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 I214 R1 12 15.1 924212 96.1% 888167 85.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
JC NZ_CP009273 4,609,810 Δ72 bp coding (391‑462/1224 nt) deoB → phosphopentomutase

New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NZ_CP009273 = 46098093 (0.190)23 (1.540) 17/156 0.1 90.6% coding (390/1224 nt) deoB phosphopentomutase
?NZ_CP009273 4609882 = 2 (0.130)coding (463/1224 nt) deoB phosphopentomutase

GTCTGGTCACTGGGAAATTGCCGGTGTCCCGGTTCTGTTTGAGTGGGGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGAT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NZ_CP009273/4609716‑4609809
‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ctggatCAACTGGGCGAAGAGCACATGAAAACCGGCAAGCCGATTTTCTATACCTCCGCTGACTCCGTGTTCCAGATTGCCTGCCATGAAGAAA  >  NZ_CP009273/4609882‑4609969
                                                                                                                                                                                      
GTCTGGTCACTGGGAAATTGCCGGTGACCCGGTTCTGGTTGAGCGGGGATATTTCTCCGATGCCGAAGACCGCTTCCCGCATGAGCTGCT                                                                                              >  2:348636/1‑90
    GGTCACTGGGAAATTGCCGGTGTCCCGGTTCTGTTTGAGTGGGGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGAT                                                                                          >  2:313030/1‑90
    GGTCACTGGGAAATTGCCGGTGTCCCGGTTCTGTTTGAGTGGGGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGAT                                                                                          >  2:131358/1‑90
         CTGGGAAATTGCCGGTGTCCCGGTTCTGTTTGAGTGGGGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAACT                                                                                     <  1:71450/90‑1
         CTGGGAAATTGCCGGTGTCCCGGTTCTGTTTGAGTGGGGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAACT                                                                                     <  2:162188/90‑1
              AAATTGCCGGTGTCCCGGTTCTGTTTGAGTGGGGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAACTGGGCG                                                                                >  2:154230/1‑90
                 TTGCCGGTGTCCCGGTTCTGTTTGAGTGGGGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAACTGGGCGAAG                                                                             <  2:328704/90‑1
                    CCGGTGTCCCGGTTCTGTTTGAGTGGGGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAACTGGGCGAAGAGC                                                                          <  2:336397/90‑1
                                   TGTTTGAGTGGGGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAACTGGGCGAAGAGCACATGAAAACCGGCA                                                           >  2:326513/1‑90
                                   TGTTTGAGTGGGGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAACTGGGCGAAGAGCACATGAAAACCGGCA                                                           >  1:140462/1‑90
                                    GTTTGAGTGGGGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAACTGGGCGAAGAGCACATGAAAACCGGCAA                                                          <  1:197165/90‑1
                                       TGAGTGGGGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAACTGGGCGAAGAGCACATGAAAACCGGCAAGCC                                                       <  2:161506/90‑1
                                       TGAGTGGGGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAACTGGGCGAAGAGCACATGAAAACCGGCAAGCC                                                       <  2:302264/90‑1
                                       TGAGTGGGGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAACTGGGCGAAGAGCACATGAAAACCGGCAAGCC                                                       <  1:366359/90‑1
                                         AGTGGGGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAACTGGGCGAAGAGCACATGAAAACCGGCAAGCCGA                                                     >  2:370490/1‑90
                                          GTGGGGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAACTGGGCGAAGAGCACATGAAAACCGGCAAGCCGAT                                                    <  2:140462/90‑1
                                            GGGGATATTTCTCCGATCACGAAAACAGCTTCCCGCGAGAGCTGCTGGATCAACTGGGCGAAGAGCACATGAAAACCGGCAAGCCGATTT                                                  <  2:304811/90‑1
                                              GGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAACTGGGCGAAGAGCACATGAAAACCGGCAAGCCGATTTTC                                                >  2:66082/1‑90
                                                         CGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAACTGGGCGAAGAGCACATGAAAACCGGCAAGCCGATTTTCTATACCTCCGC                                     >  2:119825/1‑90
                                                               CGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAACTGGGCGAAGAGCACATGAAAACCGGCAAGCCGATTTTCTATACCTCCGCTGACTC                               <  1:394235/90‑1
                                                                 AAAACAGCTTCCCGCAAGAGCTGCTGGATCAACTGGGCGAAGAGCACATGAAAACCGGCAAGCCGATTTTCTATACCTCCGCTGACTCCG                             <  1:326513/90‑1
                                                                       GCTTCCCGCAAGAGCTGCTGGATCAACTGGGCGAAGAGCACATGAAAACCGGCAAGCCGATTTTCTATACCTCCGCTGACTCCGTGTTCC                       >  2:17476/1‑90
                                                                       GCTTCCCGCAAGAGCTGCTGGATCAACTGGGCGAAGAGCACATGAAAACCGGCAAGCCGATTTTCTATACCTCCGCTGACTCCGTGTTCC                       >  1:329113/1‑90
                                                                         TTCCCGCAAGAGCTGCTGGATCAACTGGGCGAAGAGCACATGAAAACCGGCAAGCCGAT                                                    >  2:274346/1‑59
                                                                         TTCCCGCAAGAGCTGCTGGATCAACTGGGCGAAGAGCACATGAAAACCGGCAAGCCGAT                                                    <  1:274346/59‑1
                                                                                      TGCTGGATCAACTGGGCGAAGAGCACATGAAAACCGGCAAGCCGATTTTCTATACCTCCGCTGACTCCGTGTTCCAGATTGCCTGCCATG        >  2:245773/1‑90
                                                                                            ATCAACTGGGCGAAGAGCACATGAAAACCGGCAAGCCGATTTTCTATACCTCCGCTGACTCCGTGTTCCAGATTGCCTGCCATGAAGAAA  >  1:240985/1‑90
                                                                                                                                                                                      
