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 |
|
A6 F1 I0 R1
|
2892 |
75.3 |
5698161 |
66.1% |
3766484 |
59.5 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
833,282 |
T→C |
54.1% |
G580G (GGT→GGC) |
narG → |
nitrate reductase 1, alpha subunit |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 833,282 | 0 | T | C | 54.1%
| 10.2
/ 72.1
| 61 | G580G (GGT→GGC) | narG | nitrate reductase 1, alpha subunit |
| Reads supporting (aligned to +/- strand): ref base T (14/14); new base C (14/19); total (28/33) |
| Fisher's exact test for biased strand distribution p-value = 6.12e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.28e-01 |
GTCTGATCAACATGCTGATTTTCTGCGGCTGTGTCGGTCAGAGCGGGGGCGGCTGGGCGCACTATGTAGGTCAGGAAAAACTGCGTCCGCAAACCGGCTGGCAGCCGCTGGCGTTTGCCCTTGACTGGCAGCGTCC > minE/833212‑833347
|
gTCTGATCAACATGCTGATTTTCTGCGGCTGTGTCGGTCAGAGCGGGGGCGGCTGGGCGCACTATGTAGGt < 1:4566378/71‑1 (MQ=255)
gTCTGATCAACATGCTGATTTTCTGCGGCTGTGTCGGTCAGAGCGGGGGCGGCTGGGCGCACTATGTAGGt < 1:1916905/71‑1 (MQ=255)
tCTGATCAACATGCTGATTTTCTGCGGCTGTGTCGGTCAGAGCGGGGGCGGCTGGGCGCACTATGTAGGt > 1:806225/1‑70 (MQ=255)
aTCAATATGCTGATCTTCTGCGGTTGTGTCGGGCAAAGCGGTGGCGGCTGGGCACACTATGTCGGCCAg > 1:2821760/1‑69 (MQ=255)
aTCAATATGCTGATCTTCTGCGGTTGTGTCGGGCAAAGCGGTGGCGGCTGGGCACACTATGTCGGCCAGGa < 1:2944028/71‑1 (MQ=255)
aataTGCTGATCTTCTGCGGTTGTGTCGGGCAAAGCGGTGGCGGCTGGGCACACTATGTCGGCCAGGaaaa < 1:4184778/68‑1 (MQ=255)
aataTGCTGATCTTCTGCGGTTGTGTCGGGCAAAGCGGTGGCGGCTGGGCACACTATGTCGGCCAGGaaaa < 1:3016967/68‑1 (MQ=255)
aataTGCTGATCTTCTGCGGTTGTGTCGGGCAAAGCGGTGGCGGCTGGGCACACTATGTCGGCCAGGaaa > 1:2981445/4‑70 (MQ=255)
aaCATGCTGATTTTCTGCGGCTGTGTCGGTCAGAGCGGGGGCGGCTGGGCGCACTATGTAGGTCAGGaaa < 1:3493599/70‑1 (MQ=255)
aaCATGCTGATTTTCTGCGGCTGTGTCGGTCAGAGCGGGGGCGGCTGGGCGCACTATGTAGGTCAGGaaa < 1:2167987/70‑1 (MQ=255)
aTGCTGATCTTCTGCGGTTGTGTCGGGCAAAGCGGTGGCGGCTGGGCACACTATGTCGGCCAGGaaaaa > 1:4304371/1‑69 (MQ=255)
aTGCTGATCTTCTGCGGTTGTGTCGGGCAAAGCGGTGGCGGCTGGGCACACTATGTCGGCCAGGaaaaa > 1:3406557/1‑69 (MQ=255)
aTGCTGATCTTCTGCGGTTGTGTCGGGCAAAGCGGTGGCGGCTGGGCACACTATGTCGGCCAGGaaaaa > 1:4464413/1‑69 (MQ=255)
tGCTGATCTTCTGCGGTTGTGTCGGGCAAAGCGGTGGCGGCTGGGCACACTATGTCGGCCAGGaaaaa > 1:4945892/1‑68 (MQ=255)
tGCTGATCTTCTGCGGTTGTGTCGGGCAAAGCGGTGGCGGCTGGGCACACTATGTCGGCCAGGAAAAACTg > 1:3034003/1‑71 (MQ=255)
atcttCTGCGGTTGTGTCGGGCAAAGCGGTGGCGGCTGGGCACACTATGTCGGCCAGGaaaaa > 1:3438767/4‑63 (MQ=255)
