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 |
|
A3 F2 I1 R1
|
2892 |
75.3 |
5698161 |
66.1% |
3766484 |
59.5 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
Exported |
834,440 |
G→T |
24.5% |
Q966H (CAG→CAT) |
narG → |
nitrate reductase 1, alpha subunit |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | Exported | 834,440 | 0 | G | T | 24.5%
| 127.2
/ 28.5
| 61 | Q966H (CAG→CAT) | narG | nitrate reductase 1, alpha subunit |
| Reads supporting (aligned to +/- strand): ref base G (28/18); new base T (10/5); total (38/23) |
| Fisher's exact test for biased strand distribution p-value = 7.67e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.08e-01 |
CCAGCCGATGCTGAACACCGCAATTGATGCGGCAGAGATGATCCTGACACTGGCACCGGAAACCAACGGTCAGGTAGCCGTGAAAGCCTGGGCTGCCCTGAGCGAATTTACCGGTCGTGACCATACGCATCTGGCGCTG > Exported/834368‑834506
|
ccAGCCGATGCTGAACACCGCAATTGATGC‑‑CAGAGATGATCCTGACACTGGCACCGGAAACCAACGGTCAg < 1:482382/71‑1 (MQ=255)
aGCCGATGCTGAACACCGCAATTGATGCGGCAGAGATGATCCTGACACTGGCACCGGAAACCAACGGTCAg < 1:2406312/71‑1 (MQ=255)
tGCTGAACACCGCAATTGATGCGGCAGAGATGATCCTGACACTGGCACCGGAAACCAACGGTTAGGTAGcc > 1:3078595/1‑71 (MQ=255)
gCTGAACACCGCAATTGATGCGGCAGAGATGATCCTGACACTGGCACCGGAAACCAACGGTCAGGTAGCCg > 1:524524/1‑71 (MQ=255)
cTGAACACCGCAATTGATGCGGCAGAGATGATCCTGACACTGGCACCAGAAACCAACGGTCAGGTAGCCGt > 1:2728700/1‑71 (MQ=255)
ttgacacCGCCATTGACGCTTCAGAAGTGATTCTGGCACTGGCACCGGAAACCAACGGTCATGTTGCAGt > 1:3927219/4‑70 (MQ=255)
gacacCGCCATTGACGCTTCAGAAGTGATTCTGGCACTGGCACCGGAAACCAACGGTCATGTTGCAGtca > 1:2513408/2‑68 (MQ=255)
aaCACCGCAATTGATGCGGCAGAGATGATCCTGACACTGGCACCGGAAACCAACGGTCAGGTAg > 1:2180490/1‑64 (MQ=255)
aaCACCGCAATTGATGCGGCAGAGATGATCCTGACACTGGCACCGGAAACCAACGGTCAGGTAGCCGTg > 1:1513117/1‑69 (MQ=255)
aaCACCGCAATTGATGCGGCAGAGATGATCCTGACACTGGCACCGGAAACCAACGGTCAGGTAGCCGTGa > 1:1088208/1‑70 (MQ=255)
aaCACCGCAATTGATGCGGCAGAGATGATCCTGACACTGGCACCGGAAACCAACGGTCAGGTAGCCGTGa > 1:1921058/1‑70 (MQ=255)
acCGCCATTGACGCTTCAGAAGTGATTCTGGCACTGGCACCGGAAACCAACGGTCATGTTGCAGTCAAAGc < 1:5314949/71‑1 (MQ=255)
acCGCAATTGATGCGGCAGAGATGATCCTGACACTGGCACCGGAAACCACCGGTCAGGTAGCCGTGAAAGc < 1:5325265/71‑1 (MQ=255)
acCGCAATTGATGCGGCAGAGATGATCCTGACACTGGCACCGGAAACCAACGGTCAGGTAGCCGTGAAAGc < 1:2065873/71‑1 (MQ=255)
ccGCCATTGACGCTTCAGAAGTGATTCTGGCACTGGCACCGGAAACCAACGGTCATGTTGCAGTCAAAGcg < 1:2907865/71‑2 (MQ=255)
