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 |
1,261,248 |
A→C |
54.7% |
T267T (ACT→ACG) |
torY ← |
TMAO reductase III (TorYZ), cytochrome c‑type subunit |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,261,248 | 0 | A | C | 54.7%
| 24.3
/ 61.7
| 64 | T267T (ACT→ACG) | torY | TMAO reductase III (TorYZ), cytochrome c‑type subunit |
| Reads supporting (aligned to +/- strand): ref base A (20/9); new base C (16/19); total (36/28) |
| Fisher's exact test for biased strand distribution p-value = 7.93e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.99e-01 |
CGCACCCTGTAAAGACGCCTGACGCCATTGATTGCCGTATTCGTCAGCCTGCCATTCCCCGTTTACAGTGAGCGCCTTGATACCTTCTTCACTTAATGTGGCTAGCGCCAGCCGTTGACCTGCCGCCAGG > minE/1261182‑1261311
|
cgcACCCTGTAAAGACGCCTGACGCCATTGATTGCCGTATTCGTCAGCCTGCCATTCCCCGTTTACa > 1:2369516/1‑67 (MQ=255)
cgcACCCTGTAAAGACGCCTGACGCCATTGATTGCCGTATTCGTCAGCCTGCCATTCCCCGTTTACa > 1:791784/1‑67 (MQ=255)
cgcACCCTGTAAAGACGCCTGACGCCATTGATTGCCGTATTCGTCAGCCTGCCATTCCCCGTTTACa > 1:2032751/1‑67 (MQ=255)
cgcACCCTGTAAAGACGCCTGACGCCATTGATTGCCGTATTCGTCAGCCTGCCATTCCCCGTTTACa > 1:276717/1‑67 (MQ=255)
cccTGCAAAGACGCCTGACGCCATTGATTGCCGTATTCGTCAGCCTGCCATTCCCCGTTTACCGtta > 1:3142356/1‑65 (MQ=255)
cccTGCAAAGACGCCTGACGCCATTGATTGCCGTATTCGTCAGCCTGCCATTCCCCGTTTACCGTTAgc > 1:3114910/1‑69 (MQ=255)
cccTGCAAAGACGCCTGACGCCATTGATTGCCGTATTCGTCAGCCTGCCATTCCCCGTTTACCGTTAgc > 1:2346837/1‑69 (MQ=255)
cccTGCAAAGACGCCTGACGCCATTGATTGCCGTATTCGTCAGCCTGCCATTCCCCGTTTACCGTTAgc > 1:2596878/1‑69 (MQ=255)
cccTGCAAAGACGCCTGACGCCATTGATTGCCGTATTCGTCAGCCTGCCATTCCCCGTTTACCGTTAgc > 1:2053444/1‑69 (MQ=255)
cccTGCAAAGACGCCTGACGCCATTGATTGCCGTATTCGTCAGCCTGCCATTCCCCGTTTACCGTTAgc > 1:2038844/1‑69 (MQ=255)
cccTGCAAAGACGCCTGACGCCATTGATTGCCGTATTCGTCAGCCTGCCATTCCCCGTTTACCGTTAgc > 1:2841494/1‑69 (MQ=255)
cccTGCAAAGACGCCTGACGCCATTGATTGCCGTATTCGTCAGCCTGCCATTCCCCGTTTACCGTTAgc > 1:2903465/1‑69 (MQ=255)
cccTGCAAAGACGCCTGACGCCATTGATTGCCGTATTCGTCAGCCTGCCATTCCCCGTTTACCGTTAgc > 1:3266343/1‑69 (MQ=255)
cccTGCAAAGACGCCTGACGCCATTGATTGCCGTATTCGTCAGCCTGCCATTCCCCGTTTACCGTTAgc > 1:94211/1‑69 (MQ=255)
cccTGCAAAGACGCCTGACGCCATTGATTGCCGTATTCGTCAGCCTGCCATTCCCCGTTTACCGTTAgc > 1:1551577/1‑69 (MQ=255)
cccTGCAAAGACGCCTGACGCCATTGATTGCCGTATTCGTCAGCCTGCCATTCCCCGTTTACCGTTAgc > 1:843111/1‑69 (MQ=255)
cccTGCAAAGACGCCTGACGCCATTGATTGCCGTATTCGTCAGCCTGCCATTCCCCGTTTACCGTTAgc > 1:1581600/1‑69 (MQ=255)
cccTGCAAAGACGCCTGACGCCATTGATTGCCGTATTCGTCAGCCTGCCATTCCCCGTTTACCGTTAgc > 1:552984/1‑69 (MQ=255)
