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 F21 I0 R1
|
2169 |
63.0 |
3952800 |
76.2% |
3012033 |
62.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
833,258 |
G→T |
15.8% |
G572G (GGG→GGT) |
narG → |
nitrate reductase 1, alpha subunit |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 833,258 | 0 | G | T | 15.8%
| 123.5
/ 5.8
| 43 | G572G (GGG→GGT) | narG | nitrate reductase 1, alpha subunit |
| Reads supporting (aligned to +/- strand): ref base G (16/20); new base T (2/5); total (18/25) |
| Fisher's exact test for biased strand distribution p-value = 6.80e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
ATCACCTCGATATGAACTATCGTGGTCTGATCAACATGCTGATTTTCTGCGGCTGTGTCGGTCAGAGCGGGGGCGGCTGGGCGCACTATGTAGGTCAGGAAAAACTGCGTCCGCAAACCGGCTGGCAGCCGCTGGCGTTTG > minE/833188‑833328
|
aTCACCTCGATATGAACTATCGTGGTCTGATCAACATGCTGATTTTCTGCGGCTGTGTCGGTCAGAGCggg > 1:3192615/1‑71 (MQ=255)
tCACCTCGATATGAACTATCGTGGTCTGATCAACATGCTGATTTTCTGCGGCTGTGTCGGTCAGAGCgggg > 1:3019126/1‑71 (MQ=255)
cGATATGAACTATCGTGGTCTGATCAACATGCTGATTTTCTGCGGCTGTGTCGGTCAGAGCGGGGGCGGCt > 1:707151/1‑71 (MQ=255)
gATATGAACTATCGTGGTCTGATCAACATGCTGATTTTCTGCGGCTGTGTCGGTCAGAGCGGGGGCGGCt < 1:593856/70‑1 (MQ=255)
gATATGAACTATCGTGGTCTGATCAACATGCTGATTTTCTGCGGCTGTGTCGGTCAGAGCGGGGGCGGCTg < 1:2358624/71‑1 (MQ=255)
tGAACTATCGTGGTCTGATCAACATGCTGATTTTCTGCGGCTGTGTCGGTCAGAGCGGGGGCGGCTGGgc < 1:1425439/70‑1 (MQ=255)
gAACTATCGTGGTCTGATCAACATGCTGATTTTCTGCGGCTGTGTCGGTCAGAGCggggg < 1:2117250/60‑1 (MQ=255)
tCGTGGTCTGATCAACATGCTGATTTTCTGCGGCTGTGTCGGTCAGAGCGGGGGCGGCTGGGCGCACTATg > 1:3229928/1‑71 (MQ=255)
cGTGGTCTGATCAACATGCTGATTTTCTGCGGCTGTGTCGGTCAGAGCGGGGGCGGCTGGGCGCACTATg > 1:937595/1‑70 (MQ=255)
gTGGTCTGATCAACATGCTGATTTTCTGCGGCTGTGTCGGTCAGAGCGGGGGCGGCTGGGCGCACTATGt < 1:3169175/70‑1 (MQ=255)
gTCTGATCAACATGCTGATTTTCTGCGGCTGTGTCGGTCAGAGCgggg > 1:2546758/1‑48 (MQ=255)
aTCAATATGCTGATCTTCTGCGGTTGTGTCGGGCAAAGCGGTGGCGGCTGGGCACACTATGTCGGCCAg > 1:1017707/1‑69 (MQ=255)
aTCAACATGCTGATTTTCTGCGGCTGTGTCGGTCAGAGCGGGggcgg > 1:514187/1‑47 (MQ=255)
aTCAACATGCTGATTTTCTGCGGCTGTGTCGGTCAGAGCGGGggcgg > 1:2649595/1‑47 (MQ=255)
aTCAACATGCTGATTTTCTGCGGCTGTGTCGGTCAGAGCGGGggcgg > 1:2610281/1‑47 (MQ=255)
aTCAACATGCTGATTTTCTGCGGCTGTGTCGGTCAGAGCGGGggcgg > 1:2196467/1‑47 (MQ=255)
cAACATGCTGATTTTCTGCGGCTGTGTCGGTCAGAGCGGGGGCGGCTGGGCGCACTATGTAGGTCAGGaa > 1:101332/1‑70 (MQ=255)
cAACATGCTGATTTTCTGCGGCTGTGTCGGTCAGAGCGGGGGCGGCTGGGCGCACTATGTAGGTCAGGaa > 1:2285684/1‑70 (MQ=255)
cAACATGCTGATTTTCTGCGGCTGTGTCGGTCAGAGCGGGGGCGGCTGGGCGCACTATGTAGGTCAGGaa > 1:1672617/1‑70 (MQ=255)
aaCATGCTGATTTTCTGCGGCTGTGTCGGTCAGAGCGGGGGCGGCTGGGCGCACTATGTAGGTCAGGaaaa < 1:2775460/71‑1 (MQ=255)
aCATGCTGATTTTCTGCGGCTGTGTCGGTCAGAGCGGGGGCGGCTGGGCGCACTATGTAGGTCAGGaaaaa < 1:3908201/71‑1 (MQ=255)
