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 |
2,499,815 |
T→C |
34.2% |
L99L (CTT→CTC) |
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 | 2,499,815 | 0 | T | C | 34.2%
| 21.1
/ 16.3
| 35 | L99L (CTT→CTC) | uhpA | DNA‑binding response regulator in two‑component regulatory system wtih UhpB |
| Reads supporting (aligned to +/- strand): ref base T (21/2); new base C (3/9); total (24/11) |
| Fisher's exact test for biased strand distribution p-value = 1.37e-04 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
CTCCGTTCACGACAGTCCTGCGCTGGTTGAGCAGGCGCTTAACGCGGGGGCACGCGGCTTTCTTTCCAAACGCTGTAGCCCGGATGAACTCATTGCTGCGGTGCATACGGTTGCCACGGGCGGCTGTTAT > minE/2499752‑2499881
|
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 < 1:231761/68‑1 (MQ=255)
ctcCGTTCACGACAGTCCTGCGCTGGTTGAGCAGGCGCTTAACGCGGGGGCACGCGGCTTTCTTTCCa > 1:2375140/1‑68 (MQ=255)
ctcCGTTCACGACAGTCCTGCGCTGGTTGAGCAGGCGCTTAACGCGGGGGCACGCGGCTTTCTTTCCa > 1:23437/1‑68 (MQ=255)
cACGACAGTCCTGCGCTGGTTGAGCAGGCGCTTAACGCGGGGGCACGCGGCTTTCTTTCCAAACGCTGt > 1:1465106/1‑69 (MQ=255)
cACGACAGTCCTGCGCTGGTTGAGCAGGCGCTTAACGCGGGGGCACGCGGCTTTCTTTCCAAACGCTGt > 1:835612/1‑69 (MQ=255)
cACGACAGTCCTGCGCTGGTTGAGCAGGCGCTTAACGCGGGGGCACGCGGCTTTCTTTCCAAACGCTGt > 1:3341615/1‑69 (MQ=255)
cACGACAGTCCTGCGCTGGTTGAGCAGGCGCTTAACGCGGGGGCACGCGGCTTTCTTTCCAAACGCTGt > 1:3032445/1‑69 (MQ=255)
cACGACAGTCCTGCGCTGGTTGAGCAGGCGCTTAACGCGGGGGCACGCGGCTTTCTTTCCAAACGCTGt > 1:296544/1‑69 (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 > 1:2201521/1‑69 (MQ=255)
cACGACAGTCCTGCGCTGGTTGAGCAGGCGCTTAACGCGGGGGCACGCGGCTTTCTTTCCAAACGCTGt > 1:1269862/1‑69 (MQ=255)
cACGACAGTCCTGCGCTGGTTGAGCAGGCGCTTAACGCGGGGGCACGCGGCTTTCTTTCCAAACGCTGt > 1:1918663/1‑69 (MQ=255)
aGTCCGGCGCTGGTTGAGCAGGCGCTTAACGCGGGGGCGCGCGGCTTTCTCTCCAAACGCTGTAGccc < 1:1938976/68‑1 (MQ=255)
aGTCCGGCGCTGGTTGAGCAGGCGCTTAACGCGGGGGCGCGCGGCTTTCTCTCCAAACGCTGTAGccc < 1:1416488/68‑1 (MQ=255)
aGTCCGGCGCTGGTTGAGCAGGCGCTTAACGCGGGGGCGCGCGGCTTTCTCTCCAAACGCTGTAGccc < 1:2877145/68‑1 (MQ=255)
aGTCCGGCGCTGGTTGAGCAGGCGCTTAACGCGGGGGCGCGCGGCTTTCTCTCCAAACGCTGTAGccc < 1:2662021/68‑1 (MQ=255)
aGTCCGGCGCTGGTTGAGCAGGCGCTTAACGCGGGGGCGCGCGGCTTTCTCTCCAAACGCTGTAGccc < 1:1771278/68‑1 (MQ=255)
aGTCCGGCGCTGGTTGAGCAGGCGCTTAACGCGGGGGCGCGCGGCTTTCTCTCCAAACGCTGTAGccc < 1:1777837/68‑1 (MQ=255)
aGTCCGGCGCTGGTTGAGCAGGCGCTTAACGCGGGGGCGCGCGGCTTTCTCTCCAAACGCTGTAGccc < 1:1433850/68‑1 (MQ=255)
aGTCCGGCGCTGGTTGAGCAGGCGCTTAACGCGGGGGCGCGCGGCTTTCTCTCCAAACGCTGTAGccc < 1:2167085/68‑1 (MQ=255)
aGTCCGGCGCTGGTTGAGCAGGCGCTTAACGCGGGGGCGCGCGGCTTTCTCTCCAAACGCTGTAGccc < 1:1944918/68‑1 (MQ=255)
