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 |
2,282,340 |
T→C |
35.1% |
D248D (GAT→GAC) |
sthA → |
pyridine nucleotide transhydrogenase, soluble |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,282,340 | 0 | T | C | 35.1%
| 48.5
/ 42.5
| 74 | D248D (GAT→GAC) | sthA | pyridine nucleotide transhydrogenase, soluble |
| Reads supporting (aligned to +/- strand): ref base T (18/30); new base C (14/12); total (32/42) |
| Fisher's exact test for biased strand distribution p-value = 2.22e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.75e-01 |
ACTTCTGGAACAGTGGCGTAGTGATTCGTCACAACGAAGAGTACGAGAAGATCGAAGGCTGTGACGATGGTGTGATCATGCATCTGAAGTCGGGTAAAAAACTGAAAGCTGACTGCCTGCTC > minE/2282273‑2282394
|
aCTTCTGGAACAGTGGCGTAGTGATTCGTCACAACGAAGAGTACGAGAAGATCGAAGGCTGTGACGATg > 1:1429168/1‑69 (MQ=255)
aCTTCTGGAACAGTGGCGTACTGATTCGTCACAACGAAGAGTACGAGAAGATCGAAGGCTGTGACGATg > 1:580896/1‑69 (MQ=255)
ttCTGGAACAGTGGCGTAGTGATTCGTCACAACGAAGAGTACGAGAAGATCGAAGGCTGTGACGATGgt < 1:2323904/69‑1 (MQ=255)
aCAGTGGCGTAGTGATTCGTCACAACGAAGAGTACGAGAAGATCGAAGGCTGTGACGATGGTGTGAt < 1:2840021/67‑1 (MQ=255)
aCAGTGGCGTAGTGATTCGTCACAACGAAGAGTACGAGAAGATCGAAGGCTGTGACGATGGTGTGAt < 1:2309395/67‑1 (MQ=255)
aCAGTGGCGTAGTGATTCGTCACAACGAAGAGTACGAGAAGATCGAAGGCTGTGACGATGGTGTGAt < 1:1922329/67‑1 (MQ=255)
aCAGTGGCGTAGTGATTCGTCACAACGAAGAGTACGAGAAGATCGAAGGCTGTGACGATGGTGTGAt < 1:1908900/67‑1 (MQ=255)
aCAGTGGCGTAGTGATTCGTCACAACGAAGAGTACGAGAAGATCGAAGGCTGTGACGATGGTGTGAt < 1:1879890/67‑1 (MQ=255)
aCAGTGGCGTAGTGATTCGTCACAACGAAGAGTACGAGAAGATCGAAGGCTGTGACGATGGTGTGAt < 1:680033/67‑1 (MQ=255)
aCAGTGGCGTAGTGATTCGTCACAACGAAGAGTACGAGAAGATCGAAGGCTGTGACGATGGTGTGAt < 1:673236/67‑1 (MQ=255)
aCAGTGGCGTAGTGATTCGTCACAACGAAGAGTACGAGAAGATCGAAGGCTGTGACGATGGTGTGAt < 1:1567806/67‑1 (MQ=255)
aCAGTGGCGTAGTGATTCGTCACAACGAAGAGTACGAGAAGATCGAAGGCTGTGACGATGGTGTGAt < 1:2769173/67‑1 (MQ=255)
aCAGTGGCGTAGTGATTCGTCACAACGAAGAGTACGAGAAGATCGAAGGCTGTGACGATGGTGTGAt < 1:2965062/67‑1 (MQ=255)
