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 |
1,738,596 |
C→T |
41.0% |
E405E (GAG→GAA) |
lepA ← |
GTP binding membrane protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,738,596 | 0 | C | T | 41.0%
| 21.4
/ 37.4
| 56 | E405E (GAG→GAA) | lepA | GTP binding membrane protein |
| Reads supporting (aligned to +/- strand): ref base C (12/21); new base T (4/19); total (16/40) |
| Fisher's exact test for biased strand distribution p-value = 1.45e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.95e-01 |
TTTTTCTACGCACAACGTAATAACGTTGCCGAGATATGCCTGCGGCAGCAGCATGTGACACTCTGCAATCGGCTCGCGCAGTTCGTAGATGTTATTTACCGCAGGCAGCTTGGATGGGCTGTCGA > minE/1738536‑1738660
|
tttttCTACGCACAACGTAATAACGTTGCCGAGATATGCCTGCGGCAGCAGCATGTGACACTCTGCAAt > 1:873518/1‑69 (MQ=255)
cacaACGTAATAACGTTGCCGAGATATGCCTGCGGCAGCAGCATGTGACACTCTGCAATCGGCTcgcg < 1:793026/68‑1 (MQ=255)
cacaACGTAATAACGTTGCCGAGATATGCCTGCGGCAGCAGCATGTGACACTCTGCAATCGGCTcgcg < 1:2676335/68‑1 (MQ=255)
cacaACGTAATAACGTTGCCGAGATATGCCTGCGGCAGCAGCATGTGACACTCTGCAATCGGCTcgcg < 1:2230252/68‑1 (MQ=255)
cacaACGTAATAACGTTGCCGAGATATGCCTGCGGCAGCAGCATGTGACACTCTGCAATCGGCTcgcg < 1:221737/68‑1 (MQ=255)
cacaACGTAATAACGTTGCCGAGATATGCCTGCGGCAGCAGCATGTGACACTCTGCAATCGGCTcgcg < 1:607299/68‑1 (MQ=255)
aataaCGTTGCCGAGATATGCCTGCGGCAGCAGCATGTGACACTCTGCAATCGGCTCGCGCAGTTCGTa < 1:2879531/69‑1 (MQ=255)
aataaCGTTGCCGAGATATGCCTGCGGCAGCAGCATGTGACACTCTGCAATCGGCTCGCGCAGTTCGTa < 1:381365/69‑1 (MQ=255)
aataaCGTTGCCGAGATATGCCTGCGGCAGCAGCATGTGACACTCTGCAATCGGCTCGCGCAGTTCGTa < 1:2154979/69‑1 (MQ=255)
aataaCGTTGCCGAGATATGCCTGCGGCAGCAGCATGTGACACTCTGCAATCGGCTCGCGCAGTTCGTa < 1:1851245/69‑1 (MQ=255)
aataaCGTTGCCGAGATATGCCTGCGGCAGCAGCATGTGACACTCTGCAATCGGCTCGCGCAGTTCGTa < 1:1864924/69‑1 (MQ=255)
aCGTTGCCGAGATATGCCTGCGGCAGCAGCATGTGACACTCTGCAATCGGCTCGCGCAGTTCGTa > 1:2876354/1‑65 (MQ=255)
aCGTTGCCGAGATATGCCTGCGGCAGCAGCATGTGACACTCTGCAATCGGCTCGCGCAGTTCGTa > 1:3065298/1‑65 (MQ=255)
aCGTTGCCGAGATATGCCTGCGGCAGCAGCATGTGACACTCTGCAATCGGCTCGCGCAGTTCGTa > 1:350873/1‑65 (MQ=255)
aCGTTGCCGAGATATGCCTGCGGCAGCAGCATGTGACACTCTGCAATCGGCTCGCGCAGTTCGTa > 1:2080462/1‑65 (MQ=255)
aCGTTGCCGAGATATGCCTGCGGCAGCAGCATGTGACACTCTGCAATCGGCTCGCGCAGTTCGTa > 1:753658/1‑65 (MQ=255)
cGAGATATGCCTGCGGCAGCAGCATGTGACATTCTGCAATCGGCTCGCGCAGTTCGTAGATGTTAttt < 1:2412083/68‑1 (MQ=255)
cGAGATATGCCTGCGGCAGCAGCATGTGACATTCTGCAATCGGCTCGCGCAGTTCGTAGATGTTAttt < 1:1183893/68‑1 (MQ=255)
cGAGATATGCCTGCGGCAGCAGCATGTGACATTCTGCAATCGGCTCGCGCAGTTCGTAGATGTTAttt < 1:3152711/68‑1 (MQ=255)
cGAGATATGCCTGCGGCAGCAGCATGTGACATTCTGCAATCGGCTCGCGCAGTTCGTAGATGTTAttt < 1:750443/68‑1 (MQ=255)
cGAGATATGCCTGCGGCAGCAGCATGTGACATTCTGCAATCGGCTCGCGCAGTTCGTAGATGTTAttt < 1:445742/68‑1 (MQ=255)
cGAGATATGCCTGCGGCAGCAGCATGTGACATTCTGCAATCGGCTCGCGCAGTTCGTAGATGTTAttt < 1:2465501/68‑1 (MQ=255)
cGAGATATGCCTGCGGCAGCAGCATGTGACATTCTGCAATCGGCTCGCGCAGTTCGTAGATGTTAttt < 1:1145850/68‑1 (MQ=255)
cGAGATATGCCTGCGGCAGCAGCATGTGACATTCTGCAATCGGCTCGCGCAGTTCGTAGATGTTAttt < 1:2099817/68‑1 (MQ=255)
cGAGATATGCCTGCGGCAGCAGCATGTGACATTCTGCAATCGGCTCGCGCAGTTCGTAGATGTTAttt < 1:1927107/68‑1 (MQ=255)
agaTATGCCTGCGGCAGCAGCATGTGACATTCTGCAATCGGCTCGCGCAGTTc < 1:1355510/53‑1 (MQ=255)
agaTATGCCTGCGGCAGCAGCATGTGACATTCTGCAATCGGCTCGCGCAGTTc < 1:2254901/53‑1 (MQ=255)
agaTATGCCTGCGGCAGCAGCATGTGACATTCTGCAATCGGCTCGCGCAGTTc < 1:2262412/53‑1 (MQ=255)
agaTATGCCTGCGGCAGCAGCATGTGACATTCTGCAATCGGCTCGCGCAGTTc < 1:614425/53‑1 (MQ=255)
agaTATGCCTGCGGCAGCAGCATGTGACATTCTGCAATCGGCTCGCGCAGTTc < 1:129472/53‑1 (MQ=255)
agaTATGCCTGCGGCAGCAGCATGTGACATTCTGCAATCGGCTCGCGCAGTTc < 1:2835185/53‑1 (MQ=255)
agaTATGCCTGCGGCAGCAGCATGTGACATTCTGCAATCGGCTCGCGCAGTTc < 1:1917061/53‑1 (MQ=255)
agaTATGCCTGCGGCAGCAGCATGTGACATTCTGCAATCGGCTCGCGCAGTTc < 1:2010979/53‑1 (MQ=255)
agaTATGCCTGCGGCAGCAGCATGTGACATTCTGCAATCGGCTCGCCCAGTTc < 1:2774896/53‑1 (MQ=255)
atatGCCTGCGGCAGCAGCATGTGACACTCTGCAATCGGCTCGCGCAGTTCGTAGATGTTATTTACCgc > 1:192788/1‑69 (MQ=255)
atatGCCTGCGGCAGCAGCATGTGACACTCTGCAATCGGCTCGCGCAGTTCGTAGATGTTATTTACCgc > 1:2792280/1‑69 (MQ=255)
atatGCCTGCGGCAGCAGCATGTGACACTCTGCAATCGGCTCGCGCAGTTCGTAGATGTTATTTACCgc > 1:1011037/1‑69 (MQ=255)
atatGCCTGCGGCAGCAGCATGTGACACTCTGCAATCGGCTCGCGCAGTTCGTAGATGTTATTTACCgc > 1:481805/1‑69 (MQ=255)
gctgcagcaTGTGACACTCTGCAATCGGCTCGCGCAGTTCGTAGATGTTATTTACCGCAGGCAGCTTg < 1:2574665/65‑1 (MQ=255)
gcagcagcaTGTGACATTCTGCAATCGGCTCGCGCAGTTc < 1:664554/40‑1 (MQ=255)
gcagcagcaTGTGACACTCTGCAATCGGCTCGCGCAGTTCGTAGATGTTATTTACCGCAGGCAGCTTg < 1:1020302/68‑1 (MQ=255)
gcagcagcaTGTGACACTCTGCAATCGGCTCGCGCAGTTCGTAGATGTTATTTACCGCAGGCAGCTTg > 1:812014/1‑68 (MQ=255)
gcagcagcaTGTGACACTCTGCAATCGGCTCGCGCAGTTCGTAGATGTTATTTACCGCAGGCAGCTTg < 1:1220537/68‑1 (MQ=255)
gcagcagcaTGTGACACTCTGCAATCGGCTCGCGCAGTTCGTAGATGTTATTTACCGCAGGCAGCTTg < 1:1276186/68‑1 (MQ=255)
gcagcagcaTGTGACACTCTGCAATCGGCTCGCGCAGTTCGTAGATGTTATTTACCGCAGGCAGCTTg < 1:3140696/68‑1 (MQ=255)
gcagcagcaTGTGACACTCTGCAATCGGCTCGCGCAGTTCGTAGATGTTATTTACCGCAGGCAGCTTg < 1:1340099/68‑1 (MQ=255)
gcagcagcaTGTGACACTCTGCAATCGGCTCGCGCAGTTCGTAGATGTTATTTACCGCAGGCAGCTTg < 1:3382355/68‑1 (MQ=255)
gcagcagcaTGTGACACTCTGCAATCGGCTCGCGCAGTTCGTAGATGTTATTTACCGCAGGCAGCTTg < 1:1605213/68‑1 (MQ=255)
gcagcagcaTGTGACACTCTGCAATCGGCTCGCGCAGTTCGTAGATGTTATTTACCGCAGGCAGCTTg < 1:1818065/68‑1 (MQ=255)
gcagcagcaTGTGACACTCTGCAATCGGCTCGCGCAGTTCGTAGATGTTATTTACCGCAGGCAGCTTg < 1:285713/68‑1 (MQ=255)
agcagcaTGTGACACTCTGCAATCGGCTCGCGCAGTTCGTAGATGTTATTTACCGCAGGCAGCTTg < 1:2496686/66‑1 (MQ=255)
tgACACTCTGCAATCGGCTCGCGCAGTTCGTAGATGTTATTTACCGCAGGCAGCTTGGATGGGCt > 1:3314246/1‑65 (MQ=255)
gACATTCTGCAATCGGCTCGCGCAGTTCGTAGATGTTATTTACCGCTGGCAGCTTGGTTGGGCTGTCGa > 1:2802305/1‑69 (MQ=255)
gACATTCTGCAATCGGCTCGCGCAGTTCGTAGATGTTATTTACCGCTGGCAGCTTGGATGGGCTGTCGa > 1:2666454/1‑69 (MQ=255)
gACATTCTGCAATCGGCTCGCGCAGTTCGTAGATGTTATTTACCGCTGGCAGCTTGGATGGGCTGTCGa > 1:3086298/1‑69 (MQ=255)
gACATTCTGCAATCGGCTCGCGCAGTTCGTAGATGTTATTTACCGCTGGCAGCTTGGATGGGCTGTCGa > 1:3055424/1‑69 (MQ=255)
ctctGCAATCGGCTCGCGCAGTTCGTAGATGTTATTTACCGCAGGCAGCTTGGATGGGCTGTCGa > 1:2534773/1‑65 (MQ=255)
ctctGCAATCGGCTCGCGCAGTTCGTAGATGTTATTTACCGCAGGCAGCTTGGATGGGCTGTCGa > 1:2536854/1‑65 (MQ=255)
ctctGCAATCGGCTCGCGCAGTTCGTAGATGTTATTTACCGCAGGCAGCTTGGATGGGCTGTCGa > 1:138537/1‑65 (MQ=255)
ctctGCAATCGGCTCGCGCAGTTCGTAGATGTTATTTACCGCAGGCAGCTTGGATGGGCTGTCGa > 1:811957/1‑65 (MQ=255)
ctctGCAATCGGCTCGCGCAGTTCGTAGATGTTATTTACCGCAGGCAGCTTGGATGGGCTGTCGa > 1:3016824/1‑65 (MQ=255)
|
TTTTTCTACGCACAACGTAATAACGTTGCCGAGATATGCCTGCGGCAGCAGCATGTGACACTCTGCAATCGGCTCGCGCAGTTCGTAGATGTTATTTACCGCAGGCAGCTTGGATGGGCTGTCGA > minE/1738536‑1738660
|
| 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
