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 3,233,387 T→C intergenic (‑276/+8) ygjN ← / ← ygjO conserved hypothetical protein/predicted methyltransferase small domain

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb3,233,3870TC96.3% 478.4 / 1.9 190intergenic (‑276/+8)ygjN/ygjOconserved hypothetical protein/predicted methyltransferase small domain
Reads supporting (aligned to +/- strand):  ref base T (0/7);  new base C (183/0);  total (183/7)
Fisher's exact test for biased strand distribution p-value = 6.31e-13
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.68e-01

Only 100 of 191 total aligned reads displayed.

AGGCCGGATAAGGCGTTTACGCCGCATCCGGCAGGTAACTCCCAATCTTACCGACGACGTCCCAGCTTCACCG  >  W3110S.gb/3233348‑3233420
                                       |                                 
atgCCGGATAAGGCGTTTACGCCGCATCCGGCAGGTAACCCCCAATCTTACcga                     >  1:949852/3‑54 (MQ=255)
atgCCGGATAAGGCGTTTACGCCGCATCCGGCAGGTAACCCCCAATCTTACCGacgacgc               >  1:41307/3‑59 (MQ=25)
atgCCGGATAAGGCGTTTACGCCGCATCCGGCAGGTAACCCCCAATCTTACCGacgacgc               >  1:570921/3‑59 (MQ=25)
atgCCGGATAAGGCGTTTACGCCGCATCCGGCAGGTAACCCCCAATCTTACCGacgacgc               >  1:561616/3‑59 (MQ=25)
atgCCGGATAAGGCGTTTACGCCGCATCCGGCAGGTAACCCCCAATCTTACCGacgacgc               >  1:552071/3‑59 (MQ=25)
atgCCGGATAAGGCGTTTACGCCGCATCCGGCAGGTAACCCCCAATCTTACCGacgacgc               >  1:549997/3‑59 (MQ=25)
atgCCGGATAAGGCGTTTACGCCGCATCCGGCAGGTAACCCCCAATCTTACCGacgacgc               >  1:507348/3‑59 (MQ=25)
atgCCGGATAAGGCGTTTACGCCGCATCCGGCAGGTAACCCCCAATCTTACCGacgacgc               >  1:497673/3‑59 (MQ=25)
atgCCGGATAAGGCGTTTACGCCGCATCCGGCAGGTAACCCCCAATCTTACCGacgacgc               >  1:495437/3‑59 (MQ=25)
atgCCGGATAAGGCGTTTACGCCGCATCCGGCAGGTAACCCCCAATCTTACCGacgacgc               >  1:481258/3‑59 (MQ=25)
atgCCGGATAAGGCGTTTACGCCGCATCCGGCAGGTAACCCCCAATCTTACCGacgacgc               >  1:475089/3‑59 (MQ=25)
atgCCGGATAAGGCGTTTACGCCGCATCCGGCAGGTAACCCCCAATCTTACCGacgacgc               >  1:470438/3‑59 (MQ=25)
atgCCGGATAAGGCGTTTACGCCGCATCCGGCAGGTAACCCCCAATCTTACCGacgacgc               >  1:440605/3‑59 (MQ=25)
atgCCGGATAAGGCGTTTACGCCGCATCCGGCAGGTAACCCCCAATCTTACCGacgacgc               >  1:426931/3‑59 (MQ=25)
atgCCGGATAAGGCGTTTACGCCGCATCCGGCAGGTAACCCCCAATCTTACCGacgacgc               >  1:597861/3‑59 (MQ=25)
atgCCGGATAAGGCGTTTACGCCGCATCCGGCAGGTAACCCCCAATCTTACCGacgacgc               >  1:388357/3‑59 (MQ=25)
atgCCGGATAAGGCGTTTACGCCGCATCCGGCAGGTAACCCCCAATCTTACCGacgacgc               >  1:383161/3‑59 (MQ=25)
atgCCGGATAAGGCGTTTACGCCGCATCCGGCAGGTAACCCCCAATCTTACCGacgacgc               >  1:378447/3‑59 (MQ=25)
atgCCGGATAAGGCGTTTACGCCGCATCCGGCAGGTAACCCCCAATCTTACCGacgacgc               >  1:376515/3‑59 (MQ=25)
atgCCGGATAAGGCGTTTACGCCGCATCCGGCAGGTAACCCCCAATCTTACCGacgacgc               >  1:370243/3‑59 (MQ=25)
