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
A6 F28 I2 R1 52 300.6 3297834 97.8% 3225281 57.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA minE 2,563,007 G→C A357G (GCT→GGT)  lldP ← L‑lactate permease

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,563,0070GC100.0% 82.8 / NA 22A357G (GCT→GGT) lldPL‑lactate permease
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base C (22/0);  total (22/0)

CACGGCGGCATAGGCTGTAGCCTCGCTGACCACTGGCGGCATACGGGCAACCAGTTTATCGA  >  minE/2562988‑2563049
                   |                                          
cacGGCGGCATAGGCTGTACCCTCGCTGACCACTGGCGGCATACGGGc                >  1:2638961/1‑48 (MQ=255)
cacGGCGGCATAGGCTGTACCCTCGCTGACCACTGGCGGCATACGGGCAACCAGTTTATCg   >  1:1876348/1‑61 (MQ=255)
cacGGCGGCATAGGCTGTACCCTCGCTGACCACTGGCGGCATACGGGCAACCAGTTTATCg   >  1:2253277/1‑61 (MQ=255)
cacGGCGGCATAGGCTGTACCCTCGCTGACCACTGGCGGCATACGGGCAACCAGTTTATCGa  >  1:1514310/1‑62 (MQ=255)
cacGGCGGCATAGGCTGTACCCTCGCTGACCACTGGCGGCATACGGGCAACCAGTTTATCGa  >  1:593245/1‑62 (MQ=255)
cacGGCGGCATAGGCTGTACCCTCGCTGACCACTGGCGGCATACGGGCAACCAGTTTATCGa  >  1:569191/1‑62 (MQ=255)
cacGGCGGCATAGGCTGTACCCTCGCTGACCACTGGCGGCATACGGGCAACCAGTTTATCGa  >  1:494087/1‑62 (MQ=255)
cacGGCGGCATAGGCTGTACCCTCGCTGACCACTGGCGGCATACGGGCAACCAGTTTATCGa  >  1:3246798/1‑62 (MQ=255)
cacGGCGGCATAGGCTGTACCCTCGCTGACCACTGGCGGCATACGGGCAACCAGTTTATCGa  >  1:3166976/1‑62 (MQ=255)
cacGGCGGCATAGGCTGTACCCTCGCTGACCACTGGCGGCATACGGGCAACCAGTTTATCGa  >  1:2845558/1‑62 (MQ=255)
cacGGCGGCATAGGCTGTACCCTCGCTGACCACTGGCGGCATACGGGCAACCAGTTTATCGa  >  1:2517642/1‑62 (MQ=255)
cacGGCGGCATAGGCTGTACCCTCGCTGACCACTGGCGGCATACGGGCAACCAGTTTATCGa  >  1:217544/1‑62 (MQ=255)
cacGGCGGCATAGGCTGTACCCTCGCTGACCACTGGCGGCATACGGGCAACCAGTTTATCGa  >  1:2149607/1‑62 (MQ=255)
cacGGCGGCATAGGCTGTACCCTCGCTGACCACTGGCGGCATACGGGCAACCAGTTTATCGa  >  1:2050583/1‑62 (MQ=255)
cacGGCGGCATAGGCTGTACCCTCGCTGACCACTGGCGGCATACGGGCAACCAGTTTATCGa  >  1:1952313/1‑62 (MQ=255)
cacGGCGGCATAGGCTGTACCCTCGCTGACCACTGGCGGCATACGGGCAACCAGTTTATCGa  >  1:1948660/1‑62 (MQ=255)
cacGGCGGCATAGGCTGTACCCTCGCTGACCACTGGCGGCATACGGGCAACCAGTTTATCGa  >  1:1782138/1‑62 (MQ=255)
cacGGCGGCATAGGCTGTACCCTCGCTGACCACTGGCGGCATACGGGCAACCAGTTTATCGa  >  1:1674515/1‑62 (MQ=255)
cacGGCGGCATAGGCTGTACCCTCGCTGACCACTGGCGGCATACGGGCAACCAGTTTATCGa  >  1:1617482/1‑62 (MQ=255)
cacGGCGGCATAGGCTGTACCCTCGCTGACCACTGGCGGCATACGGGCAACCAGTTTATCGa  >  1:160189/1‑62 (MQ=255)
cacGGCGGCATAGGCTGTACCCTCGCTGACCACTGGCGGCATACGGGCAACCAGTTTATCGa  >  1:1245492/1‑62 (MQ=255)
cacGGCGGCATAGGCTGCACCCTCGCTGACCACTGGCGGCATACgg                  >  1:898774/1‑46 (MQ=255)
                   |                                          
CACGGCGGCATAGGCTGTAGCCTCGCTGACCACTGGCGGCATACGGGCAACCAGTTTATCGA  >  minE/2562988‑2563049

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A