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
A5 F28 I3 R2 489 0.0 1652083 58.3% 963164 55.2

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA W3110S.gb 4,258,862 A→G T399T (ACT→ACC)  plsB ← glycerol‑3‑phosphate O‑acyltransferase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb4,258,8620AG81.0% 343.6 / 60.9 189T399T (ACT→ACC) plsBglycerol‑3‑phosphate O‑acyltransferase
Reads supporting (aligned to +/- strand):  ref base A (0/36);  new base G (153/0);  total (153/36)
Fisher's exact test for biased strand distribution p-value = 1.46e-39
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.85e-01

Only 100 of 189 total aligned reads displayed.

ATCGGACGCGTGCCGCCACGCAGCATCGCCTGAATGGTCATCGACAGCGTACCAGTTTTCGGATCCAGCAAACG  >  W3110S.gb/4258809‑4258882
                                                     |                    
aTCGGACGCGTGCCGCCACGCAGCATCGCCTGAATGGTCATCGACAGCGTACCAGTTTTCgg              <  1:510892/62‑1 (MQ=255)
  cgcaCGCGTGCCGCCACGCAGCATCGCCTGAATGGTCATCGACAGCGTACCAGTTTTCGGa             <  1:634697/58‑1 (MQ=255)
  cGGACGCGTGCCGCCACGCAGCATCGCCTGAATGGTCATCGACAGCGTACCAGTTTTCGGa             <  1:475262/61‑1 (MQ=255)
  cGGACGCGTGCCGCCACGCAGCATCGCCTGAATGGTCATCGACAGCGTACCAGTTTTCGGa             <  1:1262421/61‑1 (MQ=255)
  cGGACGCGTGCCGCCACGCAGCATCGCCTGAATGGTCATCGACAGCGTACCAGTTTTCGGa             <  1:1257297/61‑1 (MQ=255)
  cGGACGCGTGCCGCCACGCAGCATCGCCTGAATGGTCATCGACAGCGTACCAGTTTTCGGa             <  1:174606/61‑1 (MQ=255)
  cGGACGCGTGCCGCCACGCAGCATCGCCTGAATGGTCATCGACAGCGTACCAGTTTTCGGa             <  1:742444/61‑1 (MQ=255)
  cGGACGCGTGCCGCCACGCAGCATCGCCTGAATGGTCATCGACAGCGTACCAGTTTTCGGa             <  1:766246/61‑1 (MQ=255)
  cGGACGCGTGCCGCCACGCAGCATCGCCTGAATGGTCATCGACAGCGTACCAGTTTTCGGa             <  1:688106/61‑1 (MQ=255)
  cGGACGCGTGCCGCCACGCAGCATCGCCTGAATGGTCATCGACAGCGTACCAGTTTTCGGa             <  1:79776/61‑1 (MQ=255)
  cGGACGCGTGCCGCCACGCAGCATCGCCTGAATGGTCATCGACAGCGTACCAGTTTTCGGa             <  1:366623/61‑1 (MQ=255)
  cGGACGCGTGCCGCCACGCAGCATCGCCTGAATGGTCATCGACAGCGTACCAGTTTTCGGa             <  1:1149878/61‑1 (MQ=255)
  cGGACGCGTGCCGCCACGCAGCATCGCCTGAATGGTCATCGACAGCGTACCAGTTTTCGGa             <  1:819302/61‑1 (MQ=255)
  cGGACGCGTGCCGCCACGCAGCATCGCCTGAATGGTCATCGACAGCGTACCAGTTTTCGGa             <  1:349439/61‑1 (MQ=255)
