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 |
2,773,593 |
T→C |
23.8% |
T429T (ACT→ACC) |
aceA → |
isocitrate lyase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,773,593 | 0 | T | C | 23.8%
| 86.7
/ 22.5
| 71 | T429T (ACT→ACC) | aceA | isocitrate lyase |
| Reads supporting (aligned to +/- strand): ref base T (25/29); new base C (7/10); total (32/39) |
| Fisher's exact test for biased strand distribution p-value = 7.85e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.65e-01 |
CGATAAAGTGACGACTATTATTCAGGGCGGCACGTCTTCAGTCACCGCGCTGACCGGCTCCACTGAAGAATCGCAGTTCTAAGCAA‑CAACAACCGTTGCTGACTGTAGGCCGGATAAGGCGTTCACGCCGCA > minE/2773530‑2773661
|
cggtAAAGTGACGACTATTATTCAGGGCGGCACGTCTTCAGTCACCGCGCTGACCGGCTCCACTgaaga > 1:2968137/4‑69 (MQ=255)
cGATAAAGTGACGACTATTATTCAGGGCGGCACGTCTTCAGTCACCGCGCTGACCGGCTCCACTggaga > 1:2145227/1‑69 (MQ=255)
cGATAAAGTGACGACTATTATTCAGGGCGGCACGTCTTCAGTCACCGCGCTGACCGGCTCCACTgaaga > 1:3409486/1‑69 (MQ=255)
cGATAAAGTGACGACTATTATTCAGGGCGGCACGTCTTCAGTCACCGCGCTGACCGGCTCCACTgaaga > 1:1139528/1‑69 (MQ=255)
cGATAAAGTGACGACTATTATTCAGGGCGGCACGTCTTCAGTCACCGCGCTGACCGGCTCCACTgaaga > 1:732115/1‑69 (MQ=255)
cGATAAAGTGACGACTATTATTCAGGGCGGCACGTCTTCAGTCACCGCGCTGACCGGCTCCACTgaaga > 1:1936377/1‑69 (MQ=255)
cGATAAAGTGACGACTATTATTCAGGGCGGCACGTCTTCAGTCACCGCGCTGACCGGCTCCACTgaaga > 1:2472058/1‑69 (MQ=255)
cGATAAAGTGACGACTATTATTCAGGGCGGCACGTCTTCAGTCAACGCGCTGACCGGCTCCACTgaaga > 1:963278/1‑69 (MQ=255)
cGATAAAGTGACGACTATTATTCAGGGAGGCACGTCTTCAGTCACCGCGCTGACCGGCTCCACTgaaga > 1:1409046/1‑69 (MQ=255)
gTGACGACTATTATTCAGGGCGGCACGTCTTCAGTCACCGCGCTGACCGGCTCCACTGAAGAATCGCAg > 1:2953904/1‑69 (MQ=255)
gTGACGACTATTATTCAGGGCGGCACGTCTTCAGTCACCGCGCTGACCGGCTCCACTGAAGAATCGCAg > 1:3154814/1‑69 (MQ=255)
gTGACGACTATTATTCAGGGCGGCACGTCTTCAGTCACCGCACTGCCCGGCTCCACTGAAGAATCGCAg > 1:730082/1‑69 (MQ=255)
tGACGACTATTATTCAGGGCGGCACGTCTTCAGTCACCGCGCTGACCGGCTCCACTGAAGATTCGCAg < 1:440067/68‑1 (MQ=255)
tGACGACTATTATTCAGGGCGGCACGTCTTCAGTCACCGCGCTGACCGGCTCCACTGAAGAATCGCAGt < 1:2904662/69‑1 (MQ=255)
tGACGACTATTATTCAGGGCGGCACGTCTTCAGTCACCGCGCTGACCGGCTCCACTGAAGAATCGCAGt < 1:189168/69‑1 (MQ=255)
