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 |
2,440,788 |
T→C |
40.0% |
intergenic (‑145/‑5) |
ilvC ← / → ilvY |
ketol‑acid reductoisomerase, NAD(P)‑binding/DNA‑binding transcriptional dual regulator |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,440,788 | 0 | T | C | 40.0%
| 28.6
/ 47.9
| 70 | intergenic (‑145/‑5) | ilvC/ilvY | ketol‑acid reductoisomerase, NAD(P)‑binding/DNA‑binding transcriptional dual regulator |
| Reads supporting (aligned to +/- strand): ref base T (15/27); new base C (19/9); total (34/36) |
| Fisher's exact test for biased strand distribution p-value = 1.41e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.88e-01 |
TTATTGCGGAAATTGATATATTCACAACGTCACATTGCAATTTTTGCAACGTCAACATCGAGGGCTGTCCCTGTGGATTTACGCGATCTGAAAACCTTCCTGCATCTGGCGGAAAGCCGCCATTTTGGC > minE/2440721‑2440849
|
ttATTGCGGAAATTGATATATTCACAACGTCACATTGCAATTTTTGCAACGTCAACATCGAGGGCTGTc < 1:71414/69‑1 (MQ=255)
ttATTGCGGAAATTGATATATTCACAACGTCACATTGCAATTTTTGCAACGTCAACATCGAGGGCTGTc > 1:2276420/1‑69 (MQ=255)
ttATTGCGGAAATTGATATATTCACAACGTCACATTGCAATTTTTGCAACGTCAACATCGAGGGCTGTc > 1:2380069/1‑69 (MQ=255)
ttATTGCGGAAATTGATATATTCACAACGTCACATTGCAATTTTTGCAACGTCAACATCGAGGGCTGTc > 1:1922940/1‑69 (MQ=255)
ttATTGCGGAAATTGATATATTCACAACGTCACATTGCAATTTTTGCAACGTCAACATCGAGGGCTGTc > 1:1637257/1‑69 (MQ=255)
ttATTGCGGAAATTGATATATTCACAACGTCACATTGCAATTTTTGCAACGTCAACATCGAGGGCTGTc > 1:3240125/1‑69 (MQ=255)
ttATTGCGGAAATTGATATATTCACAACGTCACATTGCAATTTTTGCAACGTCAACATCGAGGGCTGTc < 1:1861678/69‑1 (MQ=255)
atatTCACAACGTCACATTGCAATTTTTGCAACGTCAACATCGATGGCTGTCCCTGTGGATTTAcgcg < 1:1067610/68‑1 (MQ=255)
atatTCACAACGTCACATTGCAATTTTTGCAACGTCAACATCGAGGGCTGTCCCTGTGGATTTAcgcta < 1:2848497/69‑3 (MQ=255)
atatTCACAACGTCACATTGCAATTTTTGCAACGTCAACATCGAGGGCTGTCCCTGTGGATTTAcgcg < 1:2305615/68‑1 (MQ=255)
atatTCACAACGTCACATTGCAATTTTTGCAACGTCAACATCGAGGGCTGTCCCTGTGGATTTAcgcg < 1:2249599/68‑1 (MQ=255)
atatTCACAACGTCACATTGCAATTTTTGCAACGTCAACATCGAGGGCTGTCCCTGTGGATTTAcgcg < 1:2052505/68‑1 (MQ=255)
atatTCACAACGTCACATTGCAATTTTTGCAACGTCAACATCGAGGGCTGTCCCTGTGGATTTAcgcg < 1:2554182/68‑1 (MQ=255)
atatTCACAACGTCACATTGCAATTTTTGCAACGTCAACATCGAGGGCTGTCCCTGTGGATTTAcgcg < 1:268196/68‑1 (MQ=255)
atatTCACAACGTCACATTGCAATTTTTGCAACGTCAACATCGAGGGCTGTCCCTGTGGATTTAcgcg < 1:2777371/68‑1 (MQ=255)
atatTCACAACGTCACATTGCAATTTTTGCAACGTCAACATCGAGGGCTGTCCCTGTGGATTTAcgcg < 1:3051439/68‑1 (MQ=255)
atatTCACAACGTCACATTGCAATTTTTGCAACGTCAACATCGAGGGCTGTCCCTGTGGATTTAcgcg < 1:1414745/68‑1 (MQ=255)
atatTCACAACGTCACATTGCAATTTTTGCAACGTCAACATCGAGGGCTGTCCCTGTGGATTTAcgcg < 1:527617/68‑1 (MQ=255)
atatTCACAACGTCACATTGCAATTTTTGCAACGTCAACATCGAGGGCTGTCCCTGTGGATTTAcgcg < 1:701379/68‑1 (MQ=255)
atatTCACAACGTCACATTGCAATTTTTGCAACGTAAACATCGAGGGCTGTCCCTGTGGATTTAcgcg < 1:534321/68‑1 (MQ=255)
ttCACAACGTCACATTGCAATTTTTGCAACGTCAACATCGAGGGCTGTCCCTGTGGATTTACTCGAt > 1:3275744/1‑67 (MQ=255)
ttCACAACGTCACATTGCAATTTTTGCAACGTCAACATCGAGGGCTGTCCCTGTGGATTTACGCGATc > 1:2897323/1‑68 (MQ=255)
aaCGTCACATTGCAATTTTTGCAACGTCAACATCGAGGGCTGTCCCTGTGGATTTACGCGATCTGaaaa < 1:3085975/69‑1 (MQ=255)
aaCGTCACATTGCAATTTTTGCAACGTCAACATCGAGGGCTGTCCCTGTGGATTTACGCGATCTGaaaa < 1:3274201/69‑1 (MQ=255)
aaCGTCACATTGCAATTTTTGCAACGTCAACATCGAGGGCTGTCCCTGTGGATTTACGCGATCTGaaaa < 1:424284/69‑1 (MQ=255)
aaCGTCACATTGCAATTTTTGCAACGTCAACATCGAGGGCTGTCCCTGTGGATTTACGCGATCTGaaaa < 1:1388878/69‑1 (MQ=255)
aCGTCACATTGCAATTTTTGCAACGTCAACATCTAGGGCTGTCCCTGTGGATTTACGCGATCTGaaaa < 1:3058280/68‑1 (MQ=255)
tGCAATTTTTGCAACGTCAACATCGAGGGCTGTCCCTGTGGATTTACGCGATCTGAAAACCTTCCTGCa < 1:986648/69‑1 (MQ=255)
gCAATTTTTGCAACGTCAACATCGAGGGCTGTCCCTGTGGATTTACGCGATCTGAAAACCTTCCTGCa < 1:1080302/68‑1 (MQ=255)
gCAATTTTTGCAACGTCAACATCGAGGGCTGTCCCTGTGGATTTACGCGATCTGAAAACCTTCCTGCAt > 1:1921154/1‑69 (MQ=255)
aTTTTTGCAACGTCAACATCGAGGGCTGTCCCTGTGGATTTACGCGATCTGAAAACCTTCCTGCATCTg < 1:444953/69‑1 (MQ=255)
aTTTTTGCAACGTCAACATCGAGGGCTGTCCCTGTGGATTTACGCGATCTGAAAACCTTCCTGCATCTg < 1:1704924/69‑1 (MQ=255)
aTTTTTGCAACGTCAACATCGAGGGCTGTCCCTGTGGATTTACGCGATCTGAAAACCTTCCTGCATCTg < 1:1536382/69‑1 (MQ=255)
aTTTTTGCAACGTCAACATCGAGGGCTGTCCCTGTGGATTTACGCGATCTGAAAACCTTCCTGCATCTg < 1:498594/69‑1 (MQ=255)
aTTTTTGCAACGTCAACATCGAGGGCTGTCCCTGTGGATTTACGCGATCTGAAAACCTTCCTGCATCTg < 1:924086/69‑1 (MQ=255)
cAACGTCAACATTAAGGGCTGCGCCATTGGATTTACGCGAt > 1:891146/1‑41 (MQ=255)
cAACGTCAACATTAAGGGCTGCGCCATTGGATTTACGCGATc > 1:1798189/1‑42 (MQ=255)
cAACGTCAACATTAAGGGCTGCGCCATTGGATTTACGCGATCt > 1:1212658/1‑43 (MQ=255)
cAACGTCAACATTAAGGGCTGCGCCATTGGATTTACGCGATCt > 1:1221992/1‑43 (MQ=255)
cAACGTCAACATTAAGGGCTGCGCCATTGGATTTACGCGATCt > 1:881288/1‑43 (MQ=255)
cAACGTCAACATTAAGGGCTGCGCCATTGGATTTACGCGATCt > 1:2354022/1‑43 (MQ=255)
cAACGTCAACATTAAGGGCTGCGCCATTGGATTTACGCGATCt > 1:1486522/1‑43 (MQ=255)
cAACGTCAACATTAAGGGCTGCGCCATTGGATTTACGCGATCt > 1:376058/1‑43 (MQ=255)
cAACGTCAACATTAAGGGCTGCGCCATTGGATTTACGCGATCt > 1:3382536/1‑43 (MQ=255)
