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 |
|
A2 F1 I0 R1
|
4577 |
57.4 |
3436498 |
77.7% |
2670158 |
63.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
1,879,862 |
A→G |
42.5% |
D102D (GAT→GAC) |
mazG ← |
nucleoside triphosphate pyrophosphohydrolase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,879,862 | 0 | A | G | 42.5%
| 7.1
/ 27.7
| 40 | D102D (GAT→GAC) | mazG | nucleoside triphosphate pyrophosphohydrolase |
| Reads supporting (aligned to +/- strand): ref base A (18/5); new base G (5/12); total (23/17) |
| Fisher's exact test for biased strand distribution p-value = 3.40e-03 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.64e-01 |
CCCAACGGGCAAGCACTTCACTACTGTTTTCGGCAGAACTATCAGCAAAAACATGCGGATGGCGACGCTCTAATTTATCGCTAATAGCAGCGCAAATATCATTAAAGT > minE/1879822‑1879929
|
cccAACGGGCAAGCACTTCACTACTGTTTTCGGCAGAACTATCAGCAAAAACATGCGGATGGCGACGct < 1:350179/69‑1 (MQ=255)
cccAACGGGCAAGCACTTCACTACTGTTTTCGGCAGAACTATCAGCAAAAACATGCGGATGGCGACGct < 1:2014552/69‑1 (MQ=255)
cccAACGGGCAAGCACTTCACTACTGTTTTCGGCAGAAATATCAGCAAAAACATGCGGATGGCGACGct < 1:1941502/69‑1 (MQ=255)
cAAGCACTTCACTACTGTTTTCGGCAGAACTATCAGCAAAAACATGCg > 1:51137/1‑48 (MQ=255)
cAAGCACTTCACTACTGTTTTCGGCAGAACTATCAGCAAAAACATGCGGATGGCGACGCTCTAATTTAt > 1:746175/1‑69 (MQ=255)
cAAGCACTTCACTACTGTTTTCGGCAGAACTATCAGCAAAAACATGCGGATGGCGACGCTCTAATTTAt > 1:597518/1‑69 (MQ=255)
cACTTCACTGCTATTTTCGGCAGAACTGTCAGCAAAAACATGCGGATGGCGACGCTCTAATTTATCGCt < 1:1933781/69‑1 (MQ=255)
cACTTCACTACTGTTTTCGGCAGAACTATCAGCAAAAACATGCGGATGGCGACGCTCTAATTTATCGCt > 1:1086473/1‑69 (MQ=255)
cACTTCACTACTGTTTTCGGCAGAACTATCAGCAAAAACATGCGGATGGCGACGCTCTAATTTATCGCt > 1:652492/1‑69 (MQ=255)
cACTTCACTACTGTTTTCGGCAGAACTATCAGCAAAAACATGCGGATGGCGACGCTCTAATTTATCGCt > 1:451952/1‑69 (MQ=255)
cACTTCACTACTGTTTTCGGCAGAACTATCAGCAAAAACATGCGGATGGCGACGCTCTAATTTATCGCt < 1:3279398/69‑1 (MQ=255)
cACTTCACTACTGTTTTCGGCAGAACTATCAGCAAAAACATGCGGATGGCGACGCTCTAATTTATCGCt > 1:3104600/1‑69 (MQ=255)
cACTTCACTACTGTTTTCGGCAGAACTATCAGCAAAAACATGCGGATGGCGACGCTCTAATTTATCGCt > 1:2755380/1‑69 (MQ=255)
cACTTCACTACTGTTTTCGGCAGAACTATCAGCAAAAACATGCGGATGGCGACGCTCTAATTTATCGCt < 1:2140445/69‑1 (MQ=255)
cACTTCACTACTATTTTCGGCAGAACTGTCAGCAAAAACATGCGGATGGCGACTCTCTAATTTATCGCt < 1:3273587/69‑1 (MQ=255)
cACTTCACTACTATTTTCGGCAGAACTGTCAGCAAAAACATGCGGATGGCGACGCTCTAATTTATCGCt < 1:13007/69‑1 (MQ=255)
cACTTCACTACTATTTTCGGCAGAACTGTCAGCAAAAACATGCGGATGGCGACGCTCTAATTTATCGCt < 1:1547142/69‑1 (MQ=255)
