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 F17 I0 R2
|
276 |
45.3 |
3729697 |
93.0% |
3468618 |
60.6 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
2,773,435 |
T→C |
77.1% |
L488L (TTG→CTG) |
yfjW → |
predicted inner membrane protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 2,773,435 | 0 | T | C | 77.1%
| 123.9
/ 33.6
| 61 | L488L (TTG→CTG) | yfjW | predicted inner membrane protein |
| Reads supporting (aligned to +/- strand): ref base T (2/12); new base C (18/29); total (20/41) |
| Fisher's exact test for biased strand distribution p-value = 1.16e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.62e-01 |
TTTAGTATCAACGGGAAACATTTGTCGTTAAGGCCAGAATCGGAGATTATTATTTCTGAAGGGAGTTTGTATGGACTAGTTAATAAAAGCAAAAAAATCAAAATATATGGCACAGCAGATCTTGTTTTTGTT > W3110S.gb/2773369‑2773500
|
tttAGTATCAACGGGAAACATTTGTCGTTAAGGCCAGAATCGGAGATTATTATTTCTGAAGGGAGTTTg < 1:2938315/69‑1 (MQ=255)
tttAGTATCAACGGGAAACATTTGTCGTTAAGGCCAGAATCGGAGATTATTATTTCTGAAGGGAGTTTg < 1:1882522/69‑1 (MQ=255)
tttAGTATCAACGGGAAACATTTGTCGTTAAGGCCAGAATCGGAGATTATTATTTCTGAAGGGAGTTTg < 1:2584103/69‑1 (MQ=255)
tAGTATCAACGGGAAACATTTGTCGTTAAGGCCAGAATCGGAGATTATTATTTCTGAAGGGAGTTTGTa < 1:3029993/69‑1 (MQ=255)
tAGTATCAACGGGAAACATTTGTCGTTAAGGCCAGAATCGGAGATTATTATTTCTGAAGGGAGTTTGTa < 1:3492264/69‑1 (MQ=255)
tCAACGGGAAACATTTGTCGTTAAGGCCAGAATCGGAGATTATTATTTCTGAAGGGAGTTTGTATgg > 1:1306124/1‑67 (MQ=255)
tCAACGGGAAACATTTGTCGTTAAGGCCAGAATCGGAGATTATTATTTCTGAAGGGAGTTTGTATgg > 1:2734695/1‑67 (MQ=255)
tCAACGGGAAACATTTGTCGTTAAGGCCAGAATCGGAGATTATTATTTCTGAAGGGAGTCTGTATgg > 1:1659475/1‑67 (MQ=255)
tCAACGGGAAACATTTGTCGTTAAGGCCAGAATCGGAGATTATTATTTCTGAAGGGAGTCTGTATgg > 1:3088037/1‑67 (MQ=255)
aaCGGGAAACATTTGTCGTTAAGGCCAGAATCGGAGATTATTATTTCTGAAGGGAGTCTGTATgg > 1:1987211/1‑65 (MQ=255)
aaCGGGAAACATTTGTCGTTAAGGCCAGAATCGGAGATTATTATTTCTGAAGGGAGTCTGTATGGa > 1:1524728/1‑66 (MQ=255)
aaCGGGAAACATTTGTCGTTAAGGCCAGAATCGGAGATTATTATTTCTGAAGGGAGTCTGTATGGa > 1:3603445/1‑66 (MQ=255)
aaCGGGAAACATTTGTCGTTAAGGCCAGAATCGGAGATTATTATTTCTGAAGGGAGTCTGTATGGa > 1:2020042/1‑66 (MQ=255)
aCGGGAAACATTTGTCGTTAAGGCCAGAATCGGAGATTATTATTTCTGAAGGGAGTCTg < 1:2765577/59‑1 (MQ=255)
