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 1,060,340 C→T N221N (AAC→AAT)  torA → trimethylamine N‑oxide (TMAO) reductase I, catalytic subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb1,060,3400CT89.8% 356.6 / 20.2 157N221N (AAC→AAT) torAtrimethylamine N‑oxide (TMAO) reductase I, catalytic subunit
Reads supporting (aligned to +/- strand):  ref base C (0/16);  new base T (0/141);  total (0/157)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.32e-01

Only 100 of 157 total aligned reads displayed.

GAAGTGTATGAACAGCAAACCTCCTGGCCGCTGGTATTGCAGAACAGCAAAACCATTGTGCTGTGGGGCTCCGATTTGCTGAAAAA  >  W3110S.gb/1060296‑1060381
                                            |                                         
  aGTGTATGAACAGCAAACCTCCTGGCCGCTGGTATTGCAGAACAGCAAAACCATTGTGCtg                         <  1:528981/61‑1 (MQ=255)
  aGTGTATGAACAGCAAACCTCCTGGCCGCTGGTATTGCAGAACAGCAAAACCATTGTGCtg                         <  1:153590/61‑1 (MQ=255)
  aGTGTATGAACAGCAAACCTCCTGGCCGCTGGTATTGCAGAACAGCAAAACCATTGTGCtg                         <  1:1395445/61‑1 (MQ=255)
  aGTGTATGAACAGCAAACCTCCTGGCCGCTGGTATTGCAGAACAGCAAAACCATTGTGCtg                         <  1:314116/61‑1 (MQ=255)
  aGTGTATGAACAGCAAACCTCCTGGCCGCTGGTATTGCAGAACAGCAAAACCATTGTGCtg                         <  1:210115/61‑1 (MQ=255)
  aGTGTATGAACAGCAAACCTCCTGGCCGCTGGTATTGCAGAACAGCAAAACCATTGTGCtg                         <  1:882638/61‑1 (MQ=255)
  aGTGTATGAACAGCAAACCTCCTGGCCGCTGGTATTGCAGAACAGCAAAACCATTGTGCtg                         <  1:1337307/61‑1 (MQ=255)
  aGTGTATGAACAGCAAACCTCCTGGCCGCTGGTATTGCAGAACAGCAAAACCATTGTGCtg                         <  1:1646525/61‑1 (MQ=255)
  aGTGTATGAACAGCAAACCTCCTGGCCGCTGGTATTGCAGAACAGCAAAACCATTGTGCtg                         <  1:832241/61‑1 (MQ=255)
                         ggCCGCTGGTATTGCAGAATAGCCAAACCATTGTGCTGTGGGGCTCCGATTTGCTGaaaaa  <  1:1591054/61‑1 (MQ=255)
                         ggCCGCTGGTATTGCAGAATAGCAAAACCATTGTGCTGTGGGTCTCCGATTTGCTGaaaaa  <  1:274193/61‑1 (MQ=255)
                         ggCCGCTGGTATTGCAGAATAGCAAAACCATTGTGCTGTGGGGCTCCGATTTGCTGaaata  <  1:774859/61‑3 (MQ=255)
                         ggCCGCTGGTATTGCAGAATAGCAAAACCATTGTGCTGTGGGGCTCCGATTTGCTGaaaaa  <  1:322323/61‑1 (MQ=255)
                         ggCCGCTGGTATTGCAGAATAGCAAAACCATTGTGCTGTGGGGCTCCGATTTGCTGaaaaa  <  1:547981/61‑1 (MQ=255)
                         ggCCGCTGGTATTGCAGAATAGCAAAACCATTGTGCTGTGGGGCTCCGATTTGCTGaaaaa  <  1:275305/61‑1 (MQ=255)
