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
A11 F56 I1 R1 155 65.2 3164312 95.9% 3034575 99.8

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 1,650,904 T→C pseudogene (60/693 nt) insD1 → IS2 transposase TnpB;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,650,9040TC100.0% 39.8 / NA 13pseudogene (60/693 nt)insD1IS2 transposase TnpB;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (6/7);  total (6/7)

CAGACATGGAAAACACTGGATGACGAACTGGCCTATGGGCGCTGCTTCGCAGACAGGCAGAACTTGATGGTATGCCTGCGATCAATGCCAAACGTGTTTACCGGATCATGCGCCAGAATGCGCTGTTGC  >  NC_000913/1650810‑1650938
                                                                                              |                                  
cAGACATGGAAAACACTGGATGACGAACTGGCCTATGGGCGCTGCTTCGCAGACAGGCAGAACTTGATGGTATGCCTGCGATCAATGCCAAACGCGTTTa                               >  2:926155/1‑100 (MQ=255)
  gACATGGAAAACACTGGATGACGAACTGGCCTATGGGCGCTGCTTCGCAGACAGGCAGAACTTGATGGTATGCCTGCGATCAATGCCAAACGCGTTTAcc                             >  1:26715/1‑100 (MQ=255)
  gACATGGAAAACACTGGATGACGAACTGGCCTATGGGCGCTGCTTCGCAGACAGGCAGAACTTGATGGTATGCCTGCGATCAATGCCAAACGCGTTTAcc                             <  1:922068/100‑1 (MQ=255)
     aTGGAAAACACTGGATGACGAACTGGCCTATGGGCGCTGCTTCGCAGACAGGCAGAACTTGATGGTATGCCTGCGATCAATGCCAAACGCGTTTACCGGa                          >  2:1485189/1‑100 (MQ=255)
      tGGAAAACACTGGATGACGAACTGGCCTATGGGCGCTGCTTCGCAGACAGGCAGAACTTGATGGTATGCCTGCGATCAATGCCAAACGCGTTTACCGGAt                         <  1:676533/100‑1 (MQ=255)
      tGGAAAACACTGGATGACGAACTGGCCTATGGGCGCTGCTTCGCAGACAGGCAGAACTTGATGGTATGCCTGCGATCAATGCCAAACGCGTTTACCGGAt                         <  1:680726/100‑1 (MQ=255)
       ggAAAACACTGGATGACGAACTGGCCTATGGGCGCTGCTTCGCAGACAGGCAGAACTTGATGGTATGCCTGCGATCAATGCCAAACGCGTTTACCGGAt                         <  1:33598/99‑1 (MQ=255)
       ggAAAACACTGGATGACGAACTGGCCTATGGGCGCTGCTTCGCAGACAGGCAGAACTTGATGGTATGCCTGCGATCAATGCCAAACGCGTTTACCGGATc                        <  2:1332855/100‑1 (MQ=255)
       ggAAAACACTGGATGACGAACTGGCCTATGGGCGCTGCTTCGCAGACAGGCAGAACTTGATGGTATGCCTGCGATCAATGCCAAACGCGTTTACCGGATc                        >  2:1362310/1‑100 (MQ=255)
       ggAAAACACTGGATGACGAACTGGCCTATGGGCGCTGCTTCGCAGACAGGCAGAACTTGATGGTATGCCTGCGATCAATGCCAAACGCGTTTACCGGATc                        >  2:364191/1‑100 (MQ=255)
       ggAAAACACTGGATGACGAACTGGCCTATGGGCGCTGCTTCGCAGACAGGCAGAACTTGATGGTATGCCTGCGATCAATGCCAAACGCGTTTACCGGATc                        <  2:731734/100‑1 (MQ=255)
                tGGATGACGAACTGGCCTATGGGCGCTGCTTCGCAGACAGGCAGAACTTGATGGTATGCCTGCGATCAATGCCAAACGCGTTTACCGGATCATGCGCCAg               <  2:767527/100‑1 (MQ=255)
                             ggCCTATGGGCGCTGCTTCGCAGACAGGCAGAACTTGATGGTATGCCTGCGATCAATGCCAAACGCGTTTACCGGATCATGCGCCAGAATGCGCTGTTGc  >  1:819081/1‑100 (MQ=18)
                                                                                              |                                  
CAGACATGGAAAACACTGGATGACGAACTGGCCTATGGGCGCTGCTTCGCAGACAGGCAGAACTTGATGGTATGCCTGCGATCAATGCCAAACGTGTTTACCGGATCATGCGCCAGAATGCGCTGTTGC  >  NC_000913/1650810‑1650938

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A