gggAAACATTTGTCGTTAAGGCCAGAATCGGAGATTATTATTTCTGAAGGGAGTCTGTATGGAc > 1:1960779/1‑64 (MQ=255)
aaaCATTTGTCGTTAAGGCCAGAATCGGAGATTATTATTTCTGAAGGGAGTTTg < 1:3680896/54‑1 (MQ=255)
aaaCATTTGTCGTTAAGGCCAGAATCGGAGATTATTATTTCTGAAGGGAGTTTg < 1:3518098/54‑1 (MQ=255)
aaCATTTGTCGTTAAGGCCAGAATCGGAGATTATTATTTCTGAAGGGAGTCTGt < 1:2604441/54‑1 (MQ=255)
aaCATTTGTCGTTAAGGCCAGAATCGGAGATTATTATTTCTGAAGGGAGTCTGt < 1:2759155/54‑1 (MQ=255)
aTTTGTCGTTAAGGCCAGAATCGGAGATTATTATTTCTGAAGGGAGTCTGTATGGACTAGTTAATaaa > 1:759659/1‑68 (MQ=255)
tttGTCGTTAAGGCCAGAATCGGAGATTATTATTTCTGAAGGTAGTCTg < 1:8440/49‑1 (MQ=255)
tttGTCGTTAAGGCCAGAATCGGAGATTATTATTTCTGAAGGGAGTCTGTa < 1:1478391/51‑1 (MQ=255)
ttGTCGTTAAGGCCAGAATCGGAGATTATTATTTCTGAAGGGAGTCTg > 1:2961680/1‑48 (MQ=255)
ttGTCGTTAAGGCCAGAATCGGAGATTATTATTTCTGAAGGGAGTCTg > 1:2595873/1‑48 (MQ=255)
ttGTCGTTAAGGCCAGAATCGGAGATTATTATTTCTGAAGGGAGTCTg > 1:1457784/1‑48 (MQ=255)
ttGTCGTTAAGGCCAGAATCGGAGATTATTATTTCTGAAGGGAGTCTg > 1:1381186/1‑48 (MQ=255)
tGTCGTTAAGGCCAGAATCGGAGATTATTATTTCTGAAGGGAGTCTg < 1:2339853/47‑1 (MQ=255)
tGTCGTTAAGGCCAGAATCGGAGATTATTATTTCTGAAGGGAGTCTg < 1:2511821/47‑1 (MQ=255)
tGTCGTTAAGGCCAGAATCGGAGATTATTATTTCTGAAGGGAGTCTg < 1:206949/47‑1 (MQ=255)
tGTCGTTAAGGCCAGAATCGGAGATTATTATTTCTGAAGGGAGTCTg < 1:184287/47‑1 (MQ=255)
tGTCGTTAAGGCCAGAATCGGAGATTATTATTTCTGAAGGGAGTCTg < 1:708338/47‑1 (MQ=255)
tGTCGTTAAGGCCAGAATCGGAGATTATTATTTCTGAAGGGAGTCTg < 1:1316245/47‑1 (MQ=255)
tGTCGTTAAGGCCAGAATCGGAGATTATTATTTCTGAAGGGAGTCTg < 1:382055/47‑1 (MQ=255)
gTTAAGGCCAGAATCGGAGATTATTATTTCTGAAGGGAGTCTGTATGGACTAGTTAATAAAAGCaaaaa < 1:3650182/69‑1 (MQ=255)
tAAGGCCAGAATCGGAGATTATTATTTCTGAAGGGAGTCTGTATGGACTAGTTAATAAAAGCaaaaaa < 1:2423633/68‑1 (MQ=255)
gCCAGAATCGGAGATTATTATTTCTGAAGGGAGTTTGTATGGACTAGTTAATAAAAGCAAAAAAATCaa < 1:1451524/69‑1 (MQ=255)
gCCAGAATCGGAGATTATTATTTCTGAAGGGAGTCTGTATGGACTAGTTAATAAAAGCAAAAAAATCaa < 1:1724358/69‑1 (MQ=255)
gAATCGGAGATTATTATTTCTGAAGGGAGTCTGTATGGACTAGTTAATAAAAGCAAAAAAATCAAAata < 1:306027/69‑1 (MQ=255)
gAATCGGAGATTATTATTTCTGAAGGGAGTCTGTATGGACTAGTTAATAAAAGCAAAAAAATCAAAata < 1:520746/69‑1 (MQ=255)
aaTCGGAGATTATTATTTCTGAAGGGAGTTTGTATGGACTAGTTAATAAAAGCAAAAAAATCAAAatat < 1:2544652/69‑1 (MQ=255)
