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 |
2,669,838 |
T→C |
20.0% |
V92A (GTT→GCT) |
hcaC → |
3‑phenylpropionate dioxygenase, predicted ferredoxin subunit |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 2,669,838 | 0 | T | C | 20.0%
| 122.6
/ 27.6
| 60 | V92A (GTT→GCT) | hcaC | 3‑phenylpropionate dioxygenase, predicted ferredoxin subunit |
| Reads supporting (aligned to +/- strand): ref base T (3/45); new base C (10/2); total (13/47) |
| Fisher's exact test for biased strand distribution p-value = 2.24e-07 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.12e-01 |
TTTGCCTGAAAACGGGGAAAGCGTTATGCCTGCCCGCCACCGATCCGCTCACCACTTATCCAGTACACGTTGAAGGTGGTGACATTTTCATCGACTTACCGGAGGCGCAGCCATGAGCGA > W3110S.gb/2669769‑2669888
|
tttGCCTGAAAACGGGGAAAGCGTTATGCCTGCCCGCCACCGATCCGCTCACCACTTATCCAGTACACGtt > 1:1421831/1‑71 (MQ=255)
tttGCCTGAAAACGGGGAAAGCGTTATGCCTGCCCGCCACCGATCCGCTCACCACTTATCCAGTACACGtt > 1:11618/1‑71 (MQ=255)
gCCTGAAAACGGGGAAAGCGTTATGCCTGCCCGCCACCGATCCGCTCACCACTTATCCAGTACACGTTg > 1:2854396/1‑69 (MQ=255)
gCCTGAAAACGGGGAAAGCGTTATGCCTGCCCGCCACCGATCCGCTCACCACTTATCCAGTACACGTTg > 1:1595849/1‑69 (MQ=255)
aaGCGTTATGCCTGCCCGCCACCGATCCGCTCACCACTTATCCAGTACACGTTGAAGGTGGTGACATTTTc < 1:2649662/71‑1 (MQ=255)
aaGCGTTATGCCTGCCCGCCACCGATCCGCTCACCACTTATCCAGTACACGTTGAAGGTGGTGACATTTTc < 1:1298756/71‑1 (MQ=255)
aaGCGTTATGCCTGCCCGCCACCGATCCGCTCACCACTTATCCAGTACACGTTGAAGGTGGTGACATTTTc < 1:3037676/71‑1 (MQ=255)
aaGCGTTATGCCTGCCCGCCACCGATCCGCTCACCACTTATCCAGTACACGTTGAAGGTGGTGACATTTTc < 1:1840115/71‑1 (MQ=255)
aaGCGTTATGCCTGCCCGCCACCGATCCGCTCACCACTTATCCAGTACACGTTGAAGGTGGTGACATTTTc < 1:51258/71‑1 (MQ=255)
aaGCGTTATGCCTGCCCGCCACCGATCCGCTCACCACTTATCCAGTACACGTTGAAGGTGGTGACATTTTc < 1:1480627/71‑1 (MQ=255)
aaGCGTTATGCCTGCCCGCCACCGATCCGCTCACCACTTATCCAGTACACGTTGAAGGTGGTGACATTTTc < 1:157119/71‑1 (MQ=255)
aaGCGTTATGCCTGCCCGCCACCGATCCGCTCACCACTTATCCAGTACACGTTGAAGGTGGTGACATTTTc < 1:9558/71‑1 (MQ=255)
cGTTATGCCTGCCCGCCACCGATCCGCTCACCACTTATCCAGTACACGTTGAAGGTGGTGACATTTTCATc < 1:2606361/71‑1 (MQ=255)
cGTTATGCCTGCCCGCCACCGATCCGCTCACCACTTATCCAGTACACGTTGAAGGTGGTGACATTTTCATc < 1:559271/71‑1 (MQ=255)
cGTTATGCCTGCCCGCCACCGATCCGCTCACCACTTATCCAGTACACGTTGAAGGTGGTGACATTTTCATc < 1:2179159/71‑1 (MQ=255)
cGTTATGCCTGCCCGCCACCGATCCGCTCACCACTTATCCAGTACACGTTGAAGGTGGTGACATTTTCATc < 1:1883753/71‑1 (MQ=255)
