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
A3 F1 I1 R1 18 29.2 1933165 95.1% 1838439 75.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
JC JC REL606 4,524,522 IS186 (+) +6 bp coding (494‑499/549 nt) fimA → major type 1 subunit fimbrin (pilin)

New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? REL606 2772854 =NA (NA)16 (0.560) 14/144 1.0 100% noncoding (1/1343 nt) IS186 repeat region
?REL606 = 4524527 0 (0.000)coding (499/549 nt) fimA major type 1 subunit fimbrin (pilin)
* ? REL606 = 2774196NA (NA)22 (0.770) 20/144 0.5 100% noncoding (1343/1343 nt) IS186 repeat region
?REL606 4524522 = 0 (0.000)coding (494/549 nt) fimA major type 1 subunit fimbrin (pilin)

GAGTAATTCATCGGCACGTTAAATCATATCAGGCGTAATACCACAACCCTTAAGTTAGCGCTTATGGG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  REL606/2772921‑2772854
‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑gggTTGCGGCCCCGGTTGCAAAATAACGCGCCTGGAACGGAATGGTATTGGTTCCGTTATTCAGGGTTGTTTCT  <  REL606/4524527‑4524457
                                                                                                                                           
GAGTAACTCATCGGCACGTTAAATCATATCAGGCGCAATACCACAACCCTTAAGTTAGCGCTTATGGGTTGCGGCC                                                                 <  2:455027/76‑1
  GTAATTCATCGGCACGTTAAATCATATCAGGCGTAATACCACAACCGTTAAGTTATCGCTTATGGGTTGCGGCCCg                                                               >  1:873110/1‑75
      TTCATCGGCACGTTAAATCATATCAGGCGTAATACCACAACCCTTAAGTTAGCGCTTATGGGTTGCGGCCCCGGTT                                                           <  2:541657/76‑1
              CACGTTAAATCATATCAGGCGTAATACCACAACCCTTAAGTTAGCGCTTATGGGTTGCGGCCCCGGTTGCAAAATA                                                   <  1:375903/76‑1
                   TAAATCATATCAGGCGTAATACCACAACCCTTAAGTTAGCGCTTATGGGTTGCGGCCCCGGTTGCAAAATAACGCG                                              >  2:178930/1‑76
                         atgTCAGGCGGAATCCCACAACCCTTAAGTTAGCGCTTATGGGTGGCGGCCCCGGTTGCAAAATAACGCGCCTGGA                                        <  1:577175/73‑1
                         ATATCAGGCGTAATACCACAACCCTTAAGTTAGCGCTTATGGGTTGCGGCCCCGGTTGCAAAATAACGCGCCTGGA                                        >  2:766129/1‑76
                         ATATCAGGCGTAATACCACAACCCTTAAGTTAGCGCTTATGGGTTGCGGCCCCGGTTGCAAAATAACGCGCCTGGA                                        >  2:93426/1‑76
                              AGGCGTAATACCACAACCCTTAAGTTAGCGCTTATGGGTTGCGGCCCCGGTTGCAAAATAACGCGCCTGGAACGGA                                   <  1:704385/76‑1
                                   TAATACCACAACCCTTAAGTTAGCGATTATGGGTTGCGGCCCCGGTTGCAAAATAACGCGCCTGGAACGGAATGGT                              >  2:922806/1‑76
                                    AATACCACAACCCTTAAGTTAGCACTTATGGGTTGCGGCCCCCGTTGCAAAATAACGCGCCTGGAACGGAATGGTA                             >  1:742903/1‑76
                                          ACAACCCATAAGTTAGCGCTTATGGGTTGCGGCCCCGGTTGCAAAATAACGCGCCTGGAACGGAATGGTATTGGTT                       >  1:800596/1‑76
                                            AACCCTTAAGTTAGCGCTTATGGGTTGCGGCCCCGGTTGCAAAATAACGCGCCTGGAACGGAATGGTATTGGTTCC                     >  1:771365/1‑76
                                               CCTTAAGTTAGCGCTTATGGGTTGCGGCCCCGGTTGCAAAATAACGCGCCTGGAACGGAATGGTATTGGTTCCGTT                  >  1:390418/1‑76
                                                               ATGGGTTGCGGCCCCGGTTGCAAAATAACGCGCCTGGAACGGAATGGTATTGGTTCCGTTATTCAGGGTTGTTTCT  >  1:595242/1‑76
                                                               ATGGGTTGCGGCCCCGGTTGCAAAATAACGCGCCTGGAACGGAATGGTATTGGTTCCGTTATTCAGGGTTGTTTCT  <  2:740321/76‑1
                                                                                                                                           
GAGTAATTCATCGGCACGTTAAATCATATCAGGCGTAATACCACAACCCTTAAGTTAGCGCTTATGGG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  REL606/2772921‑2772854
‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑gggTTGCGGCCCCGGTTGCAAAATAACGCGCCTGGAACGGAATGGTATTGGTTCCGTTATTCAGGGTTGTTTCT  <  REL606/4524527‑4524457

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 38 ≤ 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

N/A