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 |
834,507 |
A→C |
42.3% |
N989H (AAT→CAT) ‡ |
narG → |
nitrate reductase 1, alpha subunit |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 834,507 | 0 | A | C | 42.3%
| ‑1.6
/ 58.3
| 45 | N989H (AAT→CAT) ‡ | narG | nitrate reductase 1, alpha subunit |
| Reads supporting (aligned to +/- strand): ref base A (19/7); new base C (12/7); total (31/14) |
| Fisher's exact test for biased strand distribution p-value = 5.28e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.95e-01 |
GTAGCCGTGAAAGCCTGGGCTGCCCTGAGCGAATTTACCGGTCGTGACCATACGCATCTGGCGCTGAATAAAGAAGACGAGAAGATCCGCTTCCGCGATATTCAGGCACAGCCGCGCAAAATTATCTCCAGCCCGA > minE/834441‑834576
|
gTAGCCGTGAAAGCCTGGGCTGCCCTGAGCGAATTTACCGGTCGTGCCCATACGCATCTGGCGCTGAATa > 1:2461451/1‑70 (MQ=255)
aGCCGTGAAAGCCTGGGCTGCCCTGAGCGAATTTACCGGTCGTGACCATACGCATCTGGCGCTGAATa > 1:5537256/1‑68 (MQ=255)
gCCGTGAAAGCCTGGGCTGCCCTGAGCGAATTTACCGGTCGTGACCATACGCATCTGGCGCTGAATAaag > 1:3476574/1‑70 (MQ=255)
aaaGCCTGGGCTGCCCTGAGCGAATTTACCGGTCGTGACCATACGCATCTGGCGCTGAATaa > 1:3609774/1‑62 (MQ=255)
aaaGCCTGGGCTGCCCTGAGCGAATTTACCGGTCGTGACCATACGCATCTGGCGCTGAATAAagaaga > 1:5674681/1‑68 (MQ=255)
aaaGCCTGGGCTGCCCTGAGCGAATTTACCGGTCGTGACCATACGCATCTGGCGCTGAATAAAGAAGAc > 1:2851789/1‑69 (MQ=255)
aaaGCCTGGGCTGCCCTGAGCGAATTTACCGGTCGTGACCATACGCATCTGGCGCTGAATAAAGAAGAc > 1:1786923/1‑69 (MQ=255)
aaGCCTGGGCTGCCCTGAGCGAATTTACCGGTCGTGACCATACGCATCTGGCGCTGAATAAAGAAGACgag < 1:5475302/71‑1 (MQ=255)
cTGCCCTGAGCGAATTTACCGGTCGTGACCATACGCATCAGGCGCTGAATAAAGAAGACGAGAAGATCCGc > 1:4356105/1‑71 (MQ=255)
cTGAGCGAATTTACCGGTCGTGACCATACGCATCTGGCGCTGAATAAAGAAGACGAGAAGATCCGCTTCcg > 1:2001859/1‑71 (MQ=255)
gAGCGAATTTACCGGTCGTGACCATACGCATCTGGGGCTGAATAAAGAAGACGAGAAGATCCGCTTCcgc > 1:3195853/1‑70 (MQ=255)
aGCGAATTTACCGGTCGTGACCATACGCATCTGGCGCTGAATAAAGAAGACGAGAAGATCCGCTTCCGCGa > 1:1934889/1‑71 (MQ=255)
aGCGAATTTACCGGTCGTGACCATACGCATCTGGCGCTGAATAAAGAAGACGAGAAGATCCGCTTCCGCGa < 1:1801173/71‑1 (MQ=255)
aGCGAATTTACCGGTCGTGACCATACGCATCTGGCGCTGAATAAAGAAGACGAGAAGATCCGCTTCCGCGa < 1:2626879/71‑1 (MQ=255)
aaTTTACCGGTCGTGACCATACGCATCTGGCGCTGAATAAAGAAGACGAGAAGATCCGCTTCCGCGatat > 1:3871637/1‑70 (MQ=255)
aaTTTACCGGTCGTGACCATACGCATCTGGCGCTGAATAAAGAAGACGAGAAGATCCGCTTCCGCGATAtt < 1:3332867/71‑1 (MQ=255)
aTTTACCGGTCGTGACCATACGCATCTGGCGCTGAATAAAGAAGACGAGAAGATCCGCTTCCGCGATAtt > 1:3796856/1‑70 (MQ=255)
taacGGTCGTGACCATACGCATCTGGCGCTGAATAAAGAAGACGAGAAGATCCGCTTCCGCGATATTCa > 1:4472993/4‑69 (MQ=255)
tACCGGTCGTGACCATACGCATCTGGCGCTGAATAAAGAAGACgaga > 1:2373374/1‑47 (MQ=255)
tACCGGTCGTGACCATACGCATCTGGCGCTGAATAAAGAAGACGAGAAGATCCGCTTCCGCGATATTCa > 1:1068834/1‑69 (MQ=255)