tttCTGCGGCTGTGTCGGTCAGAGCGGGGGCGGCTGGGCGCACTATGTAGGTCAGGAAAAACTGCGTCCg > 1:1400618/1‑70 (MQ=255)
cttCTGCGGTTGTGTCGGGCAAAGCGGTGGCGGCTGGGCACACTATGTCGGCCAGGAAAAACTGCGccca > 1:949659/2‑69 (MQ=255)
tCTGCGGCTGTGTCGGTCAGAGCGGGGGCGGCTGGGCGCACTATGTAGGTCAGGAAAAACTGCGTCCGCa < 1:5222416/70‑1 (MQ=255)
tGCGGCTGTGTCGGTCAGAGCGGGGGCGGCTGGGCGCACTATGTAGGTCAGGAAAAAc > 1:2936667/1‑58 (MQ=255)
tGCGGCTGTGTCGGTCAGAGCGGGGGCGGCTGGGCGCACTATGTAGGTCAGGAAAAAc > 1:4963301/1‑58 (MQ=255)
gCGGCTGTGTCGGTCAGAGCGGGGGCGGCTGGGCGCACTATGTAGGTCAGGaaa > 1:3734738/1‑54 (MQ=255)
ggCTGTGTCGGTCAGAGCGGGGGCGGCTGGGCGCACTATGTAGGt > 1:3760021/1‑45 (MQ=255)
ggCTGTGTCGGTCAGAGCGGGGGCGGCTGGGCGCACTATGTAGGt > 1:3400123/1‑45 (MQ=255)
gtgtCGGGCAAAGCGGTGGCGGCTGGGCACACTATGTCGGCCAGGAAAAACTGCGCCCACAAACCGGCTgg > 1:5529711/1‑71 (MQ=255)
tgtCGGTCAGAGCGGGGGCGGCTGGGCGCACTATGTAGGTCAGGAAAAACTGCGTCCGCAAACCGGCTgg < 1:1003885/70‑1 (MQ=255)
tgtCGGGCAAAGCGGTGGCGGCTGGGCACACTATGTCGGCCAGGAAAAACTGCGCCCACAAACCGGCTggt < 1:4121250/71‑2 (MQ=255)
tgtCGGGCAAAGCGGTGGCGGCTGGGCACACTATGTCGGCCAGGAAAAACTGCGCCCACAAACCGGCTgg < 1:1119725/70‑1 (MQ=255)
tCGGTCAGAGCGGGGGCGGCTGGGCGCACTATGTAGGTCAGGAAAAAc > 1:1166919/1‑48 (MQ=255)
tCGGTCAGAGCGGGGGCGGCTGGGCGCACTATGTAGGTCAGGAAAAACTGCGTCCGCaa < 1:2999885/59‑1 (MQ=255)
tCGGTCAGAGCGGGGGCGGCTGGGCGCACTATGTAGGTCAGGAAAAACTGCGTCCGCaa < 1:1294849/59‑1 (MQ=255)
cGGTCAGAGCGGGGGCGGCTGGGCGCACTATGTAGGTCAGGAAAAACTGCGTCCGCAAACCGGCTGGCAGc > 1:5440272/1‑71 (MQ=255)
ggTCAGAGCGGGGGCGGCTGGGCGCACTATGTAGGTCAGGAAAAAc > 1:3089178/1‑46 (MQ=255)
ggTCAGAGCGGGGGCGGCTGGGCGCACTATGTAGGTCAGGAAAAAc > 1:3649610/1‑46 (MQ=255)
tCAGAGCGGGGGCGGCTGGGCGCACTATGTAGGTCAGGAAAAACTGCGTCCGCAAACCGGCTGGCAGcccc < 1:3377181/71‑3 (MQ=255)
aaagCGGTGGCGGCTGGGCACACTATGTCGGCCAGGAAAAACTGCGCCCACAAACCGGCTGGTTGCCACTg < 1:616480/69‑1 (MQ=255)
agCGGGGGCGGCTGGGCGCACTATGTAGGTCAGGAAAAACTGCGTCCGCAAACCGGCTGGCAGCCGCTGGc < 1:4208992/71‑1 (MQ=255)
gCGGTGGCGGCTGGGCACACTATGTCGGCCAGGAAAAACTGCGCCCACAAACCGGCTGGTTGCCACTGGcc < 1:2457101/71‑2 (MQ=255)
cGGTGGCGGCTGGGCACACTATGTCGGCCAGGAAAAACTGCGCCCACAAACCGGCTGGTTGCCACTGGcct < 1:2909029/71‑3 (MQ=255)
tggcggcTGGGCACACTATGTCGGCCAGGAAAAACTGCGCCCACAAACCGGCTGGTTGCCACTGGCCTTTg < 1:244647/70‑1 (MQ=255)
gcggcTGGGCACACTATGTCGGCCAGGAAAAACTGCGCCCACAAACCGGCTGGTTGCCACTGGCCTTTGcg < 1:590398/71‑2 (MQ=255)
gcggcTGGGCACACTATGTCGGCCAGGAAAAACTGCGCCCACAAACCGGCTGGTTGCCACTGGCCTTTGcg < 1:1126363/71‑2 (MQ=255)