tGACGACTATTATTCAGGGCGGCACGTCTTCAGTCACCGCGCTGACCGGCTCCACTGAAGAATCGCAGt < 1:443672/69‑1 (MQ=255)
tGACGACTATTATTCAGGGCGGCACGTCTTCAGTCACCGCGCTGACCGGCTCCACTGAAGAATCGCAGt < 1:2183693/69‑1 (MQ=255)
tGACGACTATTATTCAGGGCGGCACGTCTTCAGTCACCGCGCTGACCGGCTCCACTGAAGAATCGCAGt < 1:2961140/69‑1 (MQ=255)
tGACGACTATTATTCAGGGCGGCACGTCTTCAGTCACCGCGCTGACCGGCTCCACTGAAGAACCGCAGt < 1:1724434/69‑1 (MQ=255)
acgacCATTATTCAAGGTGGCACGTCTTCAGTTACCGCGCTGACCGGCTCCACCGAAGAATCGCAGtt > 1:2227490/1‑68 (MQ=255)
acgacCATTATTCAAGGTGGCACGTCTTCAGTTACCGCGCTGACCGGCTCCACCGAAGAATCGCAGtt > 1:2495765/1‑68 (MQ=255)
acgacCATTATTCAAGGTGGCACGTCTTCAGTTACCGCGCTGACCGGCTCCACCGAAGAATCGCAGtt > 1:1025867/1‑68 (MQ=255)
acgacCATTATTCAAGGTGGCACGTCTTCAGTTACCGCGCTGACCGGCTCCACCGAAGAATCGCAGtt > 1:1870073/1‑68 (MQ=255)
acgacCATTATTCAAGGTGGCACGTCTTCAGTTACCGCGCTGACCGGCTCCACCGAAGAATCGCAGtt > 1:1211887/1‑68 (MQ=255)
acgacCATTATTCAAGGTGGCACGTCTTCAGTTACCGCGCTGACCGGCTCCACCGAAGAATCGCAGtt > 1:394601/1‑68 (MQ=255)
acgacCATTATTCAAGGTGGCACGTCTTCAGTTACCGCGCTGACCGGCTCCACCGAAGAATCGCAGtt > 1:1293963/1‑68 (MQ=255)
tCTTCAGTCACCGCGCTGACCGGCTCCACTGAAGAATCGCAGTTCTAAGCAA‑CAACAACCGTTGCTGAc > 1:3371702/1‑69 (MQ=255)
tCTTCAGTCACCGCGCTGACCGGCTCCACTGAAGAATCGCAGTTCTAAGCAA‑CAACAACCGTTGCTGAc > 1:3266745/1‑69 (MQ=255)
tCTTCAGTCACCGCGCTGACCGGCTCCACTGAAGAATCGCAGTTCTAAGCAA‑CAACAACCGTTGCTGAc > 1:3200046/1‑69 (MQ=255)
tCTTCAGTCACCGCGCTGACCGGCTCCACTGAAGAATCGCAGTTCTAAGCAA‑CAACAACCGTTGCTGAc > 1:1325991/1‑69 (MQ=255)
tCTTCAGTCACCGCGCTGACCGGCTCCACTGAAGAATCGCAGTTCTAAGCAA‑CAACAACCGTTGCTGAc > 1:2255666/1‑69 (MQ=255)
tCTTCAGTCACCGCGCTGACCGGCTCCACTGAAGAATCGCAGTTCTAAGCAA‑CAACAACCGTTGCTGAc > 1:446894/1‑69 (MQ=255)
ttCAGTCACCGCGCTGACCGGCTCCACTGAAGAATCGCAGTTCTAAGCAA‑CAACAACCGTTGCTGAc > 1:1514565/1‑67 (MQ=255)
ttCAGTCACCGCGCTGACCGGCTCCACTGAAGAATCGCAGTTCTAAGCAA‑CAACAACCGTTGCTGAc > 1:1155398/1‑67 (MQ=255)
ttCAGTCACCGCGCTGACCGGCTCCACTGAAGAATCGCAGTTCTAAGCAA‑CAACAACCGTTGCTGAc > 1:1515182/1‑67 (MQ=255)
ttCAGTCACCGCGCTGACCGGCTCCACTGAAGAATCGCAGTTCTAAGCAA‑CAACAACCGTTGCTGAc > 1:3160838/1‑67 (MQ=255)
ttCAGTCACCGCGCTGACCGGCTCCACTGAAGAATCGCAGTTCTAAGCAA‑CAACAACCGTTGCTGAc > 1:1999449/1‑67 (MQ=255)
ttCAGTCACCGCGCTGACCGGCTCCACTGAAGAATCGCAGTTCTAAGCAA‑CAACAACCGTTGCTGACTg < 1:3314502/69‑1 (MQ=255)
ttCAGTCACCGCGCTGACCGGCTCCACTGAAGAATCGCAGTTCTAAGCAA‑CAACAACCGTTGCTGACTg < 1:609453/69‑1 (MQ=255)
ttCAGTCACCGCGCTGACCGGCTCCACTGAAGAATCGCAGTTCTAAGCAA‑CAACAACCGTTGCTGACTg < 1:706520/69‑1 (MQ=255)
ttCAGTCACCGCGCTGACCGGCTCCACTGAAGAATCGCAGTTCTAAGCAA‑CAACAACCGTTGCTGACTg < 1:3230812/69‑1 (MQ=255)
ttCAGTCACCGCGCTGACCGGCTCCACTGAAGAATCGCAGTTCTAAGCAA‑CAACAACCGTTGCTGACTg < 1:391710/69‑1 (MQ=255)
ttCAGTCACCGCGCTGACCGGCTCCACTGAAGAATCGCAGTTCTAAGCAA‑CAACAACCGTTGCTGACTg < 1:2628310/69‑1 (MQ=255)
ttCAGTCACCGCGCTGACCGGCTCCACTGAAGAATCGCAGTTCTAAGCAA‑CAACAACCGTTGCTGACTg < 1:1392181/69‑1 (MQ=255)
ttCAGTCACCGCGCTGACCGGCTCCACTGAAGAATCGCAGTTCTAAGCAA‑CAACAACCGTTGCTGACTg < 1:1448739/69‑1 (MQ=255)
ttCAGTCACCGCGCTGACCGGCTCCACTGAAGAATCGCAGTTCTAAGCAA‑CAACAACCGTTGCTGACTg < 1:1487837/69‑1 (MQ=255)
ttCAGTCACCGCGCTGACCGGCTCCACTGAAGAATCGCAGTTCTAAGCAA‑CAACAACCGTTGCTGACTg < 1:158890/69‑1 (MQ=255)
ttCAGTCACCGCGCTGACCGGCTCCACTGAAGAATCGCAGTTCTAAGCAA‑CAACAACCGTTGCTGACTg < 1:1624238/69‑1 (MQ=255)
cAGTCACCGCGCTGACCGGCTCCACTGAAGAATCGCAGTTCTAAGCAA‑CAACAACCGTTGCTGACTGTa > 1:1946427/1‑69 (MQ=255)
cAGTCACCGCGCTGACAGGCTCCACTGAAGAATCGCAGTTCTAAGCAA‑CAACAACCGTTGCTGACTGTa > 1:1274111/1‑69 (MQ=255)
cACCGCGCTGACCGGCTCCACTGAAGAATCGCAGTTCTAAGCAA‑CAACAACCGTTGCTGAccg < 1:2657051/63‑3 (MQ=255)
cACCGCGCTGACCGGCTCCACTGAAGAATCGCAGTTCTAAGCAA‑CAACAACCGTTGCTGACTg < 1:91875/63‑1 (MQ=255)
cACCGCGCTGACCGGCTCCACTGAAGAATCGCAGTTCTAAGCAA‑CAACAACCGTTGCTGACTg < 1:1918960/63‑1 (MQ=255)
cACCGCGCTGACCGGCTCCACTGAAGAATCGCAGTTCTAAGCAA‑CAACAACCGTTGCTGACTg < 1:1878997/63‑1 (MQ=255)
cACCGCGCTGACCGGCTCCACTGAAGAATCGCAGTTCTAAGCAA‑CAACAACCGTTGCTGACTg < 1:1679489/63‑1 (MQ=255)
cACCGCGCTGACCGGCTCCACTGAAGAATCGCAGTTCTAAGCAA‑CAACAACCGTTGCTGACTg < 1:1655710/63‑1 (MQ=255)
cACCGCGCTGACCGGCTCCACTGAAGAATCGCAGTTCTAAGCAA‑CAACAACCGTTGCTGACTg < 1:659088/63‑1 (MQ=255)
cACCGCGCTGACCGGCTCCACTGAAGAATCGCAGTTCTAAGCAA‑CAACAACCGTTGCTGACTg < 1:3119819/63‑1 (MQ=255)