cGGGCGCGAACATACCCATCTGGCGCTGCACAAAGAGGACGAGAAGATTCGCTTTCGCGata < 1:266052/62‑1 (MQ=255)
cGGGCGCGAACATACCCATCTGGCGCTGCACAAAGAGGACGAGAAGATTCGCTTTCGCGATATTCAGGcg > 1:5275372/1‑69 (MQ=255)
cGGGCGCGAACATACCCATCTGGCGCTGCACAAAGAGGACGAGAAGATTCGCTTTCGCGATATTCAGGcg > 1:571306/1‑69 (MQ=255)
ggTCGTGACCATACGCATCTGGCGCTGAATAAAGAAGACGAGAAGATCCGCTTCCGCGATATTCAGGcaca < 1:1678312/71‑1 (MQ=255)
cGTGACCATACGCATCTGGCGCTGAATAAAGAAGACGAGAAGATCCGCTTCCGCGata > 1:2690224/1‑58 (MQ=255)
aacATACCCATCTGGCGCTGCACAAAGAGGACGAGAAGATTCGCTTTCGCGATATTCAGGCGCAGCcgcg > 1:5178234/3‑70 (MQ=255)
acATACCCATCTGGCGCTGCACAAAGAGGACGAGAAGATTCGCTTTCGCGATATTCAGGCGCAGc > 1:650790/2‑65 (MQ=255)
acATACCCATCTGGCGCTGCACAAAGAGGACGAGAAGATTCGCTTTCGCGATATTCAGGCGCAGc > 1:2943682/2‑65 (MQ=255)
acATACCCATCTGGCGCTGCACAAAGAGGACGAGAAGATTCGCTTTCGCGATATTCAGGCGCAGCcgcgt > 1:1830055/2‑69 (MQ=255)
acATACCCATCTGGCGCTGCACAAAGAGGACGAGAAGATTCGCTTTCGCGATATTCAGGCGCAGCcgcgt > 1:363581/2‑69 (MQ=255)
acATACCCATCTGGCGCTGCACAAAGAGGACGAGAAGATTCGCTTTCGCGATATTCAGGCGCAGCcgcgt > 1:4818750/2‑69 (MQ=255)
cATACGCATCTGGCGCTGAATAAAGAAGACGAGAAGATCCGCTTCCGCGATATTCAGGCACAGCCGCGCaa < 1:5646884/71‑1 (MQ=255)
cATACCCATCTGGCGCTGCACAAAGAGGACGAGAAGATTCGCTTTCGCGATATTCAGGCGCAGCCGCGTaa < 1:4857332/71‑1 (MQ=255)
cATACCCATCTGGCGCTGCACAAAGAGGACGAGAAGATTCGCTTTCGCGATATTCAGGCGCAGCCGCGTaa < 1:4841285/71‑1 (MQ=255)
aTACGCATCTGGCGCTGAATAAAGAAGACGAGAAGATCCg < 1:2931192/40‑1 (MQ=255)
tACCCATCTGGCGCTGCACAAAGAGGACGAGAAGATTCGCTTTCGCGATATTCAGGCGCAGCCGCGTaaaa > 1:4450702/1‑71 (MQ=255)
cccATCTGGCGCTGCACAAAGAGGACGAGAAGATTCGCTTTCGCGATATTCAGGCGCAGCCGCGTAAAAtt < 1:1796395/69‑1 (MQ=255)
cGCATCTGGCGCTGAATAAAGAAGACGAGAAGATCCGCTTCCGCGATATTCAGGCACAGCcgc > 1:1926493/1‑63 (MQ=255)
ccATCTGGCGCTGCACAAAGAGGACGAGAAGATTCGCTTTCGCGATATTCAGGCGCAGCCGCGTAAAATTa < 1:1309694/70‑1 (MQ=255)
tCTGGCGCTGCACAAAGAGGACGAGAAGATTCGCTTTCGCGATATTCAg < 1:4613337/49‑1 (MQ=255)
tGGCGCTGCACAAAGAGGACGAGAAGATTCGCTTTCGCGatat > 1:2538345/1‑43 (MQ=19)
tGGCGCTGCACAAAGAGGACGAGAAGATTCGCTTTCGCGat > 1:4701327/1‑41 (MQ=19)
tGGCGCTGCACAAAGAGGACGAGAAGATTCGCTTTCGCGat > 1:576717/1‑41 (MQ=19)
cgcTGCACAAAGAGGACGAGAAGATTCGCTTTCGCGATATTCAGGCGCAGCCGCGTAAAAtt < 1:4708290/62‑1 (MQ=255)
gAATAAAGAAGACGAGAAGATCCGCTTCCGCGATATTCAGGCACAGCCGCGCAAAATTATCTCCAGCCCGa > 1:2512401/1‑71 (MQ=255)
aaTAAAGAAGACGAGAAGATCCGCTTCCGCGATATTCAGGCACAGCCGCGCAAAATTATCTCCAGCCCg < 1:1233782/69‑1 (MQ=255)
aaTAAAGAAGACGAGAAGATCCGCTTCCGCGATATTCAGGCACAGCCGCGCAAAATTATCTCCAGCCCGa < 1:4425568/70‑1 (MQ=255)
|
GTAGCCGTGAAAGCCTGGGCTGCCCTGAGCGAATTTACCGGTCGTGACCATACGCATCTGGCGCTGAATAAAGAAGACGAGAAGATCCGCTTCCGCGATATTCAGGCACAGCCGCGCAAAATTATCTCCAGCCCGA > minE/834441‑834576
|
| 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