cccTGCAAAGACGCCTGACGCCATTGATTGCCGTATTCGTCAGCCTGCCATTCCCCGTTTACCGTTAgc > 1:1313661/1‑69 (MQ=255)
cccTGCAAAGACGCCTGACGCCATTGATTGCCGTATTCGTCAGCCTGACATTCCCCGTTTACCGTTAgc > 1:2954618/1‑69 (MQ=255)
aaGACGCCTGACGCCATTGATTGCCGTATTCGTCAGCCTGCCATTCCCCGTTTACCGTTAGCGCCTTGa < 1:456220/69‑1 (MQ=255)
aaGACGCCTGACGCCATTGATTGCCGTATTCGTCAGCCTGCCATTCCCCGTTTACCGTTAGCGCCTTGa < 1:992886/69‑1 (MQ=255)
aaGACGCCTGACGCCATTGATTGCCGTATTCGTCAGCCTGCCATTCCCCGTTTACCGTTAGCGCCTTGa < 1:2515960/69‑1 (MQ=255)
aaGACGCCTGACGCCATTGATTGCCGTATTCGTCAGCCTGCCATTCCCCGTTTACCGTTAGCGCCTTGa < 1:114443/69‑1 (MQ=255)
aaGACGCCTGACGCCATTGATTGCCGTATTCGTCAGCCTGCCATTCCCCGTTTACCGTTAGCGCCTTGa < 1:594380/69‑1 (MQ=255)
aaGACGCCTGACGCCATTGATTGCCGTATTCGTCAGCCTGCCATTCCCCGTTTACCGTTAGCGCCTTGa < 1:3426035/69‑1 (MQ=255)
aaGACGCCTGACGCCATTGATTGCCGTATTCGTCAGCCTGCCATTCCCCGTTTACCGTTAGCGCCTTGa < 1:2970688/69‑1 (MQ=255)
aaGACGCCTGACGCCATTGATTGCCGTATTCGTCAGCCTGCCATTCCCCGTTTACCGTTAGCGCCTTGa < 1:3003619/69‑1 (MQ=255)
aaGACGCCTGACGCCATTGATTGCCGTATTCGTCAGCCTGCCATTCCCCGTTTACCGTTAGCGCCTTGa < 1:2595410/69‑1 (MQ=255)
aaGACGCCTGACGCCATTGATTGCCGTATTCGTCAGCCTGCCATTCCCCGTTTACCGTTAGCGCCTTGa < 1:319700/69‑1 (MQ=255)
aaGACGCCTGACGCCATTGATTGCCGTATTCGTCAGCCTGCCATTCCCCGTTTACCGTTAGCGCCTTGa < 1:2341238/69‑1 (MQ=255)
aaGACGCCTGACGCCATTGATTGCCGTATTCGTCAGCCTGCCATTCCCCGTTTACCGTTAGCGCCTTGa < 1:1477306/69‑1 (MQ=255)
aaGACGCCTGACGCCATTGATTGCCGTATTCGTCAGCCTGCCATTCCCCGTTTACCGTTAGCGCCTTGa < 1:2161419/69‑1 (MQ=255)
aaGACGCCTGACGCCATTGATTGCCGTATTCGTCAGCCTGCCATTCCCCGTTTACCGTTAGCGCCTTGa < 1:209156/69‑1 (MQ=255)
aaGACGCCTGACGCCATTGATTGCCGTATTCGTCAGCCTGCCATTCCCCGTTTACCGTTAGCGCCTTGa < 1:1557841/69‑1 (MQ=255)
aaGACGCCTGACGCCATTGATTGCCGTATTCGTCAGCCTGCCATTCCCCGTTTACCGTTAGCGCCTTGa < 1:1627055/69‑1 (MQ=255)
aaGACGCCTGACGCCATTGATTGCCGTATTCGTCAGCCTGCCATTCCCCGTTTACCGTTAGCGCCTTGa < 1:1715082/69‑1 (MQ=255)
aaGACGCCTGACGCCATTGATTGCCGTATTCGTCAGCCTGCCATTCCCCGTTTACCGTTAGCGCCTTGa < 1:1815366/69‑1 (MQ=255)
aGACGCCTGACGCCATTGATTTCCGTATTCGTCAGCCTGCCATTCCCCGTTTACAGTGAGCGCCtt < 1:1700895/66‑1 (MQ=255)
aGACGCCTGACGCCATTGATTGCCGTATTCGTCAGCCTGCCATTCCCCGTTTACCGTTAGCGCCTTGa < 1:1161574/68‑1 (MQ=255)
cGTCAGCCTGCCATTCCCCGTTTATAGTGAGCGCCTTGATACCTTCTTCACTTAATGTGGCTAgcgc < 1:58798/67‑1 (MQ=255)
cGTCAGCCTGCCATTCCCCGTTTACAGTGAGCGCCTTGAt < 1:1956490/40‑1 (MQ=255)
cGTCAGCCTGCCATTCCCCGTTTACAGTGAGCGCCTTGATACCTTCTTCACTTAATGTGGCTAgcgc < 1:2962006/67‑1 (MQ=255)