gcggcTGGGCACACTATGTCGGCCAGGAAAAACTGCGCCCACAAACCGGCTGGTTGCCACTGGCCTTTGcg < 1:2734165/71‑2 (MQ=255)
gcggcTGGGCACACTATGTCGGCCAGGAAAAACTGCGCCCACAAACCGGCTGGTTGCCACTGGCCTTTGcg > 1:4792371/1‑70 (MQ=255)
gcggcTGGGCACACTATGTCGGCCAGGAAAAACTGCGCCCACAAACCGGCTGGTTGCCACTGGCCTTTGc > 1:96120/1‑70 (MQ=255)
ggcTGGGCGCACTATGTAGGTCAGGAAAAACTGCGTCCGCAAACCGGCTGGCAGCCGCTGGCGTTTGCCCt > 1:5004806/1‑71 (MQ=255)
gcTGGGCGCACTATGTAGGTCAGGAAAAACTGCGTCCGCAAACCGGCTGGCAGCCGCTGGCGTTTGCCCtt < 1:3890155/71‑1 (MQ=255)
cTGGGCACACTATGTCGGCCAGGAAAAACTGCGCCCACAAACCGGCTGGTTGCCACTGGCCTTTGCGCtcg < 1:1484523/71‑3 (MQ=255)
cTGGGCACACTATGTCGGCCAGGAAAAACTGCGCCCACAAACCGGCTGGTTGCCACTGGCCTTTGCGCtc > 1:385212/1‑69 (MQ=255)
ggCGCACTATGTAGGTCAGGAAAAACTGCGTCCGCAAACCGGCTgg > 1:907848/1‑46 (MQ=255)
ggCGCACTATGTAGGTCAGGAAAAACTGCGTCCGCAAACCGGCTGGCAGCCGCTGGCGTTTGCCCTTGAc < 1:21541/70‑1 (MQ=255)
ggCGCACTATGTAGGTCAGGAAAAACTGCGTCCGCAAACCGGCTGGCAGCCGCTGGCGTTTGCCCTTGAc < 1:1988872/70‑1 (MQ=255)
ggCGCACTATGTAGGTCAGGAAAAACTGCGTCCGCAAACCGGCTGGCAGCCGCTGGCGTTTGCCCTTGACt > 1:2654840/1‑71 (MQ=255)
cacACTATGTCGGCCAGGAAAAACTGCGCCCACAAACCGGCTGGTTGCCACTGGCCTTTGCGCTCGACTgg < 1:1095538/69‑1 (MQ=255)
cacACTATGTCGGCCAGGAAAAACTGCGCCCACAAACCGGCTGGTTGCCACTGGCCTTTGCGCTCGACTgg < 1:1788640/69‑1 (MQ=255)
gcACTATGTAGGTCAGGAAAAACTGCGTCCGCAAACCGGCTGGCAGCCGCTGGCGTTTGCCCTTGACTgg > 1:3041872/1‑70 (MQ=255)
acACTATGTCGGCCAGGAAAAACTGCGCCCACAAACCGGCTGGTTGCCACTGGCCTTTGCGCTCGACTgg > 1:5470204/2‑70 (MQ=255)
aCTATGTCGGCCAGGAAAAACTGCGCCCACAAACCGGCTGGTTGCCACTGGCCTTTGCGCTCGACTggaac < 1:1860594/71‑4 (MQ=255)
aCTATGTAGGTCAGGAAAAACTGCGTCCGCAAACCGGCTGGCAGCCGCTGGCGTTTGCCCtt > 1:1999443/1‑62 (MQ=255)
aCTATGTAGGTCAGGAAAAACTGCGTCCGCAAACCGGCTGGCAGCCGCTGGCGTTTGCCCTTGACTGGCAg < 1:2991167/71‑1 (MQ=255)
cTATGTCGGCCAGGAAAAACTGCGCCCACAAACCGGCTg < 1:4761113/39‑1 (MQ=21)
tATGTCGGCCAGGAAAAACTGCGCCCACAAACCGGCTg < 1:4127228/38‑1 (MQ=21)
tATGTCGGCCAGGAAAAACTGCGCCCACAAACCGGCTg < 1:4313406/38‑1 (MQ=21)
tATGTAGGTCAGGAAAAACTGCGTCCGCAAACCGGCTGGCAGCCGCTGGCGTTTGCCCTTGACTGGCAGCg > 1:1920352/1‑71 (MQ=255)
tGTAGGTCAGGAAAAACTGCGTCCGCAAACCGGCTg < 1:1626937/36‑1 (MQ=255)
tAGGTCAGGAAAAACTGCGTCCGCAAACCGGCTGGCAGCCGCTGGCGTTTGCCCTTGACTGGCAGCGTcc < 1:1339780/70‑1 (MQ=255)
|
GTCTGATCAACATGCTGATTTTCTGCGGCTGTGTCGGTCAGAGCGGGGGCGGCTGGGCGCACTATGTAGGTCAGGAAAAACTGCGTCCGCAAACCGGCTGGCAGCCGCTGGCGTTTGCCCTTGACTGGCAGCGTCC > minE/833212‑833347
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