atgCCGGATAAGGCGTTTACGCCGCATCCGGCAGGTAACCCCCAATCTTACCGacgacgc               >  1:370035/3‑59 (MQ=25)
atgCCGGATAAGGCGTTTACGCCGCATCCGGCAGGTAACCCCCAATCTTACCGacgacgc               >  1:338732/3‑59 (MQ=25)
atgCCGGATAAGGCGTTTACGCCGCATCCGGCAGGTAACCCCCAATCTTACCGacgacgc               >  1:32548/3‑59 (MQ=25)
atgCCGGATAAGGCGTTTACGCCGCATCCGGCAGGTAACCCCCAATCTTACCGacgacgc               >  1:317634/3‑59 (MQ=25)
atgCCGGATAAGGCGTTTACGCCGCATCCGGCAGGTAACCCCCAATCTTACCGacgacgc               >  1:28651/3‑59 (MQ=25)
atgCCGGATAAGGCGTTTACGCCGCATCCGGCAGGTAACCCCCAATCTTACCGacgacgc               >  1:778866/3‑59 (MQ=25)
atgCCGGATAAGGCGTTTACGCCGCATCCGGCAGGTAACCCCCAATCTTACCGacgacgc               >  1:994761/3‑59 (MQ=25)
atgCCGGATAAGGCGTTTACGCCGCATCCGGCAGGTAACCCCCAATCTTACCGacgacgc               >  1:979606/3‑59 (MQ=25)
atgCCGGATAAGGCGTTTACGCCGCATCCGGCAGGTAACCCCCAATCTTACCGacgacgc               >  1:962556/3‑59 (MQ=25)
atgCCGGATAAGGCGTTTACGCCGCATCCGGCAGGTAACCCCCAATCTTACCGacgacgc               >  1:932305/3‑59 (MQ=25)
atgCCGGATAAGGCGTTTACGCCGCATCCGGCAGGTAACCCCCAATCTTACCGacgacgc               >  1:924690/3‑59 (MQ=25)
atgCCGGATAAGGCGTTTACGCCGCATCCGGCAGGTAACCCCCAATCTTACCGacgacgc               >  1:921223/3‑59 (MQ=25)
atgCCGGATAAGGCGTTTACGCCGCATCCGGCAGGTAACCCCCAATCTTACCGacgacgc               >  1:899816/3‑59 (MQ=25)
atgCCGGATAAGGCGTTTACGCCGCATCCGGCAGGTAACCCCCAATCTTACCGacgacgc               >  1:888135/3‑59 (MQ=25)
atgCCGGATAAGGCGTTTACGCCGCATCCGGCAGGTAACCCCCAATCTTACCGacgacgc               >  1:880056/3‑59 (MQ=25)
atgCCGGATAAGGCGTTTACGCCGCATCCGGCAGGTAACCCCCAATCTTACCGacgacgc               >  1:836557/3‑59 (MQ=25)
atgCCGGATAAGGCGTTTACGCCGCATCCGGCAGGTAACCCCCAATCTTACCGacgacgc               >  1:806983/3‑59 (MQ=25)
atgCCGGATAAGGCGTTTACGCCGCATCCGGCAGGTAACCCCCAATCTTACCGacgacgc               >  1:1023421/3‑59 (MQ=25)
atgCCGGATAAGGCGTTTACGCCGCATCCGGCAGGTAACCCCCAATCTTACCGacgacgc               >  1:768156/3‑59 (MQ=25)
atgCCGGATAAGGCGTTTACGCCGCATCCGGCAGGTAACCCCCAATCTTACCGacgacgc               >  1:757121/3‑59 (MQ=25)
atgCCGGATAAGGCGTTTACGCCGCATCCGGCAGGTAACCCCCAATCTTACCGacgacgc               >  1:746508/3‑59 (MQ=25)
atgCCGGATAAGGCGTTTACGCCGCATCCGGCAGGTAACCCCCAATCTTACCGacgacgc               >  1:713518/3‑59 (MQ=25)
atgCCGGATAAGGCGTTTACGCCGCATCCGGCAGGTAACCCCCAATCTTACCGacgacgc               >  1:693297/3‑59 (MQ=25)
atgCCGGATAAGGCGTTTACGCCGCATCCGGCAGGTAACCCCCAATCTTACCGacgacgc               >  1:668038/3‑59 (MQ=25)
atgCCGGATAAGGCGTTTACGCCGCATCCGGCAGGTAACCCCCAATCTTACCGacgacgc               >  1:659902/3‑59 (MQ=25)
atgCCGGATAAGGCGTTTACGCCGCATCCGGCAGGTAACCCCCAATCTTACCGacgacgc               >  1:635481/3‑59 (MQ=25)
atgCCGGATAAGGCGTTTACGCCGCATCCGGCAGGTAACCCCCAATCTTACCGacgacgc               >  1:634509/3‑59 (MQ=25)
