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 F3 I0 R2
|
260 |
44.3 |
3360226 |
90.5% |
3041004 |
64.6 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
3,447,843 |
A→G |
40.0% |
V1163V (GTT→GTC) |
rpoC ← |
RNA polymerase, beta prime subunit |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 3,447,843 | 0 | A | G | 40.0%
| 32.1
/ 61.9
| 55 | V1163V (GTT→GTC) | rpoC | RNA polymerase, beta prime subunit |
| Reads supporting (aligned to +/- strand): ref base A (10/23); new base G (16/6); total (26/29) |
| Fisher's exact test for biased strand distribution p-value = 2.70e-03 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
CGGATCGCTACCGTCTACCGGGGTGATAACCAGACGACGTTTACCTTTGGTTTCTTTACCGAAGGAAACGATACCGCTGATTTCAGCCAGGATTGCCGGCTCTTTCGGACGACGTGCTTCGAAC > W3110S.gb/3447777‑3447900
|
cGGATCGCTACCGTCTACCGGGGTGATAACCAGACGACGTTTACCTTTGGTTTCTTTACCGAAGGAAACGa > 1:1870053/1‑71 (MQ=255)
cGGATCGCTACCGTCTACCGGGGTGATAACCAGACGACGTTTACCTTTGGTTTCTTTACCGAAGGAAACGa > 1:2426986/1‑71 (MQ=255)
cGGATCGCTACCGTCTACCGGGGTGATAACCAGACGACGTTTACCTTTGGTTTCTTTACCGAAGGAAACGa > 1:329959/1‑71 (MQ=255)
cGGATCGCTACCGTCTACCGGGGTGATAACCAGACGACGTTTACCTTTGGTTTCTTTACCGAAGGAAACGa > 1:1624221/1‑71 (MQ=255)
ggATCGCTACCGTCTACCGGGGTGATAACCAGACGACGTTTACCTTTGGTTTCTTTACCGAAGGAGACGAt < 1:106428/71‑1 (MQ=255)
ggATCGCTACCGTCTACCGGGGTGATAACCAGACGACGTTTACCTTTGGTTTCTTTACCGAAGGAGACGAt < 1:2068671/71‑1 (MQ=255)
cGCTACCGTCTACCGGGGTGATAACCAGACGACGTTTACCTTTGGTTTCTTTACCGAAGGAGACGATACCg > 1:1440458/1‑71 (MQ=255)
cGCTACCGTCTACCGGGGTGATAACCAGACGACGTTTACCTTTGGTTTCTTTACCGAAGGAGACGATACCg > 1:1878513/1‑71 (MQ=255)
cGCTACCGTCTACCGGGGTGATAACCAGACGACGTTTACCTTTGGTTTCTTTACCGAAGGAGACGATACCg > 1:1705778/1‑71 (MQ=255)
cGCTACCGTCTACCGGGGTGATAACCAGACGACGTTTACCTTTGGTTTCTTTACCGAAGGAGACGATACCg > 1:2585386/1‑71 (MQ=255)
cGCTACCGTCTACCGGGGTGATAACCAGACGACGTTTACCTTTGGTTTCTTTACCGAAGGAGACGATACCg > 1:2644798/1‑71 (MQ=255)
cGCTACCGTCTACCGGGGTGATAACCAGACGACGTTTACCTTTGGTTTCTTTACCGAAGGAGACGATACCg > 1:1228302/1‑71 (MQ=255)
cGCTACCGTCTACCGGGGTGATAACCAGACGACGTTTACCTTTGGTTTCTTTACCGAAGGAGACGATACCg > 1:573356/1‑71 (MQ=255)