                         ggCCGCTGGTATTGCAGAATAGCAAAACCATTGTGCTGTGGGGCTCCGATTTGCTGaaaaa  <  1:512899/61‑1 (MQ=255)
                         ggCCGCTGGTATTGCAGAATAGCAAAACCATTGTGCTGTGGGGCTCCGATTTGCTGaaaaa  <  1:512710/61‑1 (MQ=255)
                         ggCCGCTGGTATTGCAGAATAGCAAAACCATTGTGCTGTGGGGCTCCGATTTGCTGaaaaa  <  1:505129/61‑1 (MQ=255)
                         ggCCGCTGGTATTGCAGAATAGCAAAACCATTGTGCTGTGGGGCTCCGATTTGCTGaaaaa  <  1:311053/61‑1 (MQ=255)
                         ggCCGCTGGTATTGCAGAATAGCAAAACCATTGTGCTGTGGGGCTCCGATTTGCTGaaaaa  <  1:475057/61‑1 (MQ=255)
                         ggCCGCTGGTATTGCAGAATAGCAAAACCATTGTGCTGTGGGGCTCCGATTTGCTGaaaaa  <  1:468535/61‑1 (MQ=255)
                         ggCCGCTGGTATTGCAGAATAGCAAAACCATTGTGCTGTGGGGCTCCGATTTGCTGaaaaa  <  1:364685/61‑1 (MQ=255)
                         ggCCGCTGGTATTGCAGAATAGCAAAACCATTGTGCTGTGGGGCTCCGATTTGCTGaaaaa  <  1:448199/61‑1 (MQ=255)
                         ggCCGCTGGTATTGCAGAATAGCAAAACCATTGTGCTGTGGGGCTCCGATTTGCTGaaaaa  <  1:427965/61‑1 (MQ=255)
                         ggCCGCTGGTATTGCAGAATAGCAAAACCATTGTGCTGTGGGGCTCCGATTTGCTGaaaaa  <  1:411259/61‑1 (MQ=255)
                         ggCCGCTGGTATTGCAGAATAGCAAAACCATTGTGCTGTGGGGCTCCGATTTGCTGaaaaa  <  1:383889/61‑1 (MQ=255)
                         ggCCGCTGGTATTGCAGAATAGCAAAACCATTGTGCTGTGGGGCTCCGATTTGCTGaaaaa  <  1:349167/61‑1 (MQ=255)
                         ggCCGCTGGTATTGCAGAATAGCAAAACCATTGTGCTGTGGGGCTCCGATTTGCTGaaaaa  <  1:38047/61‑1 (MQ=255)
                         ggCCGCTGGTATTGCAGAATAGCAAAACCATTGTGCTGTGGGGCTCCGATTTGCTGaaaaa  <  1:364099/61‑1 (MQ=255)
                         ggCCGCTGGTATTGCAGAATAGCAAAACCATTGTGCTGTGGGGCTCCGATTTGCTGaaaaa  <  1:760597/61‑1 (MQ=255)
                         ggCCGCTGGTATTGCAGAATAGCAAAACCATTGTGCTGTGGGGCTCCGATTTGCTGaaaaa  <  1:960139/61‑1 (MQ=255)
                         ggCCGCTGGTATTGCAGAATAGCAAAACCATTGTGCTGTGGGGCTCCGATTTGCTGaaaaa  <  1:944610/61‑1 (MQ=255)
                         ggCCGCTGGTATTGCAGAATAGCAAAACCATTGTGCTGTGGGGCTCCGATTTGCTGaaaaa  <  1:930869/61‑1 (MQ=255)
                         ggCCGCTGGTATTGCAGAATAGCAAAACCATTGTGCTGTGGGGCTCCGATTTGCTGaaaaa  <  1:918588/61‑1 (MQ=255)
                         ggCCGCTGGTATTGCAGAATAGCAAAACCATTGTGCTGTGGGGCTCCGATTTGCTGaaaaa  <  1:901811/61‑1 (MQ=255)
                         ggCCGCTGGTATTGCAGAATAGCAAAACCATTGTGCTGTGGGGCTCCGATTTGCTGaaaaa  <  1:875234/61‑1 (MQ=255)
                         ggCCGCTGGTATTGCAGAATAGCAAAACCATTGTGCTGTGGGGCTCCGATTTGCTGaaaaa  <  1:843499/61‑1 (MQ=255)