cACTTCACTACTATTTTCGGCAGAACTGTCAGCAAAAACATGCGGATGGCGACGCTCTAATTTATCGCt < 1:387827/69‑1 (MQ=255)
cACTTCACTACTATTTTCGGCAGAACTGTCAGCAAAAACATGCGGATGGCGACGCTCTAATTTATCGCt < 1:36822/69‑1 (MQ=255)
cACTTCACTACTATTTTCGGCAGAACTGTCAGCAAAAACATGCGGATGGCGACGCTCTAATTTATCGCt < 1:3364389/69‑1 (MQ=255)
cACTTCACTACTATTTTCGGCAGAACTGTCAGCAAAAACATGCGGATGGCGACGCTCTAATTTATCGCt < 1:3185486/69‑1 (MQ=255)
cACTTCACTACTATTTTCGGCAGAACTGTCAGCAAAAACATGCGGATGGCGACGCTCTAATTTATCGCt < 1:1822119/69‑1 (MQ=255)
cACTTCACTACTATTTTCGGCAGAACTGTCAGCAAAAACATGCGGATGGCGACGCTCTAATTTATCGCt < 1:2962829/69‑1 (MQ=255)
cACTTCACTACTATTTTCGGCAGAACTGTCAGCAAAAACATGCGGATGGCGACGCTCTAATTTATCGCt < 1:182265/69‑1 (MQ=255)
cACTTCACTACTATTTTCGGCAGAACTGTCAGCAAAAACATGCGGATGGCGACGCTCTAATTTATCGCt < 1:1956839/69‑1 (MQ=255)
cACTTAACTACTGTTTTCGGCAGAACTATCAGCAAAAACATGCGGATGGCGACGCTCTAATTTATAGCt > 1:499193/1‑69 (MQ=255)
cACTACTGTTTTCGGCAGAACTATCAGCAAAAACATGCGGATGGCGACGCTCTAATTTATCGCTAAt > 1:2385160/1‑67 (MQ=255)
tttCGGCAGAACTGTCAGCAAAAACATGCGGATGGCGACGCTCTAATTTATCGCTAATAGCAGCGCaaa > 1:739096/1‑69 (MQ=255)
tttCGGCAGAACTGTCAGCAAAAACATGCGGATGGCGACGCTCTAATTTATCGCTAATAGCAGCGCaaa > 1:2626338/1‑69 (MQ=255)
tttCGGCAGAACTGTCAGCAAAAACATGCGGATGGCGACGCTCTAATTTATCGCTAATAGCAGCGCaaa > 1:2503387/1‑69 (MQ=255)
tttCGGCAGAACTGTCAGCAAAAACATGCGGATGGCGACGCTCTAATTTATCGCTAATAGCAGCGCaaa > 1:1643216/1‑69 (MQ=255)
tttCGGCAGAACTGTCAGCAAAAACATGCGGATGGCGACGCTCTAATTTATCGCTAATAGCAGCGCaaa > 1:1876918/1‑69 (MQ=255)
ttCGGCAGAACTATCAGCAAAAACATGCGGATGGCGACGCTCTAATTTATCGCTAATAGCAGCGCAAat > 1:1759002/1‑69 (MQ=255)
ttCGGCAGAACTATCAGCAAAAACATGCGGATGGCGACGCTCTAATTTATCGCTAATAGCAGCGCAAat > 1:1905530/1‑69 (MQ=255)
aGAACTATCAGCAAAAACATGCGGATGGCGACGCTCTAATTTATCGCTAATAGCAGCGCAAATATCAt > 1:1080597/1‑68 (MQ=255)
aGAACTATCAGCAAAAACATGCGGATGGCGACGCTCTAATTTATCGCTAATAGCAGCGCAAATATCAt > 1:3265134/1‑68 (MQ=255)
aCTATCAGCAAAAACATGCGGATGGCGACGCTCTAATTTATCGCTAATagcag > 1:246256/1‑53 (MQ=255)
cTATCAGCAAAAACATGCGGATGGCGACGCTCTAATTTATCGCTaa > 1:1447606/1‑46 (MQ=255)
cTATCAGCAAAAACATGCGGATGGCGACGCTCTAATTTATCGCTAATAGCAGCGCAAATATCATTaaa > 1:1299236/1‑68 (MQ=255)
cTATCAGCAAAAACATGCGGATGGCGACGCTCTAATTTATCGCTAATAGCAGCGCAAATATCATTaaa > 1:3012520/1‑68 (MQ=255)
aTCAGCAAAAACATGCGGATGGCGACGCTCTAATTTATCGCTAATAGCAGCGCAAATATCATTAAAGt > 1:302432/1‑68 (MQ=255)
|
CCCAACGGGCAAGCACTTCACTACTGTTTTCGGCAGAACTATCAGCAAAAACATGCGGATGGCGACGCTCTAATTTATCGCTAATAGCAGCGCAAATATCATTAAAGT > minE/1879822‑1879929
|
| 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