cGCTACCGTCTACCGGGGTGATAACCAGACGACGTTTACCTTTGGTTTCTTTACCGAAGGAGACGATACCg > 1:630809/1‑71 (MQ=255)
cTACCGTCTACCGGGGTGATAACCAGACGACGTTTACCTTTGGTTTCTTTACCGAAGGAAACGATACCGCt < 1:2115174/71‑1 (MQ=255)
cTACCGTCTACCGGGGTGATAACCAGACGACGTTTACCTTTGGTTTCTTTACCGAAGGAAACGATACCGCt < 1:2552274/71‑1 (MQ=255)
cTACCGTCTACCGGGGTGATAACCAGACGACGTTTACCTTTGGTTTCTTTACCGAAGGAAACGATACCGCt < 1:2460382/71‑1 (MQ=255)
cTACCGTCTACCGGGGTGATAACCAGACGACGTTTACCTTTGGTTTCTTTACCGAAGGAAACGATACCGCt < 1:3071742/71‑1 (MQ=255)
cTACCGTCTACCGGGGTGATAACCAGACGACGTTTACCTTTGGTTTCTTTACCGAAGGAAACGATACCGCt < 1:335481/71‑1 (MQ=255)
cTACCGTCTACCGGGGTGATAACCAGACGACGTTTACCTTTGGTTTCTTTACCGAAGGAAACGATACCGCt < 1:2042538/71‑1 (MQ=255)
cTACCGTCTACCGGGGTGATAACCAGACGACGTTTACCTTTGGTTTCTTTACCGAAGGAAACGATACCGCt < 1:1155078/71‑1 (MQ=255)
cTACCGTCTACCGGGGTGATAACCAGACGACGTTTACCTTTGGTTTCTTTACCGAAGGAAACGATACCGCt < 1:1103929/71‑1 (MQ=255)
tACCGTCTACCGGGGTGATAACCAGACGACGTTTACCTTTGGTTTCTTTACCGAAGGAAACGATACCGCt < 1:2295096/70‑1 (MQ=255)
ccGGGGTGATAACCAGACGACGTTTACCTTTGGTTTCTTTACCGAAGGAGACGATACCGCTGATTTCAGc > 1:2009784/1‑70 (MQ=255)
ccGGGGTGATAACCAGACGACGTTTACCTTTGGTTTCTTTACCGAAGGAGACGATACCGCTGATTTCAGc > 1:3252396/1‑70 (MQ=255)
ccGGGGTGATAACCAGACGACGTTTACCTTTGGTTTCTTTACCGAAGGAGACGATACCGCTGATTTCAGc > 1:1349750/1‑70 (MQ=255)
ccGGGGTGATAACCAGACGACGTTTACCTTTGGTTTCTTTACCGAAGGAGACGATACCGCTGATTTCAGc > 1:2122105/1‑70 (MQ=255)
ccGGGGTGATAACCAGACGACGTTTACCTTTGGTTTCTTTACCGAAGGAGACGATACCGCTGATTTCAGc > 1:205370/1‑70 (MQ=255)
ccGGGGTGATAACCAGACGACGATTACCTTTGGTTTCTTTACCCAAGGAGACGATACCGCTGAATTCAGc > 1:2487373/1‑70 (MQ=255)
gTGATAACCAGACGACGTTTACCTTTGGTTTCTTTACCGAAGGAAACGATACCGCt < 1:1513964/56‑1 (MQ=255)
tGATAACCAGACGACGTTTACCTTTGGTTTCTTTACCGAAGGAAACGATACCGCTGATTTCAGCCAg < 1:2105641/67‑1 (MQ=255)
tGATAACCAGACGACGTTTACCTTTGGTTTCTTTACCGAAGGAAACGATACCGCTGATTTCAGCCAg < 1:882115/67‑1 (MQ=255)
tGATAACCAGACGACGTTTACCTTTGGTTTCTTTACCGAAGGAAACGATACCGCTGATTTCAGCCAg < 1:235268/67‑1 (MQ=255)
aCCAGACGACGTTTACCTTTGGTTTCTTTACCGAAGGAAACGATACCGCTGATTTCAGCCAGGATTGCCgg > 1:2180254/1‑71 (MQ=255)
