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 F28 I1 R2 328 63.0 4687567 98.0% 4593815 65.2

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA W3110S.gb 1,646,707 C→T intergenic (‑91/+126) rem ← / ← hokD hypothetical protein/small toxic polypeptide

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb1,646,7070CT100.0% 52.7 / NA 19intergenic (‑91/+126)rem/hokDhypothetical protein/small toxic polypeptide
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (12/7);  total (12/7)

TTTAAGGGACCATCCCTCTTATCCCTGCGCGCTACTTAAGTATTTTTGATTCTATTCCGGCACCGTCCAGAACTTCAAACGCGTTGAAAATAAAAACAAAAACCCGCCGAAGCGGGTTAAGTGCGG  >  W3110S.gb/1646647‑1646772
                                                            |                                                                 
tttAAGGGACCATCCCTCTTATCCCTGCGCGCTACTTAAGTATTTTTGATTCTATTCCGGTAc                                                                 <  1:712285/63‑1 (MQ=255)
  tAAGGGATCATCCCTCTTATCCCTGCGCGCTACTTAAGTATTTTTGATTCTATTCCGGTACCGTCCAGAAc                                                       >  1:2396174/1‑71 (MQ=255)
             cccTCTTATCCCTGCGCGCTACTTAAGTATTTTTGATTCTATTCCGGTAc                                                                 >  1:2506586/1‑50 (MQ=255)
             cccTCTTATCCCTGCGCGCTACTTAAGTATTTTTGATTCTATTCCGGTAc                                                                 >  1:4415551/1‑50 (MQ=255)
              ccTCTTATCCCTGCGCGCTACTTAAGTATTTTTGATTCTATTCCGGTACCGTCCAGAACTTCAAAc                                                >  1:3169132/1‑66 (MQ=255)
                        cTGCGCGCTACTTAAGTATTTTTGATTCTATTCCGGTACCGTCCAGAACTTCAAACACGTTGAAAATaaaa                                 <  1:951090/71‑1 (MQ=255)
                           cgcgcTACTTAAGTATTTTTGATTCTATTCCGGTACCGTCCAGAACTTCAAACGCGTTGAAAATaaaaac                               >  1:2191390/1‑70 (MQ=255)
                             cgcTACTTAAGTATTTTTGATTCTATTCCGGTACCGTCCAGAACTTCAAACGCGTTGAAAATaaaaacaaa                            <  1:1683645/71‑1 (MQ=255)
                                          tttttGATTCTATTCCGGTACCGTCCAGAACTTCAAACGCGTTGAAAATaaaaacaaa                            >  1:447285/1‑58 (MQ=255)
                                          tttttGATTCTATTCCGGTACCGTCCAGAAATTCa                                                   >  1:1314384/1‑35 (MQ=25)
                                            tttGATTCTATTCCGGTACCGTCCAGAACTTCAAACGCGTTGAAAATAAAAACAAAAACCCGCCGAAGCgg             >  1:788287/1‑71 (MQ=255)
                                                aTTCTATTCCGGTACCGTCCAGAACTTCAAACGCGTTGAAAATAAAAACAAAAACCCGCCGAAGCGGGTTa         <  1:97913/71‑1 (MQ=255)
                                                aTTCTATTCCGGTACCGTCCAGAACTTCAAACGCGTTGAAAATAAAAACAAAAACCCGCCGAAGCGGGTTa         <  1:3815235/71‑1 (MQ=255)
                                                 ttCTATTCCGGTACCGTCCAGAACTTCAAACGCGTTGAAAATAAAAACAAAAACCCGCCGAAGCGGGTTa         <  1:2651495/70‑1 (MQ=255)
                                                  tCTATTCCGGTACCGTCCAGAACTTCAAACGCGTTGAAAATaaaaacaaa                            >  1:186913/1‑50 (MQ=255)
                                                   cTATTCCGGTACCGTCCAGAACTTCAAACGCGTTGAAAATAAAAACAAAAACCCGCCGAAGCGGGTTAAGt      >  1:4212718/1‑71 (MQ=255)
                                                   cTATTCCGGTACCGTCCAGAACTTCAAACGCGTTGAAAATAAAAACAAAAACCCGCCGAAGCGGGTTAAGt      >  1:462263/1‑71 (MQ=255)
                                                       tCCGGTACCGTCCAGAACTTCAAACGCGTTGAAAATAAAAACAAAAACCCGCCGAAGCGGGTTAAGTGc    <  1:3849311/69‑1 (MQ=255)
                                                        ccGGTACCGTCCAGAACTTCAAACGCGTTGAAAATAAAAACAAAAACCCGCCGAAGCGGGTTAAGTGCgg  >  1:721796/1‑70 (MQ=255)
                                                            |                                                                 
TTTAAGGGACCATCCCTCTTATCCCTGCGCGCTACTTAAGTATTTTTGATTCTATTCCGGCACCGTCCAGAACTTCAAACGCGTTGAAAATAAAAACAAAAACCCGCCGAAGCGGGTTAAGTGCGG  >  W3110S.gb/1646647‑1646772

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A