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 F28 I2 R2
|
64 |
60.0 |
3197630 |
92.7% |
2964203 |
60.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
minE |
1,522,743 |
T→C |
I121V (ATC→GTC) |
pdxB ← |
erythronate‑4‑phosphate dehydrogenase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,522,743 | 0 | T | C | 98.6%
| 256.7
/ ‑4.2
| 72 | I121V (ATC→GTC) | pdxB | erythronate‑4‑phosphate dehydrogenase |
| Reads supporting (aligned to +/- strand): ref base T (0/1); new base C (38/32); total (39/33) |
| Fisher's exact test for biased strand distribution p-value = 4.65e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.90e-01 |
TTTAATCCCTAACGCTTCCAGTCGCGCCTGCAATCGACGTCCAACGTTACCAACGCCCACGATCCCCACCGTACGGTCGTACAGTGAAAATCCATCGCGTTCGGCAAGCATCAGCAGGGAGGAGAAAA > minE/1522681‑1522808
|
tttAATCCCTAACGCTTCCAGTCGCGCCTGCAATCGACGTCCAACGTTACCAACGCCCACGACCCCCACCg > 1:939860/1‑71 (MQ=255)
ttAATCCCTAACGCTTCCAGTCGCGCCTGCAATCGCCGTCCAACGTTACCAACGCCCACGCCCCCCACCg > 1:1458141/1‑70 (MQ=255)
tCCCTAACGCTTCCAGTCGCGCCTGCAATCGACGTCCAACGTTACCAACGCCCACGACCCCCACCGTAc < 1:1604280/69‑1 (MQ=255)
cTAACGCTTCCAGTCGCGCCTGCAATCGACGTCCAACGTTACCAACGCCCACGACCCCCACCGTACGGTCg < 1:761837/71‑1 (MQ=255)
tAACGCTTCCAGTCGCGCCTGCAATCGACGTCCAACGTTACCAACGCCCACGACCCCCACCGTa > 1:100307/1‑64 (MQ=255)
tAACGCTTCCAGTCGCGCCTGCAATCGACGTCCAACGTTACCAACGCCCACGACCCCCACCGTa > 1:1451270/1‑64 (MQ=255)
tAACGCTTCCAGTCGCGCCTGCAATCGACGTCCAACGTTACCAACGCCCACGACCCCCACCGTa > 1:242287/1‑64 (MQ=255)
aCGCTTCCAGTCGCGCCTGCAATCGACGTCCAACGTTACCAACGCCCACGACCCCCACCGTAc < 1:1167621/63‑1 (MQ=255)
aCGCTTCCAGTCGCGCCTGCAATCGACGTCCAACGTTACCAACGCCCACGACCCCCACCGTACGGTCGTa < 1:1937742/70‑1 (MQ=255)
gCTTCCAGTCGCGCCTGCAATCGACGTCCAACGTTACCAACGCCCACGACCCCCACCGTACGGTCGTACAg > 1:1126927/1‑71 (MQ=255)
tCCAGTCGCGCCTGCAATCGACGTCCAACGTTACCAACGCCCACGACCCCCACCGTa < 1:2330028/57‑1 (MQ=255)
tCCAGTCGCGCCTGCAATCGACGTCCAACGTTACCAACGCCCACGACCCCCACCGTa < 1:1909766/57‑1 (MQ=255)
tCCAGTCGCGCCTGCAATCGACGTCCAACGTTACCAACGCCCACGACCCCCACCGTa < 1:1426230/57‑1 (MQ=255)
ccAGTCGCGCCTGCAATCGACGTCCAACGTTACCAACGCCCACGACCCCCACCGTa < 1:2399067/56‑1 (MQ=255)
cAGTCGCGCCTGCAATCGACGTCCAACGTTACCAACGCCCACGACCCCCACCGTACGGTCGTACAGTGaaa < 1:2843220/71‑1 (MQ=255)
cAGTCGCGCCTGCAATCGACGTCCAACGTTACCAACGCCCACGACCCCCACCGTACGGTCGTACAGTGaa > 1:1409847/1‑70 (MQ=255)
aGTCGCGCCTGCAATCGACGTCCAACGTTACCAACGCCCACGACCGCCACCGTACGGTCGTACAGTGaaaa > 1:1054213/1‑71 (MQ=255)
aGTCGCGCCTGCAATCGACGTCCAACGTTACCAACGCCCACGACCCCCACCGTACGGTCGTACAGTGaaaa > 1:383252/1‑71 (MQ=255)
aGTCGCGCCTGCAATCGACGTCCAACGTTACCAACGCCCACGACCCCCACCGTACGGTCGTACAGTGaaaa > 1:1164572/1‑71 (MQ=255)
aGTCGCGCCTGCAATCGACGTCCAACGTTACCAACGCCCACGACCCCCACCGTACGGTCGTACAGTGaaaa > 1:2472905/1‑71 (MQ=255)
aGTCGCGCCTGCAATCGACGTCCAACGTTACCAACGCCCACGACCCCCACCGTACGGTCGTACAGTGaa < 1:976275/69‑1 (MQ=255)
aGTCGCGCCTGCAATCGACGTCCAACGTTACCAACGCCCACGACCCCCACCGTACGGTCGTACAGTGaa < 1:2800828/69‑1 (MQ=255)
gTCGCGCCTGCAATCGACGTCCAACGTTACCAACGCCCACGACCCCCACCGTACGGTCGTACAGTGAAAAt > 1:3155659/1‑71 (MQ=255)
gTCGCGCCTGCAATCGACGTCCAACGTTACCAACGCCCACGACCCCCACCGTACGGTCGTACAGTGAAAAt > 1:2596798/1‑71 (MQ=255)
gcgcCTGCAATCGACGTCCAACGTTACCAACGCCCACGACCCCCACCGTACGGTCGTACAGTGAAAATCCa < 1:654147/71‑1 (MQ=255)
cgcCTGCAATCGACGTCCAACGTTACCAACGCCCACGACCCCCACCGTACGGTCGTACAGTGAAAATCCa < 1:53359/70‑1 (MQ=255)
gcCTGCAATCGACGTCCAACGTTACCAACGCCCACGACCCCCACCGTACGGTCGTACAGTGAAAATCCATc > 1:94798/1‑71 (MQ=255)
gcCTGCAATCGACGTCCAACGTTACCAACGCCCACGACCCCCACCGTACGGTCGTACAGTGAAAATCCATc > 1:2426968/1‑71 (MQ=255)
cTGCAATCGACGTCCAACGTTACCAACGCCCACGACCCCCACCGTACGGTCGTACAGTGaa < 1:1777468/61‑1 (MQ=255)
cTGCAATCGACGTCCAACGTTACCAACGCCCACGACCCCCACCGTACGGTCGTACAGTGaa < 1:2476398/61‑1 (MQ=255)
gCAATCGACGTCCAACGTTACCAACGCCCACGACCCCCACCGTACGGTCGTACAGTGAAAATCCa > 1:947209/1‑65 (MQ=255)
gCAATCGACGTCCAACGTTACCAACGCCCACGACCCCCACCGTACGGTCGTACAGTGAAAATCCATCGCGt > 1:2580561/1‑71 (MQ=255)
cAATCGACGTCCAACGTTACCAACGCCCACGACCCCCACCGTACGGTCGTACAGTGAAAATCCATCGCGt < 1:1271560/70‑1 (MQ=255)
aaTCGACGTCCAACGTTACCAACGCCCACGACCCCCACCGTACGGTCGTACAGTGAAAATCCATCGCGTTc > 1:1490778/1‑71 (MQ=255)
tCGACGTCCAACGTTACCAACGCCCACGATCCCCACCGTACGGTCGTACAGTGAAAATCCATcgcg < 1:1857063/66‑1 (MQ=255)
gACGTCCAACGTTACCAACGCCCACGACCCCCACCGTACGGTCGTACAGTGAAAATCCATCGCGTTCg < 1:1138826/68‑1 (MQ=255)
gACCTCCAACCTTACCAACGCCCACGACCCCCACCGTACGGTCCTACAGTGAAAATCCATCGCGTTCGGc > 1:1993557/1‑70 (MQ=255)
cGTCCAACGTTACCAACGCCCACGACCCCCACCGTACGGTCGTACAGTGAAAATCCATCGCGTTCGGc > 1:2993358/1‑68 (MQ=255)
cGTCCAACGTTACCAACGCCCACGACCCCCACCGTACGGTCGTACAGTGAAAATCCATCGCGTTCGGc > 1:2697199/1‑68 (MQ=255)
cGTCCAACGTTACCAACGCCCACGACCCCCACCGTACGGTCGTACAGTGAAAATCCATCGCGTTCGGc > 1:2606337/1‑68 (MQ=255)
tCCAACGTTACCAACGCCCACGACCCCCACCGTACGGTCGTACAGTGAAAATCCATCGCGTTCGGCAAGCa < 1:2597958/71‑1 (MQ=255)
ccAACGTTACCAACGCCCACGACCCCCACCGTACGGTCGTACAGTGAAAATCCATCGCGt < 1:2492760/60‑1 (MQ=255)
aaCGTTACCAACGCCCACGACCCCCACCGTACGGTCGTACAGTGAAAATCCATCGCGTTCGGCAAGCAt > 1:1225424/1‑69 (MQ=255)
aaCGTTACCAACGCCCACGACCCCCACCGTACGGTCGTACAGTGAAAATCCATCGCGTTCGGCAAGCAt > 1:2003325/1‑69 (MQ=255)
aCGTTACCAACGCCCACGACCCCCACCGTACGGTCGt < 1:65911/37‑1 (MQ=255)
aCGTTACCAACGCCCACGACCCCCACCGTACGGTCGt < 1:1755425/37‑1 (MQ=255)
aCGTTACCAACGCCCACGACCCCCACCGTACGGTCGt < 1:1843504/37‑1 (MQ=255)
aCGTTACCAACGCCCACGACCCCCACCGTACGGTCGt < 1:2598604/37‑1 (MQ=255)
aCGTTACCAACGCCCACGACCCCCACCGTACGGTCGTACAGTGAAAATCCATCGCGTTCGGCAAGCATcag < 1:1985435/71‑1 (MQ=255)
aCGTTACCAACGCCCACGACCCACACCGTACGGTCGt < 1:1761447/37‑1 (MQ=38)
aCCAACGCCCACGACCCCCACCGTACGGTCGTACAGTGAAAATCCATCGCGTTCg < 1:955086/55‑1 (MQ=255)
aCCAACGCCCACGACCCCCACCGTACGGTCGTACAGTGAAAATCCATCGCGTTCGGCAAGCATCAGCAgg > 1:2600809/1‑70 (MQ=255)
aCCAACGCCCACGACCCCCACCGTACGGTCGTACAGTGAAAATCCATCGCGTTCGGCAAGCATCAGCAgg > 1:3106140/1‑70 (MQ=255)
aCCAACGCCCACGA‑CCCCACCGTACGGTCGTACAGTGAAACTCCATCGCGTTCGGCAAGCATCAGCAgg > 1:1313237/1‑69 (MQ=255)
ccAACGCCCACGACCCCCACCGTACGGTCGTACAGTGAAAATCCATCGCGTTCGGCAAGCATCAGCAgg > 1:684222/1‑69 (MQ=255)
ccAACGCCCACGACCCCCACCGTACGGTCGTACAGTGAAAATCCATCGCGTTCGGCAAGCATCAGCAGgga < 1:1335999/71‑1 (MQ=255)
aCGCCCACGACCCCCACCGTACGGTCGTACAGTGAAAATCCATCGCGTTCGGCAAGCATCAGCAGggag > 1:431871/1‑69 (MQ=255)
aCGCCCACGACCCCCACCGTACGGTCGTACAGTGAAAATCCATCGCGTTCGGCAAGCATCAGCAGggag > 1:1467210/1‑69 (MQ=255)
aCGCCCACGACCCCCACCGTACGGTCGTACAGTGAAAATCCATCGCGTTCGGCAAGCATCAGCAGggag > 1:2263257/1‑69 (MQ=255)
aCGCCCACGACCCCCACCGTAAGGTCGTACAGTGAAAATCCATCGCGTTCGGCAAGCATCAGCAGggag > 1:1319162/1‑69 (MQ=255)
cGCCCACGACCCCCACCGTACGGTCGTACAGTGAAAATCCATCGCGTTc < 1:2018777/49‑1 (MQ=255)
cGCCCACGACCCCCACCGTACGGTCGTACAGTGAAAATCCATCGCGTTCGGCAAGCATCAGCAGggag > 1:2990618/1‑68 (MQ=255)
cccACGACCCCCACCGTACGGTCGTACAGTGAAAATCCATCGCGTTCGGCAAGCATcagca < 1:2515043/61‑1 (MQ=255)
cccACGACCCCCACCGTACGGTCGTACAGTGAAAATCCATCGCGTTCGGCAAGCATcagca < 1:661642/61‑1 (MQ=255)
cccACGACCCCCACCGTACGGTCGTACAGTGAAAATCCATCGCGTTCGGCAAGCATcagca < 1:1779873/61‑1 (MQ=255)
cACGACCCCCACCGTACGGTCGTACAGTGAAAATCCATCGCGTTCGGCAAGCATCAGCAGGGAGGAGaaaa > 1:2238034/1‑71 (MQ=255)
cACGACCCCCACCGTACGGTCGTACAGTGAAAATCCATCGCGTTCGGCAAGCATCAGCAGGGAGGAGaaaa < 1:2065874/71‑1 (MQ=255)
cACGACCCCCACCGTACGGTCGTACAGTGAAAATCCATCGCGTTCGGCAAGCATCAGCAGGGAGGAGaaaa > 1:775135/1‑71 (MQ=255)
cACGACCCCCACCGTACGGTCGTACAGTGAAAATCCATCGCGTTCGGCAAGCATCAGCAGGGAGGAGaaaa > 1:1899877/1‑71 (MQ=255)
cACGACCCCCACCGTACGGTCGTACAGTGAAAATCCATCGCGTTCGGCAAGCATCAGCAGGGAGGAGaaaa > 1:986978/1‑71 (MQ=255)
cGACCCCCACCGTACGGTCGTACAGTGAAAATCCATCGCGTTCGGCAAGCATcag > 1:2300209/1‑55 (MQ=255)
cGACCCCCACCGTACGGTCGTACAGTGAAAATCCATCGCGTTCGGCAAGCATcag > 1:1106579/1‑55 (MQ=255)
|
TTTAATCCCTAACGCTTCCAGTCGCGCCTGCAATCGACGTCCAACGTTACCAACGCCCACGATCCCCACCGTACGGTCGTACAGTGAAAATCCATCGCGTTCGGCAAGCATCAGCAGGGAGGAGAAAA > minE/1522681‑1522808
|
| 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