cGTTATGCCTGCCCGCCACCGATCCGCTCACCACTTATCCAGTACACGTTGAAGGTGGTGACATTTTCATc < 1:3253586/71‑1 (MQ=255)
cGTTATGCCTGCCCGCCACCGATCCGCTCACCACTTATCCAGTACACGTTGAAGGTGGTGACATTTTCATc < 1:3305812/71‑1 (MQ=255)
cGTTATGCCTGCCCGCCACCGATCCGCTCACCACTTATCCAGTACACGTTGAAGGTGGTGACATTTTCATc < 1:3345008/71‑1 (MQ=255)
cGTTATGCCTGCCCGCCACCGATCCGCTCACCACTTATCCAGTACACGTTGAAGGTGGTGACATTTTCATc < 1:353331/71‑1 (MQ=255)
cGTTATGCCTGCCCGCCACCGATCCGATCACCACTTATCCAGTACACGTTGAAGGTGGTGACATTTTCATc < 1:1630095/71‑1 (MQ=255)
gTTATGCCTGCCCGCCACCGATCCGCTCACCACTTATCCAGTACACGTTGAAGGTGTTGACATTTTCATc < 1:2850649/70‑1 (MQ=255)
ttATGCCTGCCCGCCACCGATCCGCTCACCACTTATCCAGTACACGCTGAAGGTGGTGACATTTTCATCGa < 1:1967792/71‑1 (MQ=255)
ttATGCCTGCCCGCCACCGATCCGCTCACCACTTATCCAGTACACGCTGAAGGTGGTGACATTTTCATCGa < 1:1980692/71‑1 (MQ=255)
aTGCCTGCCCGCCACCGATCCGCTCACCACTTATCCAGTACACGCTGaa > 1:1468978/1‑49 (MQ=255)
aTGCCTGCCCGCCACCGATCCGCTCACCACTTATCCAGTACACGCTGaa > 1:2539597/1‑49 (MQ=255)
aTGCCTGCCCGCCACCGATCCGCTCACCACTTATCCAGTACACGCTGaa > 1:436448/1‑49 (MQ=255)
aTGCCTGCCCGCCACCGATCCGCTCACCACTTATCCAGTACACGCTGaa > 1:2739160/1‑49 (MQ=255)
aTGCCTGCCCGCCACCGATCCGCTCACCACTTATCCAGTACACGCTGaa > 1:2778038/1‑49 (MQ=255)
aTGCCTGCCCGCCACCGATCCGCTCACCACTTATCCAGTACACGCTGaa > 1:1315510/1‑49 (MQ=255)
aTGCCTGCCCGCCACCGATCCGCTCACCACTTATCCAGTACACGCTGaa > 1:2023138/1‑49 (MQ=255)
aTGCCTGCCCGCCACCGATCCGCTCACCACTTATCCAGTACACGCTGaa > 1:132338/1‑49 (MQ=255)
tgcctgccCGCCACCGATCCGCTCACCACTTATCCAGTACACGTTGAAGGTGGTGACATTTTCATCGACtt < 1:2781980/71‑1 (MQ=255)
tgcctgccCGCCACCGATCCGCTCACCACTTATCCAGTACACGTTGAAGGTGGTGACATTTTCATCGACtt < 1:722863/71‑1 (MQ=255)
tgcctgccCGCCACCGATCCGCTCACCACTTATCCAGTACACGTTGAAGGTGGTGACATTTTCATCGACtt < 1:1215624/71‑1 (MQ=255)
tgcctgccCGCCACCGATCCGCTCACCACTTATCCAGTACACGTTGAAGGTGGTGACATTTTCATCGACtt < 1:1271370/71‑1 (MQ=255)
tgcctgccCGCCACCGATCCGCTCACCACTTATCCAGTACACGTTGAAGGTGGTGACATTTTCATCGACtt < 1:1327519/71‑1 (MQ=255)
tgcctgccCGCCACCGATCCGCTCACCACTTATCCAGTACACGTTGAAGGTGGTGACATTTTCATCGACtt < 1:860309/71‑1 (MQ=255)
tgcctgccCGCCACCGATCCGCTCACCACTTATCCAGTACACGTTGAAGGTGGTGACATTTTCATCGACtt < 1:1391255/71‑1 (MQ=255)
tgcctgccCGCCACCGATCCGCTCACCACTTATCCAGTACACGTTGAAGGGGGTGACATTTTCATCGACtt < 1:1337752/71‑1 (MQ=255)