cACCGCGCTGACCGGCTCCACTGAAGAATCGCAGTTCTAAGCAA‑CAACAACCGTTGCTGACTg < 1:499577/63‑1 (MQ=255)
cACCGCGCTGACCAGCTCCACTGAAGAATCGCAGTTCTAAGCAA‑CAACAACCGTTGCTGACTg < 1:2065969/63‑1 (MQ=255)
cACCGAGCTGACCGGCTCCACTGAAGAATCGCAGTTCTAAGCAA‑CAACAACCGTTGCTGACTg < 1:49953/63‑1 (MQ=255)
ccACCGAAGAATCGCAGTTCTAAGCAACCGATAAACGTTGCTGACTGTAGGCCGGATAAGGCGTTc < 1:994802/66‑1 (MQ=25)
ccACCGAAGAATCGCAGTTCTAAGCAACCGATAAACGTTGCTGACTGTAGGCCGGATAAGGCGTTc < 1:2810674/66‑1 (MQ=25)
ccACCGAAGAATCGCAGTTCTAAGCAACCGATAAACGTTGCTGACTGTAGGCCGGATAAGGCGTTc < 1:2638092/66‑1 (MQ=25)
ccACCGAAGAATCGCAGTTCTAAGCAACCGATAAACGTTGCTGACTGTAGGCCGGATAAGGCGTTc < 1:1021206/66‑1 (MQ=25)
ccACCGAAGAATCGCAGTTCTAAGCAACCGATAAACGTTGCTGACTGTAGGCCGGATAAGGCGTTc < 1:575600/66‑1 (MQ=25)
ccACCGAAGAATCGCAGTTCTAAGCAACCGATAAACGTTGCTGACTGTAGGCCGGATAAGGCGTTc < 1:2023977/66‑1 (MQ=25)
ccACCGAAGAATCGCAGTTCTAAGCAACCGATAAACGTTGCTGACTGTAGGCCGGATAAGGCGTTc < 1:376964/66‑1 (MQ=25)
ccACCGAAGAATCGCAGTTCTAAGCAACCGATAAACGTTGCTGACTGTAGGCCGGATAAGGCGTTc < 1:1749559/66‑1 (MQ=25)
ccACCGAAGAATCGCAGTTCTAAGCAACCGATAAACGTTGCTGACTGTAGGCCGGATAAGGCGTTc < 1:3286552/66‑1 (MQ=25)
ccACCGAAGAATCGCAGCTCTAAGCAACCGATAAACGTTGCTGACTGTAGGCCGGATAAGGCGTTc < 1:1363098/66‑1 (MQ=21)
tGAAGAATCTCAGTTCTAAGCAA‑CAACAACCGTTGCTGACTGTAGGCCGGATAAGGCGTTCACGCCGCa < 1:56515/69‑1 (MQ=255)
tGAAGAATCGCAGTTCTAAGCAA‑CAACAACCGTTGCTGACTGTAGGCCGGATAAGGCGTTCACGCCGCa < 1:1171823/69‑1 (MQ=255)
tGAAGAATCGCAGTTCTAAGCAA‑CAACAACCGTTGCTGACTGTAGGCCGGATAAGGCGTTCACGCCGCa < 1:99073/69‑1 (MQ=255)
tGAAGAATCGCAGTTCTAAGCAA‑CAACAACCGTTGCTGACTGTAGGCCGGATAAGGCGTTCACGCCGCa < 1:2973485/69‑1 (MQ=255)
tGAAGAATCGCAGTTCTAAGCAA‑CAACAACCGTTGCTGACTGTAGGCCGGATAAGGCGTTCACGCCGCa < 1:1511924/69‑1 (MQ=255)
tGAAGAATCGCAGTTCTAAGCAA‑CAACAACCGTTGCTGACTGTAGGCCGGATAAGGCGTTCACGCCGCa < 1:1558402/69‑1 (MQ=255)
tGAAGAATCGCAGTTCTAAGCAA‑CAACAACCGTTGCTGACTGTAGGCCGGATAAGGCGTTCACGCCGCa < 1:3227482/69‑1 (MQ=255)
|
CGATAAAGTGACGACTATTATTCAGGGCGGCACGTCTTCAGTCACCGCGCTGACCGGCTCCACTGAAGAATCGCAGTTCTAAGCAA‑CAACAACCGTTGCTGACTGTAGGCCGGATAAGGCGTTCACGCCGCA > minE/2773530‑2773661
|
| 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