cGTCAGCCTGCCATTCCCCGTTTACAGTGAGCGCCTTGATACCTTCTTCACTTAATGTGGCTAgcgc < 1:1165893/67‑1 (MQ=255)
cGTCAGCCTGCCATTCCCCGTTTACAGTGAGCGCCTTGATACCTTCTTCACTTAATGTGGCTAgcgc < 1:305525/67‑1 (MQ=255)
cGTCAGCCTGCCATTCCCCGTTTACAGTGAGCGCCTTGATACCTTCTTCACTTAATGTGGCTAgcgc < 1:1674482/67‑1 (MQ=255)
cGTCAGCCTGCCATTCCCCGTTTACAGTGAGCGCCTTGATACCTTCTTCACTTAATGTGGCTAgcgc < 1:3254370/67‑1 (MQ=255)
gTCAGCCTGCCATTCCCCGTTTACAGTGAGCGCCTTGAt < 1:2780854/39‑1 (MQ=255)
ccccGTTTACAGTGAGCGCCTTGATACCTTCTTCACTTAATGTGGCTAGCGCCAGCCGTTGACCTgcc > 1:2896253/1‑68 (MQ=255)
ccccGTTTACAGTGAGCGCCTTGATACCTTCTTCACTTAATGTGGCTAGCGCCAGCCGTTGACCTgcc > 1:1765292/1‑68 (MQ=255)
ccccGTTTACAGTGAGCGCCTTGATACCTTCTTCACTTAATGTGGCTAGCGCCAGCCGTTGACCTgcc > 1:1335475/1‑68 (MQ=255)
tACAGTGAGCGCCTTGATACCTTCTTCACTTAATGTGGCTAGCGCCAGCCGTTg > 1:2367647/1‑54 (MQ=255)
tACAGTGAGCGCCTTGATACCTTCTTCACTTAATGTGGCTAGCGCCAGCCGTTg > 1:2813184/1‑54 (MQ=255)
tACAGTGAGCGCCTTGATACCTTCTTCACTTAATGTGGCTAGCGCCAGCCGTTg > 1:1253928/1‑54 (MQ=255)
tACAGTGAGCGCCTTGATACCTTCTTCACTTAATGTGGCTAGCGCCAGCCGTTg > 1:1347984/1‑54 (MQ=255)
tACAGTGAGCGCCTTGATACCTTCTTCACTTAATGTGGCTAGCGCCAGCCGTTg > 1:410120/1‑54 (MQ=255)
tACAGTGAGCGCCTTGATACCTTCTTCACTTAATGTGGCTAGCGCCAGCCGTTg > 1:1518570/1‑54 (MQ=255)
tACAGTGAGCGCCTTGATACCTTCTTCACTTAATGTGGCTAGCGCCAGCCGTTg > 1:2067235/1‑54 (MQ=255)
tACAGTGAGCGCCTTGATACCTTCTTCACTTAATGTGGCTAGCGCCAGCCGTTg > 1:3216031/1‑54 (MQ=255)
tACAGTGAGCGCCTTGATACCTTCTTCACTTAATGTGGCTAGCGCCAGCCGTTg > 1:2737631/1‑54 (MQ=255)
tACAGTGAGCGCCTTGATACCTTCTTCACTTAATGTGGCTAGCGCCAGCCGTTGACCTGCCGCCAgg > 1:2458925/1‑67 (MQ=255)
tACAGTGAGCGCCTTGATACCTTCTTCACTTAATGTGGCTAGCGCCAGCCGTTGACCTGCCGCCAgg > 1:715728/1‑67 (MQ=255)
tACAGTGAGCGCCTTGATACCTTCTTCACTTAATGTGGCTAGCGCCAGCCGTTGACCTGCCGCCAgg > 1:788951/1‑67 (MQ=255)
tACAGTGAGCGCCTTGATACCTTCTTCACTTAATGTGGCTAGCGCCAGCCGTTGACCTGCCGCCAgg > 1:1613777/1‑67 (MQ=255)
tACAGTGAGCGCCTTGATACCTTCTTCACTTAATGTGGCTAGCGCCAGCCGTTGACCTGCCGCCAgg > 1:83845/1‑67 (MQ=255)
tACAGTGAGCGCCTTGATACCTTCTTCACTTAATGTGGCTAGCGCCAGCCGTTGACCTGCCGCCAgg > 1:1697194/1‑67 (MQ=255)
tACAGTGAGCGCCTTGATACCTTCTTCACTTAATGTGGCTAGCGCCAGCCGTTGACCTGCCGCCAgg > 1:2763991/1‑67 (MQ=255)
tACAGTGAGCGCCTTGATACCTTCCTCACTTAATGTGGCTAGCGCCAGCCGTTg > 1:1417562/1‑54 (MQ=255)
|
CGCACCCTGTAAAGACGCCTGACGCCATTGATTGCCGTATTCGTCAGCCTGCCATTCCCCGTTTACAGTGAGCGCCTTGATACCTTCTTCACTTAATGTGGCTAGCGCCAGCCGTTGACCTGCCGCCAGG > minE/1261182‑1261311
|
| 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