GTCTGGTCACTGGGAAATTGCCGGTGTCCCGGTTCTGTTTGAGTGGGGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGAT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NZ_CP009273/4609716‑4609809
‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ctggatCAACTGGGCGAAGAGCACATGAAAACCGGCAAGCCGATTTTCTATACCTCCGCTGACTCCGTGTTCCAGATTGCCTGCCATGAAGAAA  >  NZ_CP009273/4609882‑4609969

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 23 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑
Reads not counted as support for junction
read_name Not counted due to insufficient overlap past the breakpoint.
read_name Not counted due to not crossing MOB target site duplication.

GATK/CNVnator alignment

BRESEQ :: bam2aln output
GTCTGGTCACTGGGAAATTGCCGGTGTCCCGGTTCTGTTTGAGTGGGGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATAAACTGGTCGAACGCGCTAATCTGCCGGGTTACCTCGGTAACTGCCACTCTTCCGGTACGGTCATTCTGGATCAACTG  >  NZ_CP009273/4609716‑4609887
                                                                                              |                                                                             
GTCTGGTCACTGGGAAATTGCCGGTGTCCCGGTTCTGTTTGAGTGGGGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATAAACTG                                                                          >  SRR3722097.332025/1‑100 (MQ=60)
         CTGGGAAATTGCCGGTGTCCCGGTTCTGTTTGAGTGGGGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAACTGGgcgaagag                                                                 <  SRR3722097.72276/100‑9 (MQ=60)
                         GTCCCGGTTCTGTTTGAGTGGGGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAACTGGgcgaagagcacatgaaaaccggca                                                 >  SRR3722097.142104/1‑76 (MQ=60)
                                    GTTTGAGTGGGGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAACTGGgcgaagagcacatgaaaaccggcaagccgattttc                                      <  SRR3722097.199374/100‑36 (MQ=60)
                                       TGAGTGGGGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAACTGGgcgaagagcacatgaaaaccggcaagccgattttctat                                   <  SRR3722097.371391/100‑39 (MQ=60)
                                                             CACGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAACTGG                                                                         >  SRR3722097.333533/1‑40 (MQ=60)
                                                               CGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAACTGG                                                                         <  SRR3722097.277733/38‑1 (MQ=60)
                                                               CGAAAACAGCTTCCCGCAAGAGCTGCTGGATCAACTGG                                                                         <  SRR3722097.399752/38‑1 (MQ=60)
                                                                 AAAACAGCTTCCCGCAAGAGCTGCTGGATCAACTGG                                                                         <  SRR3722097.330882/36‑1 (MQ=60)
                                                                        CTTCCCGCAAGAGCTGCTGGATAACCTGGTCGAACGCGCTAATCTGCCGGGTTACCTCGGTAACTGCCACTCTTCCGGTACGGTCATTCTGGATCAACTG  <  SRR3722097.255026/100‑1 (MQ=60)
                                                                                              |                                                                             
GTCTGGTCACTGGGAAATTGCCGGTGTCCCGGTTCTGTTTGAGTGGGGATATTTCTCCGATCACGAAAACAGCTTCCCGCAAGAGCTGCTGGATAAACTGGTCGAACGCGCTAATCTGCCGGGTTACCTCGGTAACTGCCACTCTTCCGGTACGGTCATTCTGGATCAACTG  >  NZ_CP009273/4609716‑4609887

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