ccGCCATTGACGCTTCAGAAGTGATTCTGGCACTGGCACCGGAAACCAACGGTCATGTTGCAGTCAAAGcg < 1:4829589/71‑2 (MQ=255)
ccGCAATTGATGCGGCAGAGATGATCCTGACACTGGCACCGGAAACCAACGGTCAGGTAGCCGTGAAAGcc < 1:2940260/71‑1 (MQ=255)
cGCCATTGACGCTTCAGAAGTGATTCTGGCACTGGCACCGGAAACCAACGGTCATGTTGCAGTCAAAGcg < 1:2075062/70‑2 (MQ=255)
ccaTTGACGCTTCAGAAGTGATTCTGGCACTGGCACCGGAAACCAACGGTCATGTTGCAGTCAAAGCGTgg > 1:4249939/3‑71 (MQ=255)
ccaTTGACGCTTCAGAAGTGATTCTGGCACTGGCACCGGAAACCAACGGTCATGTTGCAGTCAAAGCGTgg > 1:1319085/3‑71 (MQ=255)
caTTGACGCTTCAGAAGTGATTCTGGCACTGGCACCGGAAACCAACGGTCATGTTGCAGTCAAAGCGTggc < 1:2837042/70‑2 (MQ=255)
tGATGCGGCAGAGATGATCCTGACACTGGCACCGGAAACCAACGGTCAGGTAGCCGTGAAAGCCTg > 1:5306018/1‑66 (MQ=255)
gATGCGGCAGAGATGATCCTGACACTGGCACCGGAAACCAACGGTCAGGTAGCCGTGAAAGCCTg > 1:5443950/1‑65 (MQ=255)
gATGCGGCAGAGATGATCCTGACACTGGCACCGGAAACCAACGGTCAGGTAGCCGTGAAAGCCTGGGCTGc > 1:4143126/1‑71 (MQ=255)
gATGCGGCAGAGATGATCCTGACACTGGCACCGGAAACCAACGGTCAGGTAGCCGTGAAAGCCTGGGCTGc > 1:3230775/1‑71 (MQ=255)
agagATGATCCTGACACTGGCACCGGAAACCAACGGTCAGGTAGCCGTGAAAGCCTGGGCTGCCCTGAGc > 1:1048035/1‑70 (MQ=255)
agagATGATCCTGACACTGGCACCGGAAACCAACGGTCAGGTAGCCGTGAAAGCCTGGGCTGCCCTGAGCg < 1:5142443/71‑1 (MQ=255)
atgatCCTGACACTGGCACCGGAAACCAACGGTCAGGTAGCCGTGAAAGCCTGGGCTGCCCTGAGCGaa < 1:5637538/69‑1 (MQ=255)
gatTCTGGCACTGGCCCCGGAAACCAACGGTCATGTTGCAGTCAAAGCGTggca > 1:4797438/1‑52 (MQ=255)
gatTCTGGCACTGGCACCGGAAACCAACGGTCATGTTGCAGTCAAAGCGTggca > 1:1999719/1‑52 (MQ=255)
gatTCTGGCACTGGCACCGGAAACCAACGGTCATGTTGCAGTCAAAGCGTgg > 1:3563902/1‑52 (MQ=255)
gatCCTGACACTGGCACCGGAAACCAACGGTCAGGTAGCCGTGAAAGCCTGGGCTGCCCTGAGCGaa > 1:5447706/1‑67 (MQ=255)
cTGGCACCGGAAACCAACGGTCAGGTAGCCGTGAAAGCCt < 1:166028/40‑1 (MQ=255)
cTGGCACCGGAAACCAACGGTCAGGTAGCCGTGAAAGCCt < 1:1479846/40‑1 (MQ=255)
gtcACCGGAAACCAACGGTCAGGTAGCCGTGAAAGCCTGGGCTGCCCTGa > 1:1986110/3‑50 (MQ=255)
ggCACCGGAAACCAACGGTCAGGTAGCCGTGAAAGCCTGGGCTGCCCTGa > 1:2867190/1‑50 (MQ=255)
aCCGGAAACCAACGGTCAGGTAGCCGTGAAAGCCTGGGCTGCCCTGAGCGAATTTACCGGTCGt < 1:2993730/64‑1 (MQ=255)
cGGAAACCAACGGTCAGGTAGCCGTGAAAGCCTggg > 1:920425/1‑36 (MQ=255)
cGGAAACCAACGGTCAGGTAGCCGTGAAAGCCTggg > 1:1033794/1‑36 (MQ=255)
cGGAAACCAACGGTCAGGTAGCCGTGAAAGCCTggg > 1:1487802/1‑36 (MQ=255)
ggAAACCAACGGTCAGGTAGCCGTGAAAGCCTGGGCTGCCCTGAGCGAATTTACCGGTCGTGACCATACg > 1:1766373/1‑70 (MQ=255)