  cGGACGCGTGCCGCCACGCAGCATCGCCTGAATGGTCATCGACAGCGTACCAGTTTTCGGa             <  1:1367323/61‑1 (MQ=255)
  cGGACGCGTGCCGCCACGCAGCATCGCCTGAATGGTCATCGACAGCGTACCAGTTTTCGGa             <  1:1589355/61‑1 (MQ=255)
  cGGACGCGTGCCGCCACGCAGCATCGCCTGAATGGTCATCGACAGCGTACCAGTTTTCGGa             <  1:261223/61‑1 (MQ=255)
  cGGACGCGTGCCGCCACGCAGCATCGCCTGAATGGTCATCGACAGCGTACCAGTTTTCGGa             <  1:971369/61‑1 (MQ=255)
  cGGACGCGTGCCGCCACGCAGCATCGCCTGAATGGTCATCGACAGCGTACCAGTTTTCGGa             <  1:618462/61‑1 (MQ=255)
  cGGACGCGTGCCGCCACGCAGCATCGCCTGAATGGTCATCGACAGCGTACCAGTTTTCGGa             <  1:532709/61‑1 (MQ=255)
       gcgTGCCGCCACGCAGCATCGCCTGAATGGTCATCGACAGCGTACCAGTTTTCGGa             <  1:1020446/56‑1 (MQ=255)
            cctccACGCAGCATCGCCTGAATGGTCATCGACAGCGTACCGGTTTTCGGATCCAGCAAACg  >  1:1491805/4‑62 (MQ=255)
            ccgccACGCAGCATCGCCTGAATGGTCATCGACAGCGTACCGGTTTTCGGa             >  1:103545/1‑51 (MQ=255)
            ccgccACGCAGCATCGCCTGAATGGTCATCGACAGCGTACCGGTTTTCGGATCCAGCAAAc   >  1:914300/1‑61 (MQ=255)
            ccgccACGCAGCATCGCCTGAATGGTCATCGACAGCGTACCGGTTTTCGGATCCAGCAAACg  >  1:400741/1‑62 (MQ=255)
            ccgccACGCAGCATCGCCTGAATGGTCATCGACAGCGTACCGGTTTTCGGATCCAGCAAACg  >  1:385676/1‑62 (MQ=255)
            ccgccACGCAGCATCGCCTGAATGGTCATCGACAGCGTACCGGTTTTCGGATCCAGCAAACg  >  1:422603/1‑62 (MQ=255)
            ccgccACGCAGCATCGCCTGAATGGTCATCGACAGCGTACCGGTTTTCGGATCCAGCAAACg  >  1:429270/1‑62 (MQ=255)
            ccgccACGCAGCATCGCCTGAATGGTCATCGACAGCGTACCGGTTTTCGGATCCAGCAAACg  >  1:362392/1‑62 (MQ=255)
            ccgccACGCAGCATCGCCTGAATGGTCATCGACAGCGTACCGGTTTTCGGATCCAGCAAACg  >  1:347302/1‑62 (MQ=255)
            ccgccACGCAGCATCGCCTGAATGGTCATCGACAGCGTACCGGTTTTCGGATCCAGCAAACg  >  1:331640/1‑62 (MQ=255)
            ccgccACGCAGCATCGCCTGAATGGTCATCGACAGCGTACCGGTTTTCGGATCCAGCAAACg  >  1:993338/1‑62 (MQ=255)
            ccgccACGCAGCATCGCCTGAATGGTCATCGACAGCGTACCGGTTTTCGGATCCAGCAAACg  >  1:525195/1‑62 (MQ=255)
            ccgccACGCAGCATCGCCTGAATGGTCATCGACAGCGTACCGGTTTTCGGATCCAGCAAACg  >  1:311702/1‑62 (MQ=255)
            ccgccACGCAGCATCGCCTGAATGGTCATCGACAGCGTACCGGTTTTCGGATCCAGCAAACg  >  1:545806/1‑62 (MQ=255)
            ccgccACGCAGCATCGCCTGAATGGTCATCGACAGCGTACCGGTTTTCGGATCCAGCAAACg  >  1:696959/1‑62 (MQ=255)