atgCCGGATAAGGCGTTTACGCCGCATCCGGCAGGTAACCCCCAATCTTACCGacgacgc               >  1:618302/3‑59 (MQ=25)
atgCCGGATAAGGCGTTTACGCCGCATCCGGCAGGTAACCCCCAATCTTACCGacgacgc               >  1:1235529/3‑59 (MQ=25)
atgCCGGATAAGGCGTTTACGCCGCATCCGGCAGGTAACCCCCAATCTTACCGacgacgc               >  1:285027/3‑59 (MQ=25)
atgCCGGATAAGGCGTTTACGCCGCATCCGGCAGGTAACCCCCAATCTTACCGacgacgc               >  1:1427320/3‑59 (MQ=25)
atgCCGGATAAGGCGTTTACGCCGCATCCGGCAGGTAACCCCCAATCTTACCGacgacgc               >  1:1412537/3‑59 (MQ=25)
atgCCGGATAAGGCGTTTACGCCGCATCCGGCAGGTAACCCCCAATCTTACCGacgacgc               >  1:1411624/3‑59 (MQ=25)
atgCCGGATAAGGCGTTTACGCCGCATCCGGCAGGTAACCCCCAATCTTACCGacgacgc               >  1:1376312/3‑59 (MQ=25)
atgCCGGATAAGGCGTTTACGCCGCATCCGGCAGGTAACCCCCAATCTTACCGacgacgc               >  1:1370930/3‑59 (MQ=25)
atgCCGGATAAGGCGTTTACGCCGCATCCGGCAGGTAACCCCCAATCTTACCGacgacgc               >  1:1336327/3‑59 (MQ=25)
atgCCGGATAAGGCGTTTACGCCGCATCCGGCAGGTAACCCCCAATCTTACCGacgacgc               >  1:1318521/3‑59 (MQ=25)
atgCCGGATAAGGCGTTTACGCCGCATCCGGCAGGTAACCCCCAATCTTACCGacgacgc               >  1:1300145/3‑59 (MQ=25)
atgCCGGATAAGGCGTTTACGCCGCATCCGGCAGGTAACCCCCAATCTTACCGacgacgc               >  1:1293272/3‑59 (MQ=25)
atgCCGGATAAGGCGTTTACGCCGCATCCGGCAGGTAACCCCCAATCTTACCGacgacgc               >  1:1267987/3‑59 (MQ=25)
atgCCGGATAAGGCGTTTACGCCGCATCCGGCAGGTAACCCCCAATCTTACCGacgacgc               >  1:123651/3‑59 (MQ=25)
atgCCGGATAAGGCGTTTACGCCGCATCCGGCAGGTAACCCCCAATCTTACCGacgacgc               >  1:1428145/3‑59 (MQ=25)
atgCCGGATAAGGCGTTTACGCCGCATCCGGCAGGTAACCCCCAATCTTACCGacgacgc               >  1:1232404/3‑59 (MQ=25)
atgCCGGATAAGGCGTTTACGCCGCATCCGGCAGGTAACCCCCAATCTTACCGacgacgc               >  1:1224323/3‑59 (MQ=25)
atgCCGGATAAGGCGTTTACGCCGCATCCGGCAGGTAACCCCCAATCTTACCGacgacgc               >  1:1188592/3‑59 (MQ=25)
atgCCGGATAAGGCGTTTACGCCGCATCCGGCAGGTAACCCCCAATCTTACCGacgacgc               >  1:1184282/3‑59 (MQ=25)
atgCCGGATAAGGCGTTTACGCCGCATCCGGCAGGTAACCCCCAATCTTACCGacgacgc               >  1:1165089/3‑59 (MQ=25)
atgCCGGATAAGGCGTTTACGCCGCATCCGGCAGGTAACCCCCAATCTTACCGacgacgc               >  1:1140810/3‑59 (MQ=25)
atgCCGGATAAGGCGTTTACGCCGCATCCGGCAGGTAACCCCCAATCTTACCGacgacgc               >  1:1124739/3‑59 (MQ=25)
atgCCGGATAAGGCGTTTACGCCGCATCCGGCAGGTAACCCCCAATCTTACCGacgacgc               >  1:109308/3‑59 (MQ=25)
atgCCGGATAAGGCGTTTACGCCGCATCCGGCAGGTAACCCCCAATCTTACCGacgacgc               >  1:1068432/3‑59 (MQ=25)
atgCCGGATAAGGCGTTTACGCCGCATCCGGCAGGTAACCCCCAATCTTACCGacgacgc               >  1:1060172/3‑59 (MQ=25)
atgCCGGATAAGGCGTTTACGCCGCATCCGGCAGGTAACCCCCAATCTTACCGacgacgc               >  1:1000513/3‑59 (MQ=25)
atgCCGGATAAGGCGTTTACGCCGCATCCGGCAGGTAACCCCCAATCTTACCGacgacgc               >  1:1451065/3‑59 (MQ=25)
atgCCGGATAAGGCGTTTACGCCGCATCCGGCAGGTAACCCCCAATCTTACCGacgacgc               >  1:276615/3‑59 (MQ=25)
