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 |
1,114,246 |
C→T |
35.0% |
V186V (GTG→GTA) |
pps ← |
phosphoenolpyruvate synthase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,114,246 | 0 | C | T | 35.0%
| 55.7
/ 42.1
| 77 | V186V (GTG→GTA) | pps | phosphoenolpyruvate synthase |
| Reads supporting (aligned to +/- strand): ref base C (20/30); new base T (17/10); total (37/40) |
| Fisher's exact test for biased strand distribution p-value = 6.13e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.83e-01 |
CATCACGCCAGATGATGCGAGGTCAGAGCGCACCATCCGTTGAACACCGGCGGAGAGCGCCACACCACGGTGATCGTAACCCTGGTGCACACGATAAGAGATGGCGCGATCGTTAAACAGAGAAGCAAA > minE/1114186‑1114314
|
cATCACGCCAGATGATGCGAGGTCAGAGCGCACCATCCGTTGAACACCGGCGGAGAGCGCCACACCACg > 1:1205619/1‑69 (MQ=255)
cATCACGCCAGATGATGCGAGGTCAGAGCGCACCATCCGTTGAACACCGGCGGAGAGCGCCACACCACg > 1:3396280/1‑69 (MQ=255)
cATCACGCCAGATGATGCGAGGTCAGAGCGCACCATCCGTTGAACACCGGCGGAGAGCGCCACACCACg > 1:1288593/1‑69 (MQ=255)
cATCACGCCAGATGATGCGAGGTCAGAGCGCACCATCCGTTGAACACCGGCGGAGAGCGCCACACCACg > 1:792543/1‑69 (MQ=255)
cATCACGCCAGATGATGCGAGGTCAGAGCGCACCATCCGTTGAACACCGGCGGAGAGCGCCACACCACg > 1:2100285/1‑69 (MQ=255)
aTCACGCCAGATGATGCGAGGTCAGAGCGCACCATCCGTTGAACACCGGCGGAGAGCGCCACACCACg > 1:2915385/1‑68 (MQ=255)
aTCACGCCAGATGATGCGAGGTCAGAGCGCACCATCCGTTGAACACCGGCGGAGAGCGCCACACCACg > 1:2022901/1‑68 (MQ=255)
aTCACGCCAGATGATGCGAGGTCAGAGCGCACCATCCGTTGAACACCGGCGGAGAGCGCCACACCACg > 1:329605/1‑68 (MQ=255)
aTCACGCCAGATGATGCGAGGTCAGAGCGCACCATCCGTTGAACACCGGCGGAGAGCGCCACACCACg > 1:927036/1‑68 (MQ=255)
cACGCCAGATGATGCGAGGTCAGAGCGCACCATCCGTTGAACACCGGCGGAGAGCGCCGCACCACGGTg < 1:1240062/69‑1 (MQ=255)
cACGCCAGATGATGCGAGGTCAGAGCGCACCATCCGTTGAACACCGGCGGAGAGCGCCACACCACGGTg < 1:337613/69‑1 (MQ=255)
cACGCCAGATGATGCGAGGTCAGAGCGCACCATCCGTTGAACACCGGCGGAGAGCGCCACACCACGGTg < 1:64058/69‑1 (MQ=255)
cACGCCAGATGATGCGAGGTCAGAGCGCACCATCCGTTGAACACCGGCGGAGAGCGCCACACCACGGTg < 1:287491/69‑1 (MQ=255)
cACGCCAGATGATGCGAGGTCAGAGCGCACCATCCGTTGAACACCGGCGGAGAGCGCCACACCACGGTg < 1:2421077/69‑1 (MQ=255)
cACGCCAGATGATGCGAGGTCAGAGCGCACCATCCGTTGAACACCGGCGGAGAGCGCCACACCACGGTg < 1:2198786/69‑1 (MQ=255)
cACGCCAGATGATGCGAGGTCAGAGCGCACCATCCGTTGAACACCGGCGGAGAGCGCCACACCACGGTg < 1:1822022/69‑1 (MQ=255)
cACGCCAGATGATGCGAGGTCAGAGCGCACCATCCGTTGAACACCGGCGGAGAGCGCCACACCACGGTg < 1:1513265/69‑1 (MQ=255)
cACGCCAGATGATGCGAGGTCAGAGCGCACCATCCGTTGAACACCGGCGGAGAGCGCCACACCACGGTg < 1:1181794/69‑1 (MQ=255)
cACGCCAGAAGATGCGAGGTCGGAGCGCACCATCCGCTGAACACCGGCGGAGAGCGCTACGCCACGATg < 1:423206/69‑1 (MQ=255)
cACGCCAGAAGATGCGAGGTCGGAGCGCACCATCCGCTGAACACCGