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 |
333,415 |
G→A |
30.7% |
A11A (GCG→GCA) |
ushA → |
bifunctional UDP‑sugar hydrolase and 5'‑nucleotidase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 333,415 | 0 | G | A | 30.7%
| 59.6
/ 29.5
| 65 | A11A (GCG→GCA) | ushA | bifunctional UDP‑sugar hydrolase and 5'‑nucleotidase |
| Reads supporting (aligned to +/- strand): ref base G (12/33); new base A (6/14); total (18/47) |
| Fisher's exact test for biased strand distribution p-value = 7.73e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
TTTCAACACGTTGAAATCAGGTCAGGGAGAGAAGTATGAAATTATTGCAGCGGGGCGTGGCGTTAGCGCTGTTAACCACATTTACACTGGCGAGTGAAACTGCTCTGGCGTATGAGCAGGATAAAACC > minE/333348‑333475
|
tttCAACACGTTGAAATCAGGTCAGGGAGAGAAGTATGAAATTATTGCAGCGGGGCGTGGCGTTAgcgc > 1:897202/1‑69 (MQ=255)
tttCAACACGTTGAAATCAGGTCAGGGAGAGAAGTATGAAATTATTGCAGCGGGGCGTGGCGTTAgcgc > 1:2118365/1‑69 (MQ=255)
tttCAACACGTTGAAATCAGGTCAGGGAGAGAAGTATGAAATTATTGCAGCGGGGCGTGGCGTTAgcgc > 1:2165426/1‑69 (MQ=255)
tttCAACACGTTGAAATCAGGTCAGGGAGAGAAGTATGAAATTATTGCAGCGGGGCGTGGCGTTAgcgc > 1:455519/1‑69 (MQ=255)
tttCAACACGTTGAAATCAGGTCAGGGAGAGAAGTATGAAATTATTGCAGCGGGGCGTGGCGTTAgcgc > 1:57027/1‑69 (MQ=255)
tttCAACACGTTGAAATCAGGTCAGGGAGAGAAGTATGAAATTATTGAAGCGGGGCGTGGCGTTAgcgc > 1:3217576/1‑69 (MQ=255)
tttCAACACGTTGAAATCAGGTCAGGGAGAGAAGTATGAAATTATCGCAGCGGGGCGTGGCGTTAgcgc > 1:136183/1‑69 (MQ=255)
tttCAACACGTTGAAATCAGGTCACGGAGAGAAGTATGAAATTATTGCAGCGGGGCGTGGCGTTAgcgc > 1:2104150/1‑69 (MQ=255)
ttGAAATCAGGTCAGGGAGAGAAGTATGAAATTATTGCAGCGGGGCGTGGCGTTAGCACTGTTAACcac > 1:643400/1‑69 (MQ=255)
ttGAAATCAGGTCAGGGAGAGAAGTATGAAATTATTGCAGCGGGGCGTGGCGTTAGCACTGTTAACcac > 1:1285374/1‑69 (MQ=255)
ttGAAATCAGGTCAGGGAGAGAAGTATGAAATTATTGCAGCGGGGCGTGGCGTTAGCACTGTTAACcac > 1:1056155/1‑69 (MQ=255)
ttGAAATCAGGTCAGGGAGAGAAGTATGAAATTATTGCAGCGGGGCGTGGCGTTAGCACTGTTAACcac > 1:1000765/1‑69 (MQ=255)
ttGAAATCAGGTCAGGGAGAGAAGTATGAAATTATTGCAGCGGGGCGTGGCGTTAGCACTGTTAACcac > 1:2550298/1‑69 (MQ=255)
ttGAAATCAGGTCAGGGAGAGAAGTATGAAATTATTGCAGCGGGGCGTGGCGTTAGCACTGATAACcac > 1:246615/1‑69 (MQ=255)
aaTCAGGTCAGGGAGAGAAGTATGAAATTATTGCAGCGGGGCGTGGCGTTAGCGCTGTTAACCACAtt < 1:559597/68‑1 (MQ=255)
aTCAGGTCAGGGAGAGAAGTATGAAATTATTGCAGCGGGGCGTGGCGTTAGCGCTGTTAACCACATTTa < 1:1262903/69‑1 (MQ=255)
aTCAGGTCAGGGAGAGAAGTATGAAATTATTGCAGCGGGGCGTGGCGTTAGCGCTGTTAACCACATTTa < 1:698943/69‑1 (MQ=255)
aTCAGGTCAGGGAGAGAAGTATGAAATTATTGCAGCGGGGCGTGGCGTTAGCGCTGTTAACCACATTTa < 1:3224734/69‑1 (MQ=255)
aTCAGGTCAGGGAGAGAAGTATGAAATTATTGCAGCGGGGCGTGGCGTTAGCGCTGTTAACCACATTTa < 1:1167183/69‑1 (MQ=255)
aTCAGGTCAGGGAGAGAAGTATGAAATTATTGCAGCGGGGCGTGGCGTTAGCGCTGTTAACCACATTTa < 1:2569753/69‑1 (MQ=255)
gtcaggGAGAGAAGTATGAAATTATTGCAGCGGGGCGTGGCGTTAGCGCTGTTAACCACATTTACACTg > 1:1077119/1‑69 (MQ=255)
gtcaggGAGAGAAGTATGAAATTATTGCAGCGGGGCGTGGCGTTAGCGCTGTTAACCACATTTACACTg > 1:2835964/1‑69 (MQ=255)
gagaAGTATGAAATTATTGCAGCGGGGCGTGGCGTTAGCGCTGTTAACCACATTTACACTGGCGAGTGa < 1:3277696/69‑1 (MQ=255)
gagaAGTATGAAATTATTGCAGCGGGGCGTGGCGTTAGCGCTGTTAACCACATTTACACTGGCGAGTGa < 1:721817/69‑1 (MQ=255)
gagaAGTATGAAATTATTGCAGCGGGGCGTGGCGTTAGCGCTGTTAACCACATTTACACTGGCGAGTGa < 1:2441227/69‑1 (MQ=255)
gagaAGTATGAAATTATTGCAGCGGGGCGTGGCGTTAGCGCTGTTAACCACATTTACACTGGCGAGTGa < 1:1015862/69‑1 (MQ=255)
agaAGTATGAAATTATTGCAGCGGGGCGTGGCGTTAGCGCTGTTAACCACATTTACACTGGCGAGTGaa < 1:1974373/69‑1 (MQ=255)
agaAGTATGAAATTATTGCAGCGGGGCGTGGCGTTAGCGCTGTTAACCACATTTACACTGGCGAGTGaa < 1:2077448/69‑1 (MQ=255)
agaAGTATGAAATTATTGCAGCGGGGCGTGGCGTTAGCGCTGTTAACCACATTTACACTGGCGAGTGaa < 1:1090833/69‑1 (MQ=255)
agaAGTATGAAATTATTGCAGCGGGGCGTGGCGTTAGCGCTGTTAACCACATTTACACTGGCGAGTGaa < 1:661313/69‑1 (MQ=255)
agaAGTATGAAATTATTGCAGCGGGGCGTGGCGTTAGCGCTGTTAACCACATTTACACTGGCGAGTGaa < 1:2130401/69‑1 (MQ=255)
agaAGTATGAAATTATTGCAGCGGGGCGTGGCGTTAGCGCTGTTAACCACATTTACACTGGCGAGTGaa < 1:1419013/69‑1 (MQ=255)
agaAGTATGAAATTATTGCAGCGGGGCGTGGCGTTAGCGCTGTTAACCACATTTACACTGGCGAGTGaa < 1:1439044/69‑1 (MQ=255)
agaAGTATGAAATTATTGCAGCGGGGCGTGGCGTTAGCGCTGTTAACCACATTTACACTGGCGAGTGaa < 1:1453953/69‑1 (MQ=255)
agaAGTATGAAATTATTGCAGCGGGGCGTGGCGTTAGCGCTGTTAACCACATTTACACTGGCGAGTGaa < 1:2250232/69‑1 (MQ=255)
agaAGTATGAAATTATTGCAGCGGGGCGTGGCGTTAGCGCTGTTAACCACATTTACACTGGCGAGTGaa < 1:2422132/69‑1 (MQ=255)
gaAGTATGAAATTATTGCAGCGGGGCGTGGCGTTAGCGCTGTTAACCACATTTACACTGGCGAGTGaa < 1:2868988/68‑1 (MQ=255)
tATGAAATTATTGCAGCGGGGCGTGGCGTTAGCGCTGTTAACCACATTTACACTGGCGAGTGAAACTGc < 1:418288/69‑1 (MQ=255)
tATGAAATTATTGCAGCGGGGCGTGGCGTTAGCGCTGTTAACCACATTTACACTGGCGAGTGAAACTGc < 1:1280147/69‑1 (MQ=255)
tGAAATTATTGCAGCGGGGCGTGGCGTTAGCGCTGTTAACCACATTTACACTGGCGAGTGAAACTGctc > 1:1023183/1‑69 (MQ=255)
tGAAATTATTGCAGCGGGGCGTGGCGTTAGCGCTGTTAACCACATTTACACTGGCGAGTGAAACTGctc > 1:2624033/1‑69 (MQ=255)
tGAAATTATTGCAGCGGGGCGTGGCGTTAGCGCTGTTAACCACATTTACACTGGCGAGTGAAACTGctc > 1:1398251/1‑69 (MQ=255)
tGAAATTATTGCAGCGGGGCGTGGCGTTAGCGCTGTTAACCACATTTACACTGGCGAGTGAAACTGctc > 1:1206759/1‑69 (MQ=255)
tGAAATTATTGCAGCGGGGCGTGGCGTTAGCGCTGTTAACCACATTTACACTGGCGAGTGAAACTGctc > 1:1431407/1‑69 (MQ=255)
tGAAATTATTGCAGCGGGGCGTGGCGTTAGCGCTGTTAACCACATTTACACTGGCGAGTGAAACTGctc > 1:1147216/1‑69 (MQ=255)
ttattGCAGCTGGGCGTGGCGTTAGCACTGTTAACcac < 1:3061377/38‑1 (MQ=38)
ttattGCAGCGGGGCGTGGCGTTAGCGCTGTTAACCACATTTACACTGGCGAGTGAAACTGCTCTTGCg < 1:3387408/69‑1 (MQ=255)
ttattGCAGCGGGGCGTGGCGTTAGCGCTGTTAACCACATTTACACTGGCGAGTGAAACTGCTCTGGCg < 1:1332288/69‑1 (MQ=255)
ttattGCAGCGGGGCGTGGCGTTAGCACTGTTAACcac < 1:1731591/38‑1 (MQ=255)
ttattGCAGCGGGGCGTGGCGTTAGCACTGTTAACcac < 1:342003/38‑1 (MQ=255)
ttattGCAGCGGGGCGTGGCGTTAGCACTGTTAACcac < 1:3363480/38‑1 (MQ=255)
ttattGCAGCGGGGCGTGGCGTTAGCACTGTTAACcac < 1:618646/38‑1 (MQ=255)
ttattGCAGCGGGGCGTGGCGTTAGCACTGTTAACcac < 1:2763923/38‑1 (MQ=255)
ttattGCAGCGGGGCGTGGCGTTAGCACTGTTAACcac < 1:66676/38‑1 (MQ=255)
ttattGCAGCGGGGCGTGGCGTTAGCACTGTTAACcac < 1:262874/38‑1 (MQ=255)
ttattGCAGCGGGGCGTGGCGTTAGCACTGTTAACcac < 1:2216023/38‑1 (MQ=255)
ttattGCAGCGGGGCGTGGCGTTAGCACTGTTAACcac < 1:2221558/38‑1 (MQ=255)
ttattGCAGCGGGGCGTGGCGTTAGCACTGTTAACcac < 1:1773385/38‑1 (MQ=255)
ttattGCAGCGGGGCGTGGCGTTAGCACTGTTAACcac < 1:1477112/38‑1 (MQ=255)
ttattGCAGCGGGGCGTGGCGTTAGCACTGTTAACcac < 1:2461442/38‑1 (MQ=255)
ttattGCAGCGGGGCGTGGCGTTAGCACTGTCAACcac < 1:435289/38‑1 (MQ=38)
gcgtTAGCGCTGTTAACCACATTTACACTGGCGAGTGAAACTGCTCTGGCGTATGAGCAGGATAAAAcc > 1:1952211/1‑69 (MQ=255)
gcgtTAGCGCTGTTAACCACATTTACACTGGCGAGTGAAACTGCTCTGGCGTATGAGCAGGATAAAAcc > 1:3424761/1‑69 (MQ=255)
gcgtTAGCGCTGTTAACCACATTTACACTGGCGAGTGAAACTGCTCTGGCGTATGAGCAGGATAAAAcc > 1:303416/1‑69 (MQ=255)
gcgtTAGCGCTGTTAACCACATTTACACTGGCGAGTGAAACTGCTCTGGCGTATGAGCAGGATAAAAcc > 1:2920059/1‑69 (MQ=255)
aGCGCTGTTAACCACATTTACACTGGCGAGTGAAACTGCTCTGGCg < 1:1689585/46‑1 (MQ=255)
aGCGCTGTTAACCACATTTACACTGGCGAGTGAAACTGCTCTGGCg < 1:3205715/46‑1 (MQ=255)
aGCGCTGTTAACCACATTTACACTGGCGAGTGAAACTGCTCTGGCg < 1:3137958/46‑1 (MQ=255)
aGCGCTGTTAACCACATTTACACTGGCGAGTGAAACTGCTCTGGCg < 1:1181918/46‑1 (MQ=255)
aGCGCTGTTAACCACATTTACACTGGCGAGTGAAACTGCTCTGGCg < 1:1879804/46‑1 (MQ=255)
aGCGCTGTTAACCACATTTACACTGGCGAGTGAAACTGCTCTGGCg < 1:2657338/46‑1 (MQ=255)
aGCGCTGTTAACCACATTTACACTGGCGAGTGAAACTGCTCTGGCg < 1:2501422/46‑1 (MQ=255)
aGCGCTGTTAACCACATTTACACTGGCGAGTGAAACTGCTCTGGCg < 1:1663265/46‑1 (MQ=255)
gcTGTTAACCACATTTACACTGGCGAGTGAAACTGc < 1:2525461/36‑1 (MQ=255)
|
TTTCAACACGTTGAAATCAGGTCAGGGAGAGAAGTATGAAATTATTGCAGCGGGGCGTGGCGTTAGCGCTGTTAACCACATTTACACTGGCGAGTGAAACTGCTCTGGCGTATGAGCAGGATAAAACC > minE/333348‑333475
|
| 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
