCCG                                                                                     >  SRR3721993.223253/1‑100 (MQ=60)
                                          CGTTAAAGACTGAACCTGTCCAGTCGCTGGTGCGGTGGCAACGGCGGGGTTTTTGCCGCGgtttgcggggatggggggggccctgacaggctcttttttt                                           >  SRR3721993.14700/1‑60 (MQ=60)
                                          CGTTAAAGACTGAACCTGTCCAGTCGCTGGTGCGGTGGCAACGGCGGGGTTTTTGCCGCGGTTCGCGGGgaaggggggggccccgacagtctcttttttt                                           >  SRR3721993.552971/1‑69 (MQ=60)
                                           GTTAAAGACTGAACCTGTCCAGTCGCTGGTGCGGTGGCAACGGCGGGGTTTTTTCCGCGTTTTGCGGGggtgggggggggcccgacaggctctttttttt                                          >  SRR3721993.503810/1‑68 (MQ=60)
                                                AGACTGAACCTGTCCAGTCGCTGGTGCGGTGGCAACGGCGGGGTTTTTGCCCCGGTTCGCGGGgagggggggggccctgacaggctcttttttttttttc                                     >  SRR3721993.38942/1‑63 (MQ=58)
                                                     GAACCTGTCCAGTCGCTGGTGCGGTGGCAACGGCGGGGTTTCTtccccggttcgcggggaagggggcggccatgaaagtgtctttttttctttctctttt                                >  SRR3721993.477304/1‑43 (MQ=60)
                                                                           GGTGGCAACGGCGGGGTTTCTGCCGCGTTTCGCGGGAATGGGGGCGGCCATGACAGGCTCTTTTTTTTTTATCGTGGGAATCATTTTTATTTTTTTTGTT          >  SRR3721993.615994/1‑100 (MQ=60)
                                                                               GCAACGGCGGGTTTTCTGCCGCGTTTCGCGGGAATGGGTGCGACCATGACAGTCTCTTTTTTCTGTATCGTGGAAATCATTTTCATTTTTATTGTTAGCT      <  SRR3721993.778369/100‑1 (MQ=60)
                                                                                   CGGCGGGGTTTCTGCCGCGTTTTGCGGGAATGGGTGCGACCActgtctcttatacacatctgacgctgccggcgacgtaaggggggtagatattgggggg  >  SRR3721993.59014/1‑42 (MQ=60)
                                                                                              |                                                                                        
GCCATTGGATTCGGCAATCCACTCCAGTAATTTCAGGCCACGCGTTAAAGACTGAACCTGTCCAGTCGCTGGTGCGGTGGCAACGGCGGGTTTTCTGCCGCGTTTCGCGGGAATGGGTGCGACCATGACAGTCTCTTTTTTCTGTATCGTGGAAATCATTTTCATTTTTATTGTTAGCTAATG  >  NZ_CP009273/4213431‑4213613

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