                         ggCCGCTGGTATTGCAGAATAGCAAAACCATTGTGCTGTGGGGCTCCGATTTGCTGaaaaa  <  1:83237/61‑1 (MQ=255)
                         ggCCGCTGGTATTGCAGAATAGCAAAACCATTGTGCTGTGGGGCTCCGATTTGCTGaaaaa  <  1:822352/61‑1 (MQ=255)
                         ggCCGCTGGTATTGCAGAATAGCAAAACCATTGTGCTGTGGGGCTCCGATTTGCTGaaaaa  <  1:81173/61‑1 (MQ=255)
                         ggCCGCTGGTATTGCAGAATAGCAAAACCATTGTGCTGTGGGGCTCCGATTTGCTGaaaaa  <  1:782834/61‑1 (MQ=255)
                         ggCCGCTGGTATTGCAGAATAGCAAAACCATTGTGCTGTGGGGCTCCGATTTGCTGaaaaa  <  1:514071/61‑1 (MQ=255)
                         ggCCGCTGGTATTGCAGAATAGCAAAACCATTGTGCTGTGGGGCTCCGATTTGCTGaaaaa  <  1:714920/61‑1 (MQ=255)
                         ggCCGCTGGTATTGCAGAATAGCAAAACCATTGTGCTGTGGGGCTCCGATTTGCTGaaaaa  <  1:685620/61‑1 (MQ=255)
                         ggCCGCTGGTATTGCAGAATAGCAAAACCATTGTGCTGTGGGGCTCCGATTTGCTGaaaaa  <  1:683425/61‑1 (MQ=255)
                         ggCCGCTGGTATTGCAGAATAGCAAAACCATTGTGCTGTGGGGCTCCGATTTGCTGaaaaa  <  1:634217/61‑1 (MQ=255)
                         ggCCGCTGGTATTGCAGAATAGCAAAACCATTGTGCTGTGGGGCTCCGATTTGCTGaaaaa  <  1:622526/61‑1 (MQ=255)
                         ggCCGCTGGTATTGCAGAATAGCAAAACCATTGTGCTGTGGGGCTCCGATTTGCTGaaaaa  <  1:592687/61‑1 (MQ=255)
                         ggCCGCTGGTATTGCAGAATAGCAAAACCATTGTGCTGTGGGGCTCCGATTTGCTGaaaaa  <  1:591860/61‑1 (MQ=255)
                         ggCCGCTGGTATTGCAGAATAGCAAAACCATTGTGCTGTGGGGCTCCGATTTGCTGaaaaa  <  1:572671/61‑1 (MQ=255)
                         ggCCGCTGGTATTGCAGAATAGCAAAACCATTGTGCTGTGGGGCTCCGATTTGCTGaaaaa  <  1:270983/61‑1 (MQ=255)
                         ggCCGCTGGTATTGCAGAATAGCAAAACCATTGTGCTGTGGGGCTCCGATTTGCTGaaaaa  <  1:53241/61‑1 (MQ=255)
                         ggCCGCTGGTATTGCAGAATAGCAAAACCATTGTGCTGTGGGGCTCCGATTTGCTGaaaaa  <  1:1233436/61‑1 (MQ=255)
                         ggCCGCTGGTATTGCAGAATAGCAAAACCATTGTGCTGTGGGGCTCCGATTTGCTGaaaaa  <  1:101114/61‑1 (MQ=255)
                         ggCCGCTGGTATTGCAGAATAGCAAAACCATTGTGCTGTGGGGCTCCGATTTGCTGaaaaa  <  1:1387760/61‑1 (MQ=255)
                         ggCCGCTGGTATTGCAGAATAGCAAAACCATTGTGCTGTGGGGCTCCGATTTGCTGaaaaa  <  1:1387297/61‑1 (MQ=255)
                         ggCCGCTGGTATTGCAGAATAGCAAAACCATTGTGCTGTGGGGCTCCGATTTGCTGaaaaa  <  1:138407/61‑1 (MQ=255)
                         ggCCGCTGGTATTGCAGAATAGCAAAACCATTGTGCTGTGGGGCTCCGATTTGCTGaaaaa  <  1:1375845/61‑1 (MQ=255)
                         ggCCGCTGGTATTGCAGAATAGCAAAACCATTGTGCTGTGGGGCTCCGATTTGCTGaaaaa  <  1:1357274/61‑1 (MQ=255)