atgCCGGATAAGGCGTTTACGCCGCATCCGGCAGGTAACCCCCAATCTTACCGacgacgc               >  1:275220/3‑59 (MQ=25)
atgCCGGATAAGGCGTTTACGCCGCATCCGGCAGGTAACCCCCAATCTTACCGacgacgc               >  1:265103/3‑59 (MQ=25)
atgCCGGATAAGGCGTTTACGCCGCATCCGGCAGGTAACCCCCAATCTTACCGacgacgc               >  1:257279/3‑59 (MQ=25)
atgCCGGATAAGGCGTTTACGCCGCATCCGGCAGGTAACCCCCAATCTTACCGacgacgc               >  1:241356/3‑59 (MQ=25)
atgCCGGATAAGGCGTTTACGCCGCATCCGGCAGGTAACCCCCAATCTTACCGacgacgc               >  1:228604/3‑59 (MQ=25)
atgCCGGATAAGGCGTTTACGCCGCATCCGGCAGGTAACCCCCAATCTTACCGacgacgc               >  1:20220/3‑59 (MQ=25)
atgCCGGATAAGGCGTTTACGCCGCATCCGGCAGGTAACCCCCAATCTTACCGacgacgc               >  1:175576/3‑59 (MQ=25)
atgCCGGATAAGGCGTTTACGCCGCATCCGGCAGGTAACCCCCAATCTTACCGacgacgc               >  1:1651074/3‑59 (MQ=25)
atgCCGGATAAGGCGTTTACGCCGCATCCGGCAGGTAACCCCCAATCTTACCGacgacgc               >  1:1554138/3‑59 (MQ=25)
atgCCGGATAAGGCGTTTACGCCGCATCCGGCAGGTAACCCCCAATCTTACCGacgacgc               >  1:1434284/3‑59 (MQ=25)
atgCCGGATAAGGCGTTTACGCCGCATCCGGCAGGTAACCCCCAATCTTACCGacgacgc               >  1:1457540/3‑59 (MQ=25)
atgCCGGATAAGGCGTTTACGCCGCATCCGGCAGGTAACCCCCAATCTTACCGacgacgc               >  1:1473705/3‑59 (MQ=25)
atgCCGGATAAGGCGTTTACGCCGCATCCGGCAGGTAACCCCCAATCTTACCGacgacgc               >  1:1524609/3‑59 (MQ=25)
atgCCGGATAAGGCGTTTACGCCGCATCCGGCAGGTAACCCCCAATCTTACCGacgacgc               >  1:1535206/3‑59 (MQ=25)
atgCCGGATAAGGCGTTTACGCCGCATCCGGCAGGTAACCCCCAATCTTACCGacgacgc               >  1:1610182/3‑59 (MQ=25)
atgCCGGATAAGGCGTTTACGCCGCATCCGGCAGGTAACCCCCAATCTTACCGacgacgc               >  1:1568711/3‑59 (MQ=25)
atgCCGGATAAGGCGTTTACGCCGCATCCGGCAGGTAACCCCCAATCTTACCGacgacgc               >  1:1579865/3‑59 (MQ=25)
atgCCGGATAAGGCGTTTACGCCGCATCCGGCAGGTAACCCCCAATCTTACCGacgacgc               >  1:159304/3‑59 (MQ=25)
atgCCGGATAAGGCGTTTACGCCGCATCCGGCAGGTAACCCCCAATCTTACCGacgacg                >  1:40966/3‑59 (MQ=255)
atgCCGGATAAGGCGTTTACGCCGCATCCGGCAGGTAACCCCCAATCTTACCGacgacg                >  1:1250863/3‑59 (MQ=255)
atgCCGGATAAGGCGTTTAAGCCGCATCCGGCAGGTAACCCCCAATCTTACCGacgacgc               >  1:300414/3‑59 (MQ=25)
            gCGTTTACGCCGCATCCGGCAGGTAACTCCCAATCTTACCGACGACGTCCCAGCTTCACCg  <  1:329869/61‑1 (MQ=255)
            gCGTTTACGCCGCATCCGGCAGGTAACTCCCAATCTTACCGACGACGTCCCAGCTTCACCg  <  1:9784/61‑1 (MQ=255)
            gCGTTTACGCCGCATCCGGCAGGTAACTCCCAATCTTACCGACGACGTCCCAGCTTCACCg  <  1:1621611/61‑1 (MQ=255)
             cGTTTACGCCGCATCCGGCAGGTAACTCCCAATCTTACCGACGACGTCCCAGCTTCACCg  <  1:201099/60‑1 (MQ=255)
                                       |                                 
AGGCCGGATAAGGCGTTTACGCCGCATCCGGCAGGTAACTCCCAATCTTACCGACGACGTCCCAGCTTCACCG  >  W3110S.gb/3233348‑3233420

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