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 |
2,499,803 |
A→G |
28.5% |
A95A (GCA→GCG) |
uhpA → |
DNA‑binding response regulator in two‑component regulatory system wtih UhpB |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,499,803 | 0 | A | G | 28.5%
| 37.8
/ 15.5
| 42 | A95A (GCA→GCG) | uhpA | DNA‑binding response regulator in two‑component regulatory system wtih UhpB |
| Reads supporting (aligned to +/- strand): ref base A (28/2); new base G (3/9); total (31/11) |
| Fisher's exact test for biased strand distribution p-value = 2.28e-05 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.27e-01 |
ATGGCGACGATTATGCTCTCCGTTCACGACAGTCCTGCGCTGGTTGAGCAGGCGCTTAACGCGGGGGCACGCGGCTTTCTTTCCAAACGCTGTAGCCCGGATGAACTCATTGCTGCGGTGCATACGGTTGC > minE/2499735‑2499865
|
aTGGCGACGATTATGCTCTCCGTTCACGACAGTCCTGCGCTGGTTGAGCAGGCGCTTAACGCGGGGGCa > 1:2556394/1‑69 (MQ=255)
tGGCGACGATTATGCTCTCCGTTCACGACAGTCCTGCGCTGGTTGAGCAGGCGCTTAACGCGGGGGCAc > 1:2254621/1‑69 (MQ=255)
gCGACGATTATGCTCTCCGTTCACGACAGTCCTGCGCTGGTTGAGCAGGCGCTTAACGCGGGGGCAcgc > 1:1207043/1‑69 (MQ=255)
gCGACGATTATGCTCTCCGTTCACGACAGTCCTGCGCTGGTTGAGCAGGCGCTTAACGCGGGGGCAcgc > 1:580872/1‑69 (MQ=255)
gCGACGATTATGCTCTCCGTTCACGACAGTCCTGCGCTGGTTGAGCAGGCGCTTAACGCGGGGGCAcg > 1:1119032/1‑68 (MQ=255)
tATGCTCTCCGTTCACGACAGTCCTGCGCTGGTTGAGCAGGCGCTTAACGCGGGGGCACGCGGctttct > 1:1284168/1‑69 (MQ=255)
tATGCTCTCCGTTCACGACAGTCCTGCGCTGGTTGAGCAGGCGCTTAACGCGGGGGCACGCGGctttct > 1:2352116/1‑69 (MQ=255)
tATGCTCTCCGTTCACGACAGTCCTGCGCTGGTTGAGCAGGCGCTTAACGCGGGGGCACGCGGctttct > 1:2309334/1‑69 (MQ=255)
ctcCGTTCACGACAGTCCTGCGCTTGTTGAGCAGGCGCTCAACGCGGGGGCACGCGGCTTTCTTTCCaa > 1:1658479/1‑69 (MQ=255)
ctcCGTTCACGACAGTCCTGCGCTGGTTGAGCAGGCGCTTAACGCGGGGGCACGCGGCTTTCTTTCCaa > 1:898698/1‑69 (MQ=255)
ctcCGTTCACGACAGTCCTGCGCTGGTTGAGCAGGCGCTTAACGCGGGGGCACGCGGCTTTCTTTCCaa > 1:333084/1‑69 (MQ=255)
ctcCGTTCACGACAGTCCTGCGCTGGTTGAGCAGGCGCTTAACGCGGGGGCACGCGGCTTTCTTTCCaa > 1:126139/1‑69 (MQ=255)
ctcCGTTCACGACAGTCCTGCGCTGGTTGAGCAGGCGCTTAACGCGGGGGCACGCGGCTTTCTTTCCaa > 1:1635948/1‑69 (MQ=255)
ctcCGTTCACGACAGTCCTGCGCTGGTTGAGCAGGCGCTTAACGCGGGGGCACGCGGCTTTCTTTCCa > 1:2375140/1‑68 (MQ=255)
ctcCGTTCACGACAGTCCTGCGCTGGTTGAGCAGGCGCTTAACGCGGGGGCACGCGGCTTTCTTTCCa > 1:23437/1‑68 (MQ=255)
ctcCGTTCACGACAGTCCTGCGCTGGTTGAGCAGGCGCTTAACGCGGGGGCACGCGGCTTTCTTTCCa < 1:231761/68‑1 (MQ=255)
cACGACAGTCCTGCGCTGGTTGAGCAGGCGCTTAACGCGGGGGCACGCGGCTTTCTTTCCAAACGCTGt > 1:1465106/1‑69 (MQ=255)
cACGACAGTCCTGCGCTGGTTGAGCAGGCGCTTAACGCGGGGGCACGCGGCTTTCTTTCCAAACGCTGt > 1:2788761/1‑69 (MQ=255)
cACGACAGTCCTGCGCTGGTTGAGCAGGCGCTTAACGCGGGGGCACGCGGCTTTCTTTCCAAACGCTGt > 1:2623021/1‑69 (MQ=255)
