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 I215 R1 7 24.6 1459714 95.1% 1388188 84.6

Breseq alignment

N/A

GATK/CNVnator alignment

BRESEQ :: bam2aln output
ACCCCGTCTGGTCACTGGGAAATTGCCGGTGTCCCGGTTCTGTTTGAGTGGGGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATAAACTGGTCGAACGCGCTAATCTGCCGGGTTACCTCGGTAACTGCCACTCTT  >  NZ_CP009273/4609711‑4609861
                                                                                                   |                                                   
ACCCCGTCTGGTCACTGGGAAATTGCCGGTGTCCCGGTTCTGTTTGAGTGGGGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATC                                                     >  SRR3722098.69313/1‑100 (MQ=60)
   GCGTCTGGTCACTGGGAAATTGCCGGTGTCCCGGTTCTGTTTGAGTGGGGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAAC                                                  <  SRR3722098.651858/100‑1 (MQ=60)
   CCGTCTGGTCACTGGGAAATTGCCGGTGTCCCGGTTCTGTTTGAGTGGGGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAAC                                                  <  SRR3722098.671881/100‑1 (MQ=60)
    CGTCTGGTCACTGGGAAATTGCCGGTGTCCCGGTTCTGTTTGAGTGGGGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAACT                                                 >  SRR3722098.255506/1‑100 (MQ=60)
             ACTGGGAAATTGCCGGTGTCCCGGTTCTGTTTGAGTGGGGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAACTGGgcgaaga                                        >  SRR3722098.327823/1‑93 (MQ=60)
              CTGGGAAATTGCCGGTGTCCCGGTTCTGTTTGAGTGGGGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAACTGGgcgaagag                                       <  SRR3722098.609291/100‑9 (MQ=60)
                      TTGCCGGTGTCCCGGTTCTGTTTGAGTGGGGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAACTGGgcgaagagcacatgaa                               <  SRR3722098.607121/100‑17 (MQ=60)
                            GTGTCCCGGTTCTGTTTGAGTGGGGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAACTGGgcgaagagcacatgaaaaccgg                         >  SRR3722098.559032/1‑78 (MQ=60)
                                       CTGTTTGAGTGGGGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAACTGGgcgaagagcacatgaaaaccggcaagccgattt              >  SRR3722098.140233/1‑67 (MQ=60)
                                       CTGTTTGAGTGGGGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAACTGGgcgaagagcacatgaaaaccggcaagccgattt              >  SRR3722098.386357/1‑67 (MQ=60)
                                             GAGTGGGGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAACTGGgcgaagagcacatgaaaaccggcaagccgattttctata        >  SRR3722098.47110/1‑61 (MQ=60)
                                                   GGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAACTGG                                               >  SRR3722098.718506/1‑55 (MQ=60)
                                                   GGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATAAACTGGTCGAACGCGCTAATCTGCCGGGTTACCTCGGTAACTGCCACTCTT  >  SRR3722098.272315/1‑100 (MQ=60)
                                                          TCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAACTGG                                               <  SRR3722098.19900/48‑1 (MQ=60)
                                                              CGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAACTGG                                               <  SRR3722098.40850/44‑1 (MQ=60)
                                                                ATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAACTGG                                               <  SRR3722098.268660/42‑1 (MQ=60)
                                                                      AAAACAGCTTCCCGCAAGAGCTGCTGGATCAACTGG                                               <  SRR3722098.246084/36‑1 (MQ=60)
                                                                      AAAACAGCTTCCCGCAAGAGCTGCTGGATCAACTGG                                               <  SRR3722098.80227/36‑1 (MQ=60)
                                                                                                   |                                                   
ACCCCGTCTGGTCACTGGGAAATTGCCGGTGTCCCGGTTCTGTTTGAGTGGGGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATAAACTGGTCGAACGCGCTAATCTGCCGGGTTACCTCGGTAACTGCCACTCTT  >  NZ_CP009273/4609711‑4609861

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