gCCACCGATCCGCTCACCACTTATCCAGTACACGTTGAAGGTGGTGACATTTTCATCGACTTACCGGAGgc < 1:609132/71‑1 (MQ=255)
gCCACCGATCCGCTCACCACTTATCCAGTACACGTTGAAGGTGGTGACATTTTCATCGACTTACCGGAGgc < 1:836042/71‑1 (MQ=255)
gCCACCGATCCGCTCACCACTTATCCAGTACACGTTGAAGGTGGTGACATTTTCATCGACTTACCGGAGgc < 1:2913677/71‑1 (MQ=255)
gCCACCGATCCGCTCACCACTTATCCAGTACACGTTGAAGGTGGTGACATTTTCATCGACTTACCGGAGgc < 1:185384/71‑1 (MQ=255)
cGATCCGCTCACCACTTCTCCAGTACACGTTGAAGGTGGTGACATTTTCATCGACtt < 1:3330984/57‑1 (MQ=255)
cGATCCGCTCACCACTTATCCAGTACACGTTGAAGGTGGTGACATTTTCATCGACTTACCGGAGGCGCAGc < 1:2767997/71‑1 (MQ=255)
cGATCCGCTCACCACTTATCCAGTACACGTTGAAGGTGGTGACATTTTCATCGACTTACCGGAGGCGCAGc < 1:2886458/71‑1 (MQ=255)
cGATCCGCTCACCACTTATCCAGTACACGTTGAAGGTGGTGACATTTTCATCGACTTACCGGAGGCGCAGc < 1:330873/71‑1 (MQ=255)
ccGCTCACCACTTATCCAGTACACGTTGAAGGTGGTGACATTTTCATCGACTTACCGGAGGCGCAGCCAt > 1:2381187/1‑70 (MQ=255)
ccGCTCACCACTTATCCAGTACACGCTGAAGGTGGTGACATTTTCATCGACTTACCGGAg > 1:3049595/1‑60 (MQ=255)
ccGCTCACCACTTATCCAGTACACGCTGAAGGTGGTGACATTTTCATCGACTTACCGGAg > 1:1872299/1‑60 (MQ=255)
cGCTCACCACTTATCCAGTACACGTTGAAGGTGGTGACATTTTCATCGACTTACCGGAGGCGCAGc < 1:2430510/66‑1 (MQ=255)
caccacTTATCCAGTACACGTTGAAGGTGGTGACATTTTCATCGACTTACCGGAGGCGCTGc < 1:3214002/62‑1 (MQ=255)
accacTTATCCAGTACACGTTGAAGGTGGTGACATTTTCATCGACTTACCGGAGGCGCAGCCATGAGCGa < 1:956981/70‑1 (MQ=255)
accacTTATCCAGTACACGTTGAAGGTGGTGACATTTTCATCGACTTACCGGAGGCGCAGCCATGAGCGa < 1:3231882/70‑1 (MQ=255)
accacTTATCCAGTACACGTTGAAGGTGGTGACATTTTCATCGACTTACCGGAGGCGCAGCCATGAGCGa < 1:2271703/70‑1 (MQ=255)
accacTTATCCAGTACACGTTGAAGGTGGTGACATTTTCATCGACTTACCGGAGGCGCAGCCATGAGCGa < 1:2211721/70‑1 (MQ=255)
accacTTATCCAGTACACGTTGAAGGTGGTGACATTTTCATCGACTTACCGGAGGCGCAGCCATGAGCGa < 1:2117043/70‑1 (MQ=255)
accacTTATCCAGTACACGTTGAAGGTGGTGACATTTTCATCGACTTACCGGAGGCGCAGCCATGAGCGa < 1:1678385/70‑1 (MQ=255)
accacTTATCCAGTACACGTTGAAGGTGGTGACATTTTCATCGACTTACCGGAGGCGCAGCCATGAGCGa < 1:1638898/70‑1 (MQ=255)
ccacTTATCCAGTACACGTTGAAGGTGGTGACATTTTCATCGACTTACCGGAGGCGCAGCCATGAGCGa < 1:2458628/69‑1 (MQ=255)
ccacTTATCCAGTACACGTTGAAGGTGGTGACATTTTCATCGACTTACCGGAGGCGCAGCCATGAGCGa < 1:183864/69‑1 (MQ=255)
|
TTTGCCTGAAAACGGGGAAAGCGTTATGCCTGCCCGCCACCGATCCGCTCACCACTTATCCAGTACACGTTGAAGGTGGTGACATTTTCATCGACTTACCGGAGGCGCAGCCATGAGCGA > W3110S.gb/2669769‑2669888
|
| 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
