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 I198 R1 96 36.2 2313912 84.6% 1957569 85.2

Breseq alignment

N/A

GATK/CNVnator alignment

BRESEQ :: bam2aln output
CGCAAGCAACTTCGCGGATTATCTGCTGAAAAACCGTCTGAAGAGCCGCAGCAACGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTGCCGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGTCCGCCAGGCGTCACGGAAATATGGCGTTGATGAGTCGCTGATTCTGGCAATTATG  >  NZ_CP009273/3098241‑3098433
                                                                                               |                                                                                                 
CGCAAGCAACTTCGCGGATTATCTGCTGAAAAACCGTCTGAAGAGCCGCAGCAACGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTGCCGAAC                                                                                               <  SRR3722077.105267/100‑1 (MQ=60)
     GCAACTTCGCGGATTATCTGCTGAAAAACCGTCTGAAGAGCCGCAGCAACGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTGCCGAACCACCT                                                                                          <  SRR3722077.675778/100‑1 (MQ=60)
         CTTCGCGGATTATCTGCTGAAAAACCGTCTGAAGAGCCGCAGCAACGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTGCCGAACCtgtctctt                                                                                      >  SRR3722077.262521/1‑92 (MQ=60)
           TCGCGGATTATCTGCTGAAAAACCGTCTGAAGAGCCGCAGCAACGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTGCCGAACCACCTTGATAA                                                                                    <  SRR3722077.1110741/100‑1 (MQ=60)
           TCGCGGATTATCTGCTGAAAAACCGTCTGAAGAGCCGCAGCAACGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAA                                                                                   <  SRR3722077.194792/100‑1 (MQ=60)
           TCGCGGATTATCTGCTGAAAAACCGTCTGAAGAGCCGCAGCAACGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAA                                                                                   <  SRR3722077.957076/100‑1 (MQ=60)
             GCGGATTATCTGCTGAAAAACCGTCTGAAGAGCCGCAGCAACGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACG                                                                                 <  SRR3722077.218705/100‑1 (MQ=60)
                          ctcggagatgtgtataagagacagGCAACGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATAT                                                                    <  SRR3722077.994074/76‑1 (MQ=60)
                            AAAAACCGTCTGAAGAGCCGCAGCAACGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCT                                                                  <  SRR3722077.660290/100‑1 (MQ=60)
                                  CGTCTGAAGAGCCGCAGCAACGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTGCCGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCA                                                             >  SRR3722077.111893/1‑100 (MQ=60)
                                             CCGCAGCAACGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTGCCGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGTCCGCCAG                                                  <  SRR3722077.952596/100‑1 (MQ=60)
                                                              GTATCATCTACAGCGTCACCATTAACATGGTGCCGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGTCCGCCAGGCGTCACGGAAATATGG                                 >  SRR3722077.466325/1‑100 (MQ=60)
                                                              GTATCATCTACAGCGTCACCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGTCCGCCAGGCGTCACGGAAATATGGC                                >  SRR3722077.375443/1‑100 (MQ=60)
                                                                    TCTACAGCGTCACCATTAACATGGTGCCGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGTCCGCCAGGCGTCACGGAAATATGGCGTTGA                           >  SRR3722077.814840/1‑100 (MQ=60)
                                                                                CCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGTCCGCCAGGCGTCACGGAAATATGGCGTTGATGAGTCGCTGATT              >  SRR3722077.261236/1‑100 (MQ=60)
                                                                                CCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGTCCGCCAGGCGTCACGGAAATATGGCGTTGATGAGTCGCTGATT              >  SRR3722077.355979/1‑100 (MQ=60)
                                                                                CCATTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGTCCGCCAGGCGTCACGGAAATATGGCGTTGATGAGTCGCTGATT              >  SRR3722077.206410/1‑100 (MQ=60)
                                                                                   TTAACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGTCCGCCAGGCGTCACGGAAATATGGCGTTGATGAGTCGCTGATTCct           >  SRR3722077.240947/1‑98 (MQ=60)
                                                                                     AACATGGTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGTCCGCCAGGCGTCACGGAAATATGGCGTTGATGAGTCGCTGATTCTGGC         >  SRR3722077.517883/1‑100 (MQ=60)
                                                                                           GTG‑CGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGTCCGCCAGGCGTCACGGAAATATGGCGTTGATGAGTCGCTGATTCTGGCAATTAT   >  SRR3722077.411223/1‑100 (MQ=60)
                                                                                             GCCGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGTCCGCCAGGCGTCACGGAAATATGGCGTTGATGAGTCGCTGATTCTGGCAATTATG  >  SRR3722077.355851/1‑100 (MQ=60)
                                                                                               |                                                                                                 
CGCAAGCAACTTCGCGGATTATCTGCTGAAAAACCGTCTGAAGAGCCGCAGCAACGGGCTGCGTATCATCTACAGCGTCACCATTAACATGGTGCCGAACCACCTTGATAAACGTGCGCACAAATATCTCGGCATGGTCCGCCAGGCGTCACGGAAATATGGCGTTGATGAGTCGCTGATTCTGGCAATTATG  >  NZ_CP009273/3098241‑3098433

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