cACGACAGTCCTGCGCTGGTTGAGCAGGCGCTTAACGCGGGGGCACGCGGCTTTCTTTCCAAACGCTGt > 1:2394510/1‑69 (MQ=255)
cACGACAGTCCTGCGCTGGTTGAGCAGGCGCTTAACGCGGGGGCACGCGGCTTTCTTTCCAAACGCTGt > 1:2366145/1‑69 (MQ=255)
cACGACAGTCCTGCGCTGGTTGAGCAGGCGCTTAACGCGGGGGCACGCGGCTTTCTTTCCAAACGCTGt > 1:296544/1‑69 (MQ=255)
cACGACAGTCCTGCGCTGGTTGAGCAGGCGCTTAACGCGGGGGCACGCGGCTTTCTTTCCAAACGCTGt > 1:2201521/1‑69 (MQ=255)
cACGACAGTCCTGCGCTGGTTGAGCAGGCGCTTAACGCGGGGGCACGCGGCTTTCTTTCCAAACGCTGt > 1:3032445/1‑69 (MQ=255)
cACGACAGTCCTGCGCTGGTTGAGCAGGCGCTTAACGCGGGGGCACGCGGCTTTCTTTCCAAACGCTGt > 1:1269862/1‑69 (MQ=255)
cACGACAGTCCTGCGCTGGTTGAGCAGGCGCTTAACGCGGGGGCACGCGGCTTTCTTTCCAAACGCTGt > 1:3341615/1‑69 (MQ=255)
cACGACAGTCCTGCGCTGGTTGAGCAGGCGCTTAACGCGGGGGCACGCGGCTTTCTTTCCAAACGCTGt > 1:1918663/1‑69 (MQ=255)
cACGACAGTCCTGCGCTGGTTGAGCAGGCGCTTAACGCGGGGGCACGCGGCTTTCTTTCCAAACGCTGt > 1:835612/1‑69 (MQ=255)
aGTCCGGCGCTGGTTGAGCAGGCGCTTAACGCGGGGGCGCGCGGCTTTCTCTCCAAACGCTGTAGccc < 1:1777837/68‑1 (MQ=255)
aGTCCGGCGCTGGTTGAGCAGGCGCTTAACGCGGGGGCGCGCGGCTTTCTCTCCAAACGCTGTAGccc < 1:2877145/68‑1 (MQ=255)
aGTCCGGCGCTGGTTGAGCAGGCGCTTAACGCGGGGGCGCGCGGCTTTCTCTCCAAACGCTGTAGccc < 1:2662021/68‑1 (MQ=255)
aGTCCGGCGCTGGTTGAGCAGGCGCTTAACGCGGGGGCGCGCGGCTTTCTCTCCAAACGCTGTAGccc < 1:1416488/68‑1 (MQ=255)
aGTCCGGCGCTGGTTGAGCAGGCGCTTAACGCGGGGGCGCGCGGCTTTCTCTCCAAACGCTGTAGccc < 1:1433850/68‑1 (MQ=255)
aGTCCGGCGCTGGTTGAGCAGGCGCTTAACGCGGGGGCGCGCGGCTTTCTCTCCAAACGCTGTAGccc < 1:2167085/68‑1 (MQ=255)
aGTCCGGCGCTGGTTGAGCAGGCGCTTAACGCGGGGGCGCGCGGCTTTCTCTCCAAACGCTGTAGccc < 1:1944918/68‑1 (MQ=255)
aGTCCGGCGCTGGTTGAGCAGGCGCTTAACGCGGGGGCGCGCGGCTTTCTCTCCAAACGCTGTAGccc < 1:1938976/68‑1 (MQ=255)
aGTCCGGCGCTGGTTGAGCAGGCGCTTAACGCGGGGGCGCGCGGCTTTCTCTCCAAACGCTGTAGccc < 1:1771278/68‑1 (MQ=255)
ccTGCGCTGGTTGAGCAGGCGCTTAACGCGGGGGCACGCGGCTTTCTTTCCAAACGCTGTAGCCCGGa > 1:3081793/1‑68 (MQ=255)
ccTGCGCTGGTTGAGCAGGCGCTTAACGCGGGGGCACGCGGCTTTCTTTCCAAACGCTGTAGCCCGGa > 1:3379186/1‑68 (MQ=255)
ggTTGAGCAGGCGCTTAACGCGGGGGCGCGCGGCTTTCTCTCCAAACGCTGTAGCCCGGATGAACTCAt > 1:1948247/1‑69 (MQ=255)
ggTTGAGCAGGCGCTTAACGCGGGGGCGCGCGGCTTTCTCTCCAAACGCTGTAGCCCGGATGAACTCAt > 1:510101/1‑69 (MQ=255)
ggTTGAGCAGGCGCTTAACGCGGGGGCGCGCGGCTTTCTCTCCAAACGCTGTAGCCCGGATGAACTCAt > 1:1063870/1‑69 (MQ=255)
gggggCACGCGGCTTTCTTTCCAAACGCTGTAGCCCGGATGAACTCATTGCTGCGGTGCATACGGTTGc < 1:740299/69‑1 (MQ=255)
|
ATGGCGACGATTATGCTCTCCGTTCACGACAGTCCTGCGCTGGTTGAGCAGGCGCTTAACGCGGGGGCACGCGGCTTTCTTTCCAAACGCTGTAGCCCGGATGAACTCATTGCTGCGGTGCATACGGTTGC > minE/2499735‑2499865
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