aCAGTGGCGTAGTGATTCGTCACAACGAAGAGTACGAGAAGATCGAAGGCTGTGACGATGGTGTGAt < 1:1365561/67‑1 (MQ=255)
aCAGTGGCGTAGTGATTCGTCACAACGAAGAGTACGAGAAGATCGAAGGCTGTGACGATGGTGTGAt < 1:3221296/67‑1 (MQ=255)
aCAGTGGCGTAGTGATTCGTCACAACGAAGAGTACGAGAAGATCGAAGGCTGTGACGATGGTGTGAt < 1:1180555/67‑1 (MQ=255)
aCAGTGGCGTAGTGATTCGTCACAACGAAGAGTACGAGAAGATCGAAGGCTGTGACGATGGTGTGAt < 1:1135550/67‑1 (MQ=255)
aCAGTGGCGTAGTGATTCGTCACAACGAAGAGTACGAGAAGATCGAAGGCTGTGACGATGGTGTGAt < 1:108927/67‑1 (MQ=255)
aCAGTGGCGTAGTGATTCGTCACAACGAAGAGTACGAGAAGATCGAAGGCTGTGACGATGGTGTGAt < 1:3307190/67‑1 (MQ=255)
cAGTGGCGTAGTGATTCGTCACAACGAAGAGTACGAGAAGATCGAAGGCTGTGACGATGGTGTGAt < 1:324803/66‑1 (MQ=255)
gTGGCGTAGTGATTCGTCACAACGAAGAGTACGAGAAGATCGAAGGCTGTGACGATGGTGTGATCATg > 1:1372178/1‑68 (MQ=255)
gTGGCGTAGTGATTCGTCACAACGAAGAGTACGAGAAGATCGAAGGCTGTGACGATGGTGTGATCATg > 1:3089064/1‑68 (MQ=255)
gTGGCGTAGTGATTCGTCACAACGAAGAGTACGAGAAGATCGAAGGCTGTGACGATGGTGTGATCATGc > 1:3317639/1‑69 (MQ=255)
gTGGCGTAGTGATTCGTCACAACGAAGAGTACGAGAAGATCGAAGGCTGTGACGATGGTGTGATCATGc > 1:716334/1‑69 (MQ=255)
cGTAGTGATTCGTCACAACGAAGAGTACGAGAAGATCGAAGGCTGTGACGATGGTGTGAt < 1:237646/60‑1 (MQ=255)
gATTCGTCACAACGAAGAGTACGAGAAGATCGAAGGCTGTGACGATGGTGTGAt < 1:2164103/54‑1 (MQ=255)
tCGTCACAACGAAGAGTACGAGAAGATCGAAGGCTGTGACGATGGTGTGATCa > 1:2563838/1‑53 (MQ=255)
tCGTCACAACGAAGAGTACGAGAAGATCGAAGGCTGTGACGATGGTGTGATCATGCATCTGAAGTCgg > 1:2153970/1‑68 (MQ=255)
tCGTCACAACGAAGAGTACGAGAAGATCGAAGGCTGTGACGATGGTGTGATCATGCATCTGAAGTCgg > 1:1373841/1‑68 (MQ=255)
acaACGAAGAGTACGAGAAGATCGAAGGCTGTGACGACGGTGTGATCATGCATCTGAAGTCGGGTaaaa > 1:2106634/1‑69 (MQ=255)
acaACGAAGAGTACGAGAAGATCGAAGGCTGTGACGACGGTGTGATCATGCATCTGAAGTCGGGTaaaa > 1:3305947/1‑69 (MQ=255)
acaACGAAGAGTACGAGAAGATCGAAGGCTGTGACGACGGTGTGATCATGCATCTGAAGTCGGGTaaaa > 1:3280435/1‑69 (MQ=255)
acaACGAAGAGTACGAGAAGATCGAAGGCTGTGACGACGGTGTGATCATGCATCTGAAGTCGGGTaaaa > 1:1170357/1‑69 (MQ=255)
acaACGAAGAGTACGAGAAGATCGAAGGCTGTGACGACGGTGTGATCATGCATCTGAAGTCGGGTaaaa > 1:722524/1‑69 (MQ=255)
acaACGAAGAGTACGAGAAGATCGAAGGCTGTGACGACGGTGTGATCATGCATCTGAAGTCGGGTaaaa > 1:3146958/1‑69 (MQ=255)