aCATGCTGATTTTCTGCGGCTGTGTCGGTCAGAGCGGGGGCGGCTGGGCGCACTATGTAGGTCAGGaaaaa < 1:2876246/71‑1 (MQ=255)
cATGCTGATTTTCTGCGGCTGTGTCGGTCAGAGCGGGGGCGGCTGGGCGCACTATGt > 1:14721/1‑57 (MQ=255)
cATGCTGATTTTCTGCGGCTGTGTCGGTCAGAGCGGGGGCGGCTGGGCGCACTATGTAGGTCAGGAAAAAc > 1:2136151/1‑71 (MQ=255)
aTGCTGATTTTCTGCGGCTGTGTCGGTCAGAGCGGGGGCGGCTGGGCGCACTATGTAGGTCAGGAAAAACt > 1:1388559/1‑71 (MQ=255)
tGCTGATCTTCTGCGGTTGTGTCGGGCAAAGCGGTGGCGGCTGGGCACACTATGTCGGCCAGGAAAAACTg < 1:2421184/71‑1 (MQ=255)
tGCTGATCTTCTGCGGTTGTGTCGGGCAAAGCGGTGGCGGCTGGGCACACTATGTCGGCCAGGAAAAACTg > 1:2992050/1‑71 (MQ=255)
cTGATTTTCTGCGGCTGTGTCGGTCAGAGCGGGGGCGGCTGGGCGCACTATGTAGGTCAGGAAAAACTGCg < 1:1008393/71‑1 (MQ=255)
tGATCTTCTGCGGTTGTGTCGGGCAAAGCGGTGGCGGCTGGgc < 1:320456/43‑1 (MQ=255)
gATTTTCTGCGGCTGTGTCGGTCAGAGCGGGGGCGGCTGGGCGCACTATGTAGGTCAGGAAAAACTGCGt > 1:3474505/1‑70 (MQ=255)
tCTGCGGCTGTGTCGGTCAGAGCGGGGGCGGCTGGGCGCACTATGTAGGTCAGGaaa < 1:3760383/57‑1 (MQ=255)
cTGCGGTTGTGTCGGGCAAAGCGGTGGCGGCTGGGCACACTATGTCGGCCAGGAAAAACTGCGCCcaca < 1:780955/69‑1 (MQ=255)
cTGCGGCTGTGTCGGTCAGAGCGGGGGCGGCTGGGCGCACTATGTAGGTCAGGAAAAACTGCGTCCGCaa < 1:2464834/70‑1 (MQ=255)
gCGGCTGTGTCGGTCAGAGCGGGGGCGGCTGGGCGCACTATGTAGGTCAGGAAAAACTGCGTCCGCAAAcc > 1:2004451/1‑71 (MQ=255)
gttgtgTCGGGCAAAGCGGTGGCGGCTGGGCACACTATGTCGGCCAGGAAAAACTGCGCCCACAAACCGGc < 1:2975396/69‑1 (MQ=255)
gCTGTGTCGGTCAGAGCGGGGGCGGCTGGGCGCACTATGTAGGTCAGGaaa < 1:1182187/51‑1 (MQ=255)
tCGGTCAGAGCGGGGGCGGCTGGGCGCACTATGTAGGTCAGGAAAAACTGCGTCCGCAAACCGGCTGGc < 1:3643274/69‑1 (MQ=255)
tCGGGCAGAGCGGGGGCGGCTGGGCGCACTATGTAGGTCAGGAAAAACTGCGGCCGCAAACCGGCTGGCAg < 1:3522510/71‑1 (MQ=255)
tCAGAGCGGGGGCGGCTGGGCGCACTATGTAGGTCAGGAAAAACTGCGTCCGCAAACCGGCTGGCAGCCGc < 1:2587079/71‑1 (MQ=255)
tCAGAGCGGGGGCGGCTGGGCGCACTATGTAGGTCAGGAAAAACTGCGTCCGCAAACCGGCTGGCAGCCGc < 1:852018/71‑1 (MQ=255)
gagCGGGGGCGGCTGGGCGCACTATGTAGGTCAGGAAAAACTGCGTcc > 1:3593555/1‑48 (MQ=255)
gagCGGGGGCGGCTGGGCGAACTATGTAGGTCAGGAAAAACTGCGTCCGCa < 1:1821906/51‑1 (MQ=255)
agCGGGGGCGGCTGGGCGCACTATGTAGGTCAGGAAAAACTGCGTCCGCAAACCGGCTGGCAGCAGCTGGc < 1:2408/71‑1 (MQ=255)
gCGGTGGCGGCTGGGCACACTATGTCGGCCAGGAAAAACTGCGCCCACAAACCGGCTGGTTGCCACTGGcc < 1:3840797/71‑2 (MQ=255)
gCGGGGGCGGCTGGGCGCACTATGTAGGTCAGGAAAAACTGCGTCCGCAAACCGGCTGGCAGCCGCTGGCg < 1:3947740/71‑1 (MQ=255)
cGGGGGCGGCTGGGCGCACTATGTAGGTCAGGaaa < 1:111556/35‑1 (MQ=255)
cGGGGGCGGCTGGGCGCACTATGTAGGTCAGGAAAAACTGCGTCCGCAAACCGGCTGGCAGCCGCTGGCGt < 1:3939621/71‑1 (MQ=255)
gggCGGCTGGGCGCACTATGTAGGTCAGGAAAAACTGCGTCCGCAAACCGGCTGGCAGCCGCTGGCGTTTg > 1:1326532/1‑71 (MQ=255)
|
ATCACCTCGATATGAACTATCGTGGTCTGATCAACATGCTGATTTTCTGCGGCTGTGTCGGTCAGAGCGGGGGCGGCTGGGCGCACTATGTAGGTCAGGAAAAACTGCGTCCGCAAACCGGCTGGCAGCCGCTGGCGTTTG > minE/833188‑833328
|
| 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