            ccgccACGCAGCATCGCCTGAATGGTCATCGACAGCGTACCGGTTTTCGGATCCAGCAAACg  >  1:1001638/1‑62 (MQ=255)
            ccgccACGCAGCATCGCCTGAATGGTCATCGACAGCGTACCGGTTTTCGGATCCAGCAAACg  >  1:934415/1‑62 (MQ=255)
            ccgccACGCAGCATCGCCTGAATGGTCATCGACAGCGTACCGGTTTTCGGATCCAGCAAACg  >  1:924157/1‑62 (MQ=255)
            ccgccACGCAGCATCGCCTGAATGGTCATCGACAGCGTACCGGTTTTCGGATCCAGCAAACg  >  1:881451/1‑62 (MQ=255)
            ccgccACGCAGCATCGCCTGAATGGTCATCGACAGCGTACCGGTTTTCGGATCCAGCAAACg  >  1:858375/1‑62 (MQ=255)
            ccgccACGCAGCATCGCCTGAATGGTCATCGACAGCGTACCGGTTTTCGGATCCAGCAAACg  >  1:846882/1‑62 (MQ=255)
            ccgccACGCAGCATCGCCTGAATGGTCATCGACAGCGTACCGGTTTTCGGATCCAGCAAACg  >  1:808580/1‑62 (MQ=255)
            ccgccACGCAGCATCGCCTGAATGGTCATCGACAGCGTACCGGTTTTCGGATCCAGCAAACg  >  1:789460/1‑62 (MQ=255)
            ccgccACGCAGCATCGCCTGAATGGTCATCGACAGCGTACCGGTTTTCGGATCCAGCAAACg  >  1:720674/1‑62 (MQ=255)
            ccgccACGCAGCATCGCCTGAATGGTCATCGACAGCGTACCGGTTTTCGGATCCAGCAAACg  >  1:562117/1‑62 (MQ=255)
            ccgccACGCAGCATCGCCTGAATGGTCATCGACAGCGTACCGGTTTTCGGATCCAGCAAACg  >  1:669074/1‑62 (MQ=255)
            ccgccACGCAGCATCGCCTGAATGGTCATCGACAGCGTACCGGTTTTCGGATCCAGCAAACg  >  1:667435/1‑62 (MQ=255)
            ccgccACGCAGCATCGCCTGAATGGTCATCGACAGCGTACCGGTTTTCGGATCCAGCAAACg  >  1:644180/1‑62 (MQ=255)
            ccgccACGCAGCATCGCCTGAATGGTCATCGACAGCGTACCGGTTTTCGGATCCAGCAAACg  >  1:639520/1‑62 (MQ=255)
            ccgccACGCAGCATCGCCTGAATGGTCATCGACAGCGTACCGGTTTTCGGATCCAGCAAACg  >  1:631705/1‑62 (MQ=255)
            ccgccACGCAGCATCGCCTGAATGGTCATCGACAGCGTACCGGTTTTCGGATCCAGCAAACg  >  1:608907/1‑62 (MQ=255)
            ccgccACGCAGCATCGCCTGAATGGTCATCGACAGCGTACCGGTTTTCGGATCCAGCAAACg  >  1:587652/1‑62 (MQ=255)
            ccgccACGCAGCATCGCCTGAATGGTCATCGACAGCGTACCGGTTTTCGGATCCAGCAAACg  >  1:57971/1‑62 (MQ=255)
            ccgccACGCAGCATCGCCTGAATGGTCATCGACAGCGTACCGGTTTTCGGATCCAGCAAACg  >  1:575494/1‑62 (MQ=255)
            ccgccACGCAGCATCGCCTGAATGGTCATCGACAGCGTACCGGTTTTCGGATCCAGCAAACg  >  1:1215407/1‑62 (MQ=255)
            ccgccACGCAGCATCGCCTGAATGGTCATCGACAGCGTACCGGTTTTCGGATCCAGCAAACg  >  1:1382524/1‑62 (MQ=255)
            ccgccACGCAGCATCGCCTGAATGGTCATCGACAGCGTACCGGTTTTCGGATCCAGCAAACg  >  1:1354460/1‑62 (MQ=255)