                         ggCCGCTGGTATTGCAGAATAGCAAAACCATTGTGCTGTGGGGCTCCGATTTGCTGaaaaa  <  1:1348095/61‑1 (MQ=255)
                         ggCCGCTGGTATTGCAGAATAGCAAAACCATTGTGCTGTGGGGCTCCGATTTGCTGaaaaa  <  1:1346757/61‑1 (MQ=255)
                         ggCCGCTGGTATTGCAGAATAGCAAAACCATTGTGCTGTGGGGCTCCGATTTGCTGaaaaa  <  1:1320510/61‑1 (MQ=255)
                         ggCCGCTGGTATTGCAGAATAGCAAAACCATTGTGCTGTGGGGCTCCGATTTGCTGaaaaa  <  1:1316273/61‑1 (MQ=255)
                         ggCCGCTGGTATTGCAGAATAGCAAAACCATTGTGCTGTGGGGCTCCGATTTGCTGaaaaa  <  1:1265712/61‑1 (MQ=255)
                         ggCCGCTGGTATTGCAGAATAGCAAAACCATTGTGCTGTGGGGCTCCGATTTGCTGaaaaa  <  1:1430331/61‑1 (MQ=255)
                         ggCCGCTGGTATTGCAGAATAGCAAAACCATTGTGCTGTGGGGCTCCGATTTGCTGaaaaa  <  1:1203469/61‑1 (MQ=255)
                         ggCCGCTGGTATTGCAGAATAGCAAAACCATTGTGCTGTGGGGCTCCGATTTGCTGaaaaa  <  1:119910/61‑1 (MQ=255)
                         ggCCGCTGGTATTGCAGAATAGCAAAACCATTGTGCTGTGGGGCTCCGATTTGCTGaaaaa  <  1:1194128/61‑1 (MQ=255)
                         ggCCGCTGGTATTGCAGAATAGCAAAACCATTGTGCTGTGGGGCTCCGATTTGCTGaaaaa  <  1:1185442/61‑1 (MQ=255)
                         ggCCGCTGGTATTGCAGAATAGCAAAACCATTGTGCTGTGGGGCTCCGATTTGCTGaaaaa  <  1:1173683/61‑1 (MQ=255)
                         ggCCGCTGGTATTGCAGAATAGCAAAACCATTGTGCTGTGGGGCTCCGATTTGCTGaaaaa  <  1:1099500/61‑1 (MQ=255)
                         ggCCGCTGGTATTGCAGAATAGCAAAACCATTGTGCTGTGGGGCTCCGATTTGCTGaaaaa  <  1:1095052/61‑1 (MQ=255)
                         ggCCGCTGGTATTGCAGAATAGCAAAACCATTGTGCTGTGGGGCTCCGATTTGCTGaaaaa  <  1:1078976/61‑1 (MQ=255)
                         ggCCGCTGGTATTGCAGAATAGCAAAACCATTGTGCTGTGGGGCTCCGATTTGCTGaaaaa  <  1:1042644/61‑1 (MQ=255)
                         ggCCGCTGGTATTGCAGAATAGCAAAACCATTGTGCTGTGGGGCTCCGATTTGCTGaaaaa  <  1:101331/61‑1 (MQ=255)
                         ggCCGCTGGTATTGCAGAATAGCAAAACCATTGTGCTGTGGGGCTCCGATTTGCTGaaaaa  <  1:1575883/61‑1 (MQ=255)
                         ggCCGCTGGTATTGCAGAATAGCAAAACCATTGTGCTGTGGGGCTCCGATTTGCTGaaaaa  <  1:240114/61‑1 (MQ=255)
                         ggCCGCTGGTATTGCAGAATAGCAAAACCATTGTGCTGTGGGGCTCCGATTTGCTGaaaaa  <  1:239486/61‑1 (MQ=255)
                         ggCCGCTGGTATTGCAGAATAGCAAAACCATTGTGCTGTGGGGCTCCGATTTGCTGaaaaa  <  1:196190/61‑1 (MQ=255)
                         ggCCGCTGGTATTGCAGAATAGCAAAACCATTGTGCTGTGGGGCTCCGATTTGCTGaaaaa  <  1:185970/61‑1 (MQ=255)
                         ggCCGCTGGTATTGCAGAATAGCAAAACCATTGTGCTGTGGGGCTCCGATTTGCTGaaaaa  <  1:178765/61‑1 (MQ=255)