cAACGTCAACATTAAGGGCTGCGCCATTGGATTTACGCGATCt > 1:923339/1‑43 (MQ=255)
cAACGTCAACATTAAGGGCTGCGCCATTGGATTTACGCGATCt > 1:1664822/1‑43 (MQ=255)
cAACGTCAACATTAAGGGCTGCGCCATTGGATTTACGCGATCt > 1:3103045/1‑43 (MQ=255)
cAACGTCAACATTAAGGGCTGCGCCATTGGATTTACGCGATCt > 1:1726577/1‑43 (MQ=255)
cAACGTCAACATTAAGGGCTGCGCCATTGGATTTACGCGATCt > 1:2344025/1‑43 (MQ=255)
cAACGTCAACATTAAGGGCTGCGCCATTGGATTTACGCGATCt > 1:2493854/1‑43 (MQ=255)
cAACGTCAACATTAAGGGCTGCGCCATTGGATTTACGCGATCt > 1:2945288/1‑43 (MQ=255)
cAACGTCAACATTAAGGGCTGCGCCATTGGATTTACGCGATCt > 1:200558/1‑43 (MQ=255)
cAACGTCAACATTAAGGGCTGCGCCATTGGATTTACGCGATCt > 1:1858880/1‑43 (MQ=255)
cAACGTCAACATTAAGGGCTGCGCCATTGGATTTACGCGATCt > 1:1814280/1‑43 (MQ=255)
aCGTCAACATTAAGGTCTGCGCCATTGGATTTACGCGATCTGAAAACCTTCCTGCATCTGGCGGAAAgc < 1:434076/69‑1 (MQ=25)
aCGTCAACATTAAGGGCTGCGCCATTGGATTTACGCGATCTGAAAACCTTCCTGCATCTGGCTGAAAgc < 1:3404/69‑1 (MQ=255)
aCGTCAACATTAAGGGCTGCGCCATTGGATTTACGCGATCTGAAAACCTTCCTGCATCTGGCGGAAAgc < 1:2705439/69‑1 (MQ=25)
aCGTCAACATTAAGGGCTGCGCCATTGGATTTACGCGATCTGAAAACCTTCCTGCATCTGGCGGAAAgc < 1:2701718/69‑1 (MQ=25)
aCGTCAACATTAAGGGCTGCGCCATTGGATTTACGCGATCTGAAAACCTTCCTGCATCTGGCGGAAAgc < 1:1544860/69‑1 (MQ=25)
aCGTCAACATTAAGGGCTGCGCCATTGGATTTACGCGATCTGAAAACCTTCCTGCATCTGGCGGAAAgc < 1:2649123/69‑1 (MQ=25)
aCGTCAACATTAAGGGCTGCGCCATTGGATTTACGCGATCTGAAAACCTTCCTGCATCTGGCGGAAAgc < 1:3211018/69‑1 (MQ=25)
aCGTCAACATTAAGGGCTGCGCCATTGGATTTACGCGATCTGAAAACCTTCCTGCATCTGGCGGAAAgc < 1:2149214/69‑1 (MQ=25)
aCGTCAACATTAAGGGCTGCGCCATTGGATTTACGCGATCTGAAAACCTTCCTGCATCTGGCGGAAAgc < 1:3057633/69‑1 (MQ=25)
ggCTGTCCCTGTGGATTTACGCGATCTGAAAACCTTCCTGCATCTGGCGGAAAGCCGCCATTTTGGc > 1:2897739/1‑67 (MQ=255)
ggCTGTCCCTGTGGATTTACGCGATCTGAAAACCTTCCTGCATCTGGCGGAAAGCCGCCATTTTGGc > 1:2777024/1‑67 (MQ=255)
ggCTGTCCCTGTGGATTTACGCGATCTGAAAACCTTCCTGCATCTGGCGGAAAGCCGCCATTTTGGc > 1:307134/1‑67 (MQ=255)
ggCTGTCCCTGTGGATTTACGCGATCTGAAAACCTTCCTGCATCTGGCGGAAAGCCGCCATTTTGGc > 1:2044088/1‑67 (MQ=255)
ggCTGTCCCTGTGGATTTACGCGATCTGAAAACCTTCCTGCATCTGGCGGAAAGCCGCCATTTTGGc > 1:1046095/1‑67 (MQ=255)
ggCTGTCCCTGTGGATTTACGCGATCTGAAAACCTTCCTGCATCTGGCGGAAAGCCGCCATTTTGGc > 1:2548672/1‑67 (MQ=255)
ggCTGTCCCTGTGGATTTACGCGATCTGAAAACCTTCCTGCATCTGGCGGAAAGCCGCCATTTTGGc > 1:1016497/1‑67 (MQ=255)
|
TTATTGCGGAAATTGATATATTCACAACGTCACATTGCAATTTTTGCAACGTCAACATCGAGGGCTGTCCCTGTGGATTTACGCGATCTGAAAACCTTCCTGCATCTGGCGGAAAGCCGCCATTTTGGC > minE/2440721‑2440849
|
| 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