acaACGAAGAGTACGAGAAGATCGAAGGCTGTGACGACGGTGTGATCATGCATCTGAAGTCGGGTaaaa > 1:2818943/1‑69 (MQ=255)
acaACGAAGAGTACGAGAAGATCGAAGGCTGTGACGACGGTGTGATCATGCATCTGAAGTCGGGTaaaa > 1:1428033/1‑69 (MQ=255)
acaACGAAGAGTACGAGAAGATCGAAGGCTGTGACGACGGTGTGATCATGCATCTGAAGTCGGGTaaaa > 1:1481654/1‑69 (MQ=255)
acaACGAAGAGTACGAGAAGATCGAAGGCTGTGACGACGGTGTGATCATGCATCTGAAGTCGGGTaaaa > 1:2696792/1‑69 (MQ=255)
acaACGAAGAGTACGAGAAGATCGAAGGCTGTGACGACGGTGTGATCATGCATCTGAAGTCGGGTaaaa > 1:2095810/1‑69 (MQ=255)
acaACGAAGAGTACGAGAAGATCGAAGGCTGTGACGACGGTGTGATCATGCATCTGAAGTCGGGTaaaa > 1:709961/1‑69 (MQ=255)
acaACGAAGAGTACGAGAAGATCGAAGGCTGTGACGACGGTGTGATCATGCATCTGAAGTCGGGTaaaa > 1:231358/1‑69 (MQ=255)
acaACGAAGAGTACGAGAAGATCGAAGGCTGTGACGACGGTGTGATCATGCATCTGAAGTCGGGTaaa > 1:3003450/1‑68 (MQ=255)
aaCGAAGAGTACGAGAAGATCGAAGGCTGTGACGACGGTGTGATCATGCATCTGAAGTCGGGTaaaaa < 1:1751100/68‑1 (MQ=255)
aaCGAAGAGTACGAGAAGATCGAAGGCTGTGACGACGGTGTGATCATGCATCTGAAGTCGGGTaaaaa < 1:2114028/68‑1 (MQ=255)
aaCGAAGAGTACGAGAAGATCGAAGGCTGTGACGACGGTGTGATCATGCATCTGAAGTCGGGTaaaaa < 1:2141357/68‑1 (MQ=255)
aaCGAAGAGTACGAGAAGATCGAAGGCTGTGACGACGGTGTGATCATGCATCTGAAGTCGGGTaaaaa < 1:1294706/68‑1 (MQ=255)
aaCGAAGAGTACGAGAAGATCGAAGGCTGTGACGACGGTGTGATCATGCATCTGAAGTCGGGTaaaaa < 1:405890/68‑1 (MQ=255)
aaCGAAGAGTACGAGAAGATCGAAGGCTGTGACGACGGTGTGATCATGCATCTGAAGTCGGGTaaaaa < 1:417244/68‑1 (MQ=255)
aaCGAAGAGTACGAGAAGATCGAAGGCTGTGACGACGGTGTGATCATGCATCTGAAGTCGGGTaaaaa < 1:2340019/68‑1 (MQ=255)
aaCGAAGAGTACGAGAAGATCGAAGGCTGTGACGACGGTGTGATCATGCATCTGAAGTCGGGTaaaaa < 1:2802030/68‑1 (MQ=255)
aaCGAAGAGTACGAGAAGATCGAAGGCTGTGACGACGGTGTGATCATGCATCTGAAGTCGGGTaaaaa < 1:2501960/68‑1 (MQ=255)
aaCGAAGAGTACGAGAAGATCGAAGGCTGTGACGACGGTGTGATCATGCATCTGAAGTCGGGTaaaaa < 1:1826934/68‑1 (MQ=255)
aaCGAAGAGTACGAGAAGATCGAAGGCTGTGACGACGGTGTCATCATGCATCTGAAGTCGGGTaaaaa < 1:3019181/68‑1 (MQ=255)
agagTACGGGAAGATCGAAGGCTGTGACGATGGTGTGATCATGCATCTGAAGTCGGGTAAAAGACTGaa > 1:696160/1‑69 (MQ=255)
agagTACGAGAAGATCGAAGGCTGTGACGATGGTGTGATCATGCATCTGAAGTCGGGTAAAAAACTGaa > 1:719083/1‑69 (MQ=255)