aTCGGAGATTATTATTTCTGAAGGGAGTCTGTATGGACTAGTTAATAAAAGCAAAAAAATCAAAatata < 1:2633674/69‑1 (MQ=255)
aTCGCAGATTATTATTTCTGAAGGGAGTCTGTATGGACTAGTTAATAAAAGCAAAAAAATCAAAata < 1:785020/67‑1 (MQ=255)
tattattTCTGAAGGGAGTTTGTATGGACTAGTtaata < 1:922356/38‑1 (MQ=255)
tattattTCTGAAGGGAGTCTGTATGGACTAGTTAATAAAAGCaaaaaa < 1:3230654/49‑1 (MQ=255)
tattattTCTGAAGGGAGTCTGTATGGACTAGTTAATAAAAGCaaaaaa < 1:3238107/49‑1 (MQ=255)
tattattTCTGAAGGGAGTCTGTATGGACTAGTTAATAAAAGCaaaaaa < 1:796385/49‑1 (MQ=255)
tattattTCTGAAGGGAGTCTGTATGGACTAGTTAATAAAAGCAAAAAAATCAAAatatat > 1:604809/1‑61 (MQ=255)
tattattTCTGAAGGGAGTCTGTATGGACTAGTTAATAAAAGCAAAAAAATCAAAatatat > 1:166518/1‑61 (MQ=255)
tattattTCTGAAGGGAGTCTGTATGGACTAGTTAATAAAAGCAAAAAAATCAAAatatat > 1:1629515/1‑61 (MQ=255)
attattTCTGAAGGGAGTCTGTATGGACTAGTTAATAAAAGCAAAAAAATCAAAATATATGGcac > 1:1842213/1‑65 (MQ=255)
attattTCTGAAGGGAGTCTGTATGGACTAGTTAATAAAAGCAAAAAAATCAAAATATATGGcac > 1:400905/1‑65 (MQ=255)
attattTCTGAAGGGAGTCTGTATGGACTAGTTAATAAAAGCAAAAAAATCAAAATATATGGCAcagca < 1:3552394/69‑1 (MQ=255)
tCTGAAGGGAGTTTGTATGGACTAGTTAATAAAAGCAAAAAAATCAAAATATATGGCACAGCAGATCtt < 1:1288576/69‑1 (MQ=255)
cTGAAGGGAGTCTGTATGGACTAGTTAATAAAAGCAAAAAAATCAAAATATATGGCACAGCAGATCTTg > 1:2785976/1‑69 (MQ=255)
gggAGTCTGTATGGACTAGTTAATAAAAGCAAAAAAATCAAAATATATGGCACAGCAGATCTTGtt < 1:2639406/66‑1 (MQ=255)
gggAGTCTGTATGGACTAGTTAATAAAAGCAAAAAAATCAAAATATATGGCACAGCAGATCTTGtt < 1:148082/66‑1 (MQ=255)
gggAGTCTGTATGGACTAGTTAATAAAAGCAAAAAAATCAAAATATATGGCACAGCAGATCTTGtt < 1:991559/66‑1 (MQ=255)
ggAGTTTGTATGGACTAGTTAATAAAAGCAAAAAAATCAAAATATATGGCACAGCAGATCTTGTTTttg < 1:1394944/69‑1 (MQ=255)
aGTCTGTATGGACTAGTTAATAAAAGCAAAAAAATCAAAATATATGGCACAGCAGATCTTGTTTttgtt < 1:2449733/69‑1 (MQ=255)
aGTCTGTATGGACTAGTTAATAAAAGCAAAAAAATCAAAATATATGGCACAGCAGATCTTGTTTttgtt < 1:1839774/69‑1 (MQ=255)
aGTCTGTATGGACTAGTTAATAAAAGCAAAAAAATCAAAATATATGGCACAGCAGATCTTGTTTttgtt < 1:117513/69‑1 (MQ=255)
|
TTTAGTATCAACGGGAAACATTTGTCGTTAAGGCCAGAATCGGAGATTATTATTTCTGAAGGGAGTTTGTATGGACTAGTTAATAAAAGCAAAAAAATCAAAATATATGGCACAGCAGATCTTGTTTTTGTT > W3110S.gb/2773369‑2773500
|
| 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