ccTGCGCTGGTTGAGCAGGCGCTTAACGCGGGGGCACGCGGCTTTCTTTCCAAACGCTGTAGCCCGGa > 1:3379186/1‑68 (MQ=255)
ccTGCGCTGGTTGAGCAGGCGCTTAACGCGGGGGCACGCGGCTTTCTTTCCAAACGCTGTAGCCCGGa > 1:3081793/1‑68 (MQ=255)
ggTTGAGCAGGCGCTTAACGCGGGGGCGCGCGGCTTTCTCTCCAAACGCTGTAGCCCGGATGAACTCAt > 1:1063870/1‑69 (MQ=255)
ggTTGAGCAGGCGCTTAACGCGGGGGCGCGCGGCTTTCTCTCCAAACGCTGTAGCCCGGATGAACTCAt > 1:510101/1‑69 (MQ=255)
ggTTGAGCAGGCGCTTAACGCGGGGGCGCGCGGCTTTCTCTCCAAACGCTGTAGCCCGGATGAACTCAt > 1:1948247/1‑69 (MQ=255)
gggggCACGCGGCTTTCTTTCCAAACGCTGTAGCCCGGATGAACTCATTGCTGCGGTGCATACGGTTGc < 1:740299/69‑1 (MQ=255)
tttctttcCAAACGCTGTAGCCCGGATGAACTCATTGCTGCGGTGCATACGGTTGCCACGGGCGGCTg > 1:224441/1‑68 (MQ=255)
ttctttcCAAACGCTGTAGCCCGGATGAACTCATTGCTGCGGTGCATACGGTTTCCACGggcg < 1:2691433/63‑1 (MQ=255)
ttctttcCAAACGCTGTAGCCCGGATGAACTCATTGCTGCGGTGCATACGGTTGCCACGggcg < 1:2041151/63‑1 (MQ=255)
ttctttcCAAACGCTGTAGCCCGGATGAACTCATTGCTGCGGTGCATACGGTTGCCACGggcg < 1:1505528/63‑1 (MQ=255)
ttctttcCAAACGCTGTAGCCCGGATGAACTCATTGCTGCGGTGCATACGGTTGCCACGGGCGGCTGtt < 1:1938806/69‑1 (MQ=255)
ttctttcCAAACGCTGTAGCCCGGATGAACTCATTGCTGCGGTGCATACGGTTGCCACGGGCGGCTGtt < 1:1960439/69‑1 (MQ=255)
ttctttcCAAACGCTGTAGCCCGGATGAACTCATTGCTGCGGTGCATACGGTTGCCACGGGCGGCTGtt < 1:3153254/69‑1 (MQ=255)
ttctttcCAAACGCTGTAGCCCGGATGAACTCATTGCTGCGGTGCATACGGTTGCCACGGGCGGCTGtt < 1:3265920/69‑1 (MQ=255)
ttctttcCAAACGCTGTAGCCCGGATGAACTCATTGCTGCGGTGCATACGGTTGCCACGGGCGGCTGtt > 1:1195177/1‑69 (MQ=255)
ttctttcCAAACGCTGTAGCCCGGATGAACTCATTGCTGCGGTGCATACGGTTGCCACGGGCGGCTGtt < 1:2418888/69‑1 (MQ=255)
ttctttcCAAACGCTGTAGCCCGGATGAACTCATTGCTGCGGTGCATACGGTTGCCACGGGCGGCTGtt < 1:3432070/69‑1 (MQ=255)
ttctttcCAAACGCTGTAGCCCGGATGAACTCATTGCTGCGGTGCATACGGTTGCCACGGGCGGCTGtt < 1:542678/69‑1 (MQ=255)
ttctttcCAAACGCTGTAGCCCGGATGAACTCATTGCTGCGGTGCATACGGTTGCCACGGGCGGCTGtt < 1:769468/69‑1 (MQ=255)
ttctttcCAAACGCTGTAGCCCGGATGAACTCATTGCTGCGGTGCATACGGTTGCCACGGGCGGCTGt > 1:458201/1‑68 (MQ=255)
ctttcCAAACGCTGTAGCCCGGATGAACTCATTGCTGCGGTGCATACGGtt < 1:1233700/51‑1 (MQ=255)
ctttcAAAACGCTGTAGCCCGGATGAACTCATTGCTGCGGTGCATACGGtt < 1:1733285/51‑1 (MQ=255)
tttcCAAACGCTGTAGCCCGGATGAACTCATTGCTGCGGTGCATACGGTTGCCACGGGCGGCTGTTa < 1:1892741/67‑1 (MQ=255)
tttcCAAACGCTGTAGCCCGGATGAACTCATTGCTGCGGTGCATACGGTTGCCACGGGCGGCTGTTa < 1:1246333/67‑1 (MQ=255)
tttcCAAACGCTGTAGCCCGGATGAACTCATTGCTGCGGTGCATACGGTTGCCACGGGCGGCTGTTAt < 1:1080158/68‑1 (MQ=255)
|
CTCCGTTCACGACAGTCCTGCGCTGGTTGAGCAGGCGCTTAACGCGGGGGCACGCGGCTTTCTTTCCAAACGCTGTAGCCCGGATGAACTCATTGCTGCGGTGCATACGGTTGCCACGGGCGGCTGTTAT > minE/2499752‑2499881
|
| 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