            ccgccACGCAGCATCGCCTGAATGGTCATCGACAGCGTACCGGTTTTCGGATCCAGCAAACg  >  1:1340623/1‑62 (MQ=255)
            ccgccACGCAGCATCGCCTGAATGGTCATCGACAGCGTACCGGTTTTCGGATCCAGCAAACg  >  1:130516/1‑62 (MQ=255)
            ccgccACGCAGCATCGCCTGAATGGTCATCGACAGCGTACCGGTTTTCGGATCCAGCAAACg  >  1:1290444/1‑62 (MQ=255)
            ccgccACGCAGCATCGCCTGAATGGTCATCGACAGCGTACCGGTTTTCGGATCCAGCAAACg  >  1:1280324/1‑62 (MQ=255)
            ccgccACGCAGCATCGCCTGAATGGTCATCGACAGCGTACCGGTTTTCGGATCCAGCAAACg  >  1:1255980/1‑62 (MQ=255)
            ccgccACGCAGCATCGCCTGAATGGTCATCGACAGCGTACCGGTTTTCGGATCCAGCAAACg  >  1:12486/1‑62 (MQ=255)
            ccgccACGCAGCATCGCCTGAATGGTCATCGACAGCGTACCGGTTTTCGGATCCAGCAAACg  >  1:123829/1‑62 (MQ=255)
            ccgccACGCAGCATCGCCTGAATGGTCATCGACAGCGTACCGGTTTTCGGATCCAGCAAACg  >  1:1230740/1‑62 (MQ=255)
            ccgccACGCAGCATCGCCTGAATGGTCATCGACAGCGTACCGGTTTTCGGATCCAGCAAACg  >  1:1403872/1‑62 (MQ=255)
            ccgccACGCAGCATCGCCTGAATGGTCATCGACAGCGTACCGGTTTTCGGATCCAGCAAACg  >  1:1186477/1‑62 (MQ=255)
            ccgccACGCAGCATCGCCTGAATGGTCATCGACAGCGTACCGGTTTTCGGATCCAGCAAACg  >  1:1136728/1‑62 (MQ=255)
            ccgccACGCAGCATCGCCTGAATGGTCATCGACAGCGTACCGGTTTTCGGATCCAGCAAACg  >  1:1125735/1‑62 (MQ=255)
            ccgccACGCAGCATCGCCTGAATGGTCATCGACAGCGTACCGGTTTTCGGATCCAGCAAACg  >  1:1121145/1‑62 (MQ=255)
            ccgccACGCAGCATCGCCTGAATGGTCATCGACAGCGTACCGGTTTTCGGATCCAGCAAACg  >  1:110938/1‑62 (MQ=255)
            ccgccACGCAGCATCGCCTGAATGGTCATCGACAGCGTACCGGTTTTCGGATCCAGCAAACg  >  1:1096547/1‑62 (MQ=255)
            ccgccACGCAGCATCGCCTGAATGGTCATCGACAGCGTACCGGTTTTCGGATCCAGCAAACg  >  1:109067/1‑62 (MQ=255)
            ccgccACGCAGCATCGCCTGAATGGTCATCGACAGCGTACCGGTTTTCGGATCCAGCAAACg  >  1:1057983/1‑62 (MQ=255)
            ccgccACGCAGCATCGCCTGAATGGTCATCGACAGCGTACCGGTTTTCGGATCCAGCAAACg  >  1:1045527/1‑62 (MQ=255)
            ccgccACGCAGCATCGCCTGAATGGTCATCGACAGCGTACCGGTTTTCGGATCCAGCAAACg  >  1:1040259/1‑62 (MQ=255)
            ccgccACGCAGCATCGCCTGAATGGTCATCGACAGCGTACCGGTTTTCGGATCCAGCAAACg  >  1:154555/1‑62 (MQ=255)
            ccgccACGCAGCATCGCCTGAATGGTCATCGACAGCGTACCGGTTTTCGGATCCAGCAAACg  >  1:286601/1‑62 (MQ=255)
            ccgccACGCAGCATCGCCTGAATGGTCATCGACAGCGTACCGGTTTTCGGATCCAGCAAACg  >  1:251354/1‑62 (MQ=255)