gAAACCAACGGTCATGTTGCAGTCAAAGCGTGGCAGGCGCTGGGCGAGATCACCGGGCGCGAACATAc > 1:3798077/1‑68 (MQ=255)
gAAACCAACGGTCATGTTGCAGTCAAAGCGTGGCAGGCGCTGGGCGAGATCACCGGGCGCGAACATACCCa > 1:1453460/1‑71 (MQ=255)
gAAACCAACGGTCAGGTAGCCGTGAAAGCCTGGGCTGCCCTGAGCGAATTTACCGGTCGTGACCATACGc > 1:976663/1‑70 (MQ=255)
gAAACCAACGGTCAGGTAGCCGTGAAAGCCTGGGCTGCCCTGAGCGAATTTACCGGTCGTGACCATACGCa > 1:139084/1‑71 (MQ=255)
gAAACCAACGGTCAGGTAGCCGTGAAAGCCTGGGCTGCCCTGAGCGAATTTACCGGTCGTGACCATACGCa < 1:1737948/71‑1 (MQ=255)
aaaCCAACGGTCAGGTAGCCGTGAAAGCCTGGGCTGCCCTGAGCGAATTTACCGGTCGt > 1:3198639/1‑59 (MQ=255)
aaaCCAACGGTCAGGTAGCCGTGAAAGCCTGGGCTGCCCTGAGCGAATTTACCGGTCGt < 1:4408041/59‑1 (MQ=255)
aaaCCAACGGTCAGGTAGCCGTGAAAGCCTGGGCTGCCCTGAGCGAATTTACCGGTCGTg > 1:518618/1‑60 (MQ=255)
aCCAACGGTCATGTTGCAGTCAAAGCGTGGCAGGCGCTGGGCGAGATCACCGGGCGCGAACATACCCATCt > 1:836391/1‑71 (MQ=255)
aCCAACGGTCAGGTAGCCGTGAAAGCCTGGGCTGCCCTGAGCGAATTTACCGGTCGTGa < 1:3742897/59‑1 (MQ=255)
aCCAACGGTCAGGTAGCCGTGAAAGCCTGGGCTGCCCTGAGCGAATTTACCGGTCGTGa < 1:3147622/59‑1 (MQ=255)
ccAACGGTCAGGTAGCCGTGAAAGCCTGGGCTGCCCTGAGCGAATTTACCGGTCGTGACCa < 1:4148986/61‑1 (MQ=255)
ccAACGGTCAGGTAGCCGTGAAAGCCTGGGCTGCCCTGAGCGAATTTACCGGTCGTGACCATACGCATCTg < 1:4765093/71‑1 (MQ=255)
cAACGGTCAGGTAGCCGTGAAAGCCTGGGCTGCCCTGAGCGAATTTACCGGTCGt > 1:2733766/1‑55 (MQ=255)
cAACGGTCAGGTAGCCGTGAAAGCCTGGGCTGCCCTGAGCGAATTTACCGGTCGTGACCATACGCATCTg < 1:4758660/70‑1 (MQ=255)
aCGGTCAGGTAGCCGTGAAAGCCTGGGCTGCCCTGAGCGAAtt > 1:3574503/1‑43 (MQ=255)
aCGGTCAGGTAGCCGTGAAAGCCTGGGCTGCCCTGAGCGAATTTACCGGTCGTGACCATACGCATCTGgcg < 1:1617288/71‑1 (MQ=255)
cGGTCAGGTAGCCGTGAAAGCCTGGGCTGCCCTGAGCGAATTTACCGGTCGTGACCATACGCATCTGgcg > 1:1951297/1‑70 (MQ=255)
cGGTCAGGTAGCCGTGAAAGCCTGGGCTGCCCTGAGCGAATTTACCGGTCGTGACCATACGCATCTGgcg > 1:1671944/1‑70 (MQ=255)
ggTCAGGTAGCCGTGAAAGCCTGGGCTGCCCTGAGCGAATTTACCGGTCGTGACCa < 1:4297539/56‑1 (MQ=255)
gTCAGGTAGCCGTGAAAGCCTGGGCTGCCCTGAGCGAATTTACCGGTCGTGACCATACGCATCTGGCGCTg < 1:1907621/71‑1 (MQ=255)
cAGGTAGCCGTGAAAGCCTGGGCTGCCCTGAGCGAATTTACCGGTCg > 1:2598438/1‑47 (MQ=255)
|
CCAGCCGATGCTGAACACCGCAATTGATGCGGCAGAGATGATCCTGACACTGGCACCGGAAACCAACGGTCAGGTAGCCGTGAAAGCCTGGGCTGCCCTGAGCGAATTTACCGGTCGTGACCATACGCATCTGGCGCTG > Exported/834368‑834506
|
| 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