agagTACGAGAAGATCGAAGGCTGTGACGATGGTGTGATCATGCATCTGAAGTCGGGTAAAAAACTGaa > 1:3053905/1‑69 (MQ=255)
agagTACGAGAAGATCGAAGGCTGTGACGATGGTGTGATCATGCATCTGAAGTCGGGTAAAAAACTGaa > 1:2479359/1‑69 (MQ=255)
agagTACGAGAAGATCGAAGGCTGTGACGATGGTGTGATCATGCATCTGAAGTCGGGTAAAAAACTGaa > 1:807896/1‑69 (MQ=255)
gagTACGAGAAGAGCGAAGGCTGTGACGATGGTGTGAt < 1:687004/38‑1 (MQ=255)
tACGAGAAGATCGAAGGCTGTGACGACGGTGTGATCATGCATCTGAAGTCGGGTaaaaa < 1:2517163/59‑1 (MQ=255)
aCGAGAAGATCGAAGGCTGTGACGATGGTGTGATCATGCATCTGAAGTCGGGTAAAAAACTGAAAGCTg < 1:806309/69‑1 (MQ=255)
cGAGAAGATCGAAGGCTGTGACGATGGTGTGATCATGCATCTGAAGTCGGGTAAAAAACTGAAAGCTGa > 1:2934867/1‑69 (MQ=255)
cGAGAAGATCGAAGGCTGTGACGATGGTGTGATCATGCATCTGAAGTCGGGTAAAAAACTGAAAGCTGa > 1:1003575/1‑69 (MQ=255)
cGAGAAGATCGAAGGCTGTGACGATGGTGTGATCATGCATCTGAAGTCGGGTAAAAAACTGAAAGCTGa > 1:2014801/1‑69 (MQ=255)
cGAGAAGATCGAAGGCTGTGACGATGGTGTGATCATGCATCTGAAGTCGGGTAAAAAACTGAAAGCTGa > 1:1241049/1‑69 (MQ=255)
gAAGGCTGTGACGATGGTGTGATCATGCATCTGAAGTCGGGTAAAAAACTGAAAGCTGACTGCCTGctc < 1:2842226/69‑1 (MQ=255)
gAAGGCTGTGACGATGGTGTGATCATGCATCTGAAGTCGGGTAAAAAACTGAAAGCTGACTGCCTGctc < 1:2762277/69‑1 (MQ=255)
gAAGGCTGTGACGATGGTGTGATCATGCATCTGAAGTCGGGTAAAAAACTGAAAGCTGACTGCCTGctc < 1:2635252/69‑1 (MQ=255)
gAAGGCTGTGACGATGGTGTGATCATGCATCTGAAGTCGGGTAAAAAACTGAAAGCTGACTGCCTGctc < 1:2143723/69‑1 (MQ=255)
gAAGGCTGTGACGATGGTGTGATCATGCATCTGAAGTCGGGTAAAAAACTGAAAGCTGACTGCCTGctc < 1:1412829/69‑1 (MQ=255)
gAAGGCTGTGACGATGGTGTGATCATGCATCTGAAGTCGGGTAAAAAACTGAAAGCTGACTGCCTGctc < 1:1033105/69‑1 (MQ=255)
gAAGGCTGTGACGATGGTGTCATCATGCATCTGAAGTCGGGTAAAAAACTGAAAGCTGACTGCCTGctc < 1:533467/69‑1 (MQ=255)
gACGATGGTGTGATCATGCATCTGAAGTCGGGTAAAAAACTGAAAGCTGACTGCCTGctc < 1:2530207/60‑1 (MQ=255)
acgacgGTGTGATCATGTATCTGAAGTCGGGTaaaaa < 1:2066211/37‑1 (MQ=38)
|
ACTTCTGGAACAGTGGCGTAGTGATTCGTCACAACGAAGAGTACGAGAAGATCGAAGGCTGTGACGATGGTGTGATCATGCATCTGAAGTCGGGTAAAAAACTGAAAGCTGACTGCCTGCTC > minE/2282273‑2282394
|
| 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