aCCAGACGACGTTTACCTTTGGTTTCTTTACCGAAGGAAACGATACCGCTGATTTCAGCCAGGATTGCCgg > 1:1055099/1‑71 (MQ=255)
aCCAGAAGACGTTTACCTTTGGTTTCTTTACCGAAGGAAACGATACCGCTGATTTCAGCCAGGATTGCCgg > 1:430082/1‑71 (MQ=255)
aGACGACGTTTACCTTTGGTTTCTTTACCGAAGGAGACGa > 1:944820/1‑40 (MQ=255)
aGACGACGTTTACCTTTGGTTTCTTTACCGAAGGAGACGa > 1:757260/1‑40 (MQ=255)
acgacgTTTACCTTTGGTTTCTTTACCGAAGGAAACGATACCGCTGATTTCAGCCAGGAtt < 1:171923/61‑1 (MQ=255)
acgacgTTTACCTTTGGTTTCTTTACCGAAGGAAACGATACCGCTGATTTCAGCCAGGAtt < 1:1309856/61‑1 (MQ=255)
acgacgTTTACCTTTGGTTTCTTTACCGAAGGAAACGATACCGCTGATTTCAGCCAGGAtt < 1:99111/61‑1 (MQ=255)
acgacgTTTACCTTTGGTTTCTTTACCGAAGGAAACGATACCGCTGATTTCAGCCAGGAtt < 1:1140273/61‑1 (MQ=255)
acgacgTTTACCTTTGGTTTCTTTACCGAAGGAAACGATACCGCTGATTTCAGCCAGGAtt < 1:1716064/61‑1 (MQ=255)
acgacgTTTACCTTTGGTTTCTTTACCGAAGGAAACGATACCGCTGATTTCAGCCAGGAtt < 1:78395/61‑1 (MQ=255)
acgacgTTTACCTTTGGTTTCTTTACCGAAGGAAACGATACCGCTGATTTCAGCCAGGAtt < 1:2302239/61‑1 (MQ=255)
acgacgTTTACCTTTGGTTTCTTTACCGAAGGAAACGATACCGATGATTTCAGCCAGGAtt < 1:1319028/61‑1 (MQ=255)
acgTTTACCTTTGGTTTCTTTACCGAAGGAGACGATACCGCTGATTTCAGCCAGGATTGCCGGCTCTTTCg < 1:2038439/71‑1 (MQ=255)
acgTTTACCTTTGGTTTCTTTACCGAAGGAGACGATACCGCTGATTTCAGCCAGGATTGCCGGCTCTTTCg < 1:1409830/71‑1 (MQ=255)
acgTTTACCTTTGGTTTCTTTACCGAAGGAGACGATACCGCTGATTTCAGCCAGGATTGCCGGCTCTTTCg < 1:2304200/71‑1 (MQ=255)
ttACCTTTGGTTTCTTTACCGAAGGAAACGATACCGCt < 1:1700541/38‑1 (MQ=255)
tttCTTTACCGAAGGAAACGATACCGCTGATTTCAGCCAGGATTGCCGGCTCTTTCGGACGACGTGCTTc > 1:2785892/1‑70 (MQ=255)
tttCTTTACCGAAGGAAACGATACCGCTGATTTCAGCCAGGATTGCCGGCTCTTTCGGACGACGTGCTTc > 1:2324136/1‑70 (MQ=255)
tttCTTTACCGAAGGAAACGATACCGCTGATTTCAGCCAGGATTGCCGGCTCTTTCGGACGACGTGCTTc > 1:208957/1‑70 (MQ=255)
cTTTACCGAAGGAAACGATACCGCTGATTTCAGCCAGGATTGCCGGCTCTTTCGGACGACGTGCTTCGaa < 1:1941559/70‑1 (MQ=255)
tACCGAAGGAGACGATACCGCTGATTTCAGCCAGGATTGCCGGCTCTTTCGGACGACGTGCTTCGAAc < 1:2325733/68‑1 (MQ=255)
|
CGGATCGCTACCGTCTACCGGGGTGATAACCAGACGACGTTTACCTTTGGTTTCTTTACCGAAGGAAACGATACCGCTGATTTCAGCCAGGATTGCCGGCTCTTTCGGACGACGTGCTTCGAAC > W3110S.gb/3447777‑3447900
|
| 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