            ccgccACGCAGCATCGCCTGAATGGTCATCGACAGCGTACCGGTTTTCGGATCCAGCAAACg  >  1:241074/1‑62 (MQ=255)
            ccgccACGCAGCATCGCCTGAATGGTCATCGACAGCGTACCGGTTTTCGGATCCAGCAAACg  >  1:216013/1‑62 (MQ=255)
            ccgccACGCAGCATCGCCTGAATGGTCATCGACAGCGTACCGGTTTTCGGATCCAGCAAACg  >  1:194577/1‑62 (MQ=255)
            ccgccACGCAGCATCGCCTGAATGGTCATCGACAGCGTACCGGTTTTCGGATCCAGCAAACg  >  1:175963/1‑62 (MQ=255)
            ccgccACGCAGCATCGCCTGAATGGTCATCGACAGCGTACCGGTTTTCGGATCCAGCAAACg  >  1:167616/1‑62 (MQ=255)
            ccgccACGCAGCATCGCCTGAATGGTCATCGACAGCGTACCGGTTTTCGGATCCAGCAAACg  >  1:1620164/1‑62 (MQ=255)
            ccgccACGCAGCATCGCCTGAATGGTCATCGACAGCGTACCGGTTTTCGGATCCAGCAAACg  >  1:1603085/1‑62 (MQ=255)
            ccgccACGCAGCATCGCCTGAATGGTCATCGACAGCGTACCGGTTTTCGGATCCAGCAAACg  >  1:1581588/1‑62 (MQ=255)
            ccgccACGCAGCATCGCCTGAATGGTCATCGACAGCGTACCGGTTTTCGGATCCAGCAAACg  >  1:302618/1‑62 (MQ=255)
            ccgccACGCAGCATCGCCTGAATGGTCATCGACAGCGTACCGGTTTTCGGATCCAGCAAACg  >  1:1518499/1‑62 (MQ=255)
            ccgccACGCAGCATCGCCTGAATGGTCATCGACAGCGTACCGGTTTTCGGATCCAGCAAACg  >  1:1508877/1‑62 (MQ=255)
            ccgccACGCAGCATCGCCTGAATGGTCATCGACAGCGTACCGGTTTTCGGATCCAGCAAACg  >  1:1482253/1‑62 (MQ=255)
            ccgccACGCAGCATCGCCTGAATGGTCATCGACAGCGTACCGGTTTTCGGATCCAGCAAACg  >  1:1479104/1‑62 (MQ=255)
            ccgccACGCAGCATCGCCTGAATGGTCATCGACAGCGTACCGGTTTTCGGATCCAGCAAACg  >  1:1457004/1‑62 (MQ=255)
            ccgccACGCAGCATCGCCTGAATGGTCATCGACAGCGTACCGGTTTTCGGATCCAGCAAACg  >  1:1444223/1‑62 (MQ=255)
            ccgccACGCAGCATCGCCTGAATGGTCATCGACAGCGTACCGGTTTTCGGATCCAGCAAACg  >  1:1439724/1‑62 (MQ=255)
            ccgccACGCAGCATCGCCTGAATGGTCATCGACAGCGTACCGGTTTTCGGATCCAGCAAACg  >  1:1425632/1‑62 (MQ=255)
            ccgccACGCAGCATCGCCTGAATGGTCATCGACAGCGTACCGGTTTTCGGATCCAGCAAACg  >  1:1411961/1‑62 (MQ=255)
            ccgccACGCAGCATCGCCTGAATGGACATCGACAGCGTACCGGTTTTCGGATCCAGCAAACg  >  1:655653/1‑62 (MQ=255)
                   gcagcaTCGCCTGAATGGTCATCGACAGCGTACCAGTTTTCGGa             <  1:245769/44‑1 (MQ=255)
                                                     |                    
ATCGGACGCGTGCCGCCACGCAGCATCGCCTGAATGGTCATCGACAGCGTACCAGTTTTCGGATCCAGCAAACG  >  W3110S.gb/4258809‑4258882

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A