                         ggCCGCTGGTATTGCAGAATAGCAAAACCATTGTGCTGTGGGGCTCCGATTTGCTGaaaaa  <  1:170831/61‑1 (MQ=255)
                         ggCCGCTGGTATTGCAGAATAGCAAAACCATTGTGCTGTGGGGCTCCGATTTGCTGaaaaa  <  1:163908/61‑1 (MQ=255)
                         ggCCGCTGGTATTGCAGAATAGCAAAACCATTGTGCTGTGGGGCTCCGATTTGCTGaaaaa  <  1:1628986/61‑1 (MQ=255)
                         ggCCGCTGGTATTGCAGAATAGCAAAACCATTGTGCTGTGGGGCTCCGATTTGCTGaaaaa  <  1:162691/61‑1 (MQ=255)
                         ggCCGCTGGTATTGCAGAATAGCAAAACCATTGTGCTGTGGGGCTCCGATTTGCTGaaaaa  <  1:1621421/61‑1 (MQ=255)
                         ggCCGCTGGTATTGCAGAATAGCAAAACCATTGTGCTGTGGGGCTCCGATTTGCTGaaaaa  <  1:1613938/61‑1 (MQ=255)
                         ggCCGCTGGTATTGCAGAATAGCAAAACCATTGTGCTGTGGGGCTCCGATTTGCTGaaaaa  <  1:1431152/61‑1 (MQ=255)
                         ggCCGCTGGTATTGCAGAATAGCAAAACCATTGTGCTGTGGGGCTCCGATTTGCTGaaaaa  <  1:1550551/61‑1 (MQ=255)
                         ggCCGCTGGTATTGCAGAATAGCAAAACCATTGTGCTGTGGGGCTCCGATTTGCTGaaaaa  <  1:1543920/61‑1 (MQ=255)
                         ggCCGCTGGTATTGCAGAATAGCAAAACCATTGTGCTGTGGGGCTCCGATTTGCTGaaaaa  <  1:153642/61‑1 (MQ=255)
                         ggCCGCTGGTATTGCAGAATAGCAAAACCATTGTGCTGTGGGGCTCCGATTTGCTGaaaaa  <  1:1495602/61‑1 (MQ=255)
                         ggCCGCTGGTATTGCAGAATAGCAAAACCATTGTGCTGTGGGGCTCCGATTTGCTGaaaaa  <  1:147780/61‑1 (MQ=255)
                         ggCCGCTGGTATTGCAGAATAGCAAAACCATTGTGCTGTGGGGCTCCGATTTGCTGaaaaa  <  1:1455774/61‑1 (MQ=255)
                         ggCCGCTGGTATTGCAGAATAGCAAAACCATTGTGCTGTGGGGCTCCGATTTGCTGaaaaa  <  1:1442482/61‑1 (MQ=255)
                         ggCCGATGGTATTGCAGAATAGCAAAACCATTGTGCTGTGGGGCTCCGATTTGCTGaaaaa  <  1:1569475/61‑1 (MQ=255)
                          gCCGCTGGTATTGCATAATAGCAAAACCATTGTGCTGTGGGGCTCCGATTTGCTGaaaaa  <  1:707599/60‑1 (MQ=255)
                          gCCGCTGGTATTGCAGAATAGCAAAACCATTGTGCTGTGGGGCTCCGATTTGCTGaaaaa  <  1:653470/60‑1 (MQ=255)
                          gCCGCTGGTATTGCAGAATAGCAAAACCATTGTGCTGTGGGGCTCCGATTTGCTGaaaaa  <  1:54880/60‑1 (MQ=255)
                           ccGCTGGTATTGCAGAATAGCAAAACCATTGTGCTGTGGGGCTCCGATTTGCTGaaaaa  <  1:327961/59‑1 (MQ=255)
                                            |                                         
GAAGTGTATGAACAGCAAACCTCCTGGCCGCTGGTATTGCAGAACAGCAAAACCATTGTGCTGTGGGGCTCCGATTTGCTGAAAAA  >  W3110S.gb/1060296‑1060381

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

GATK/CNVnator alignment

N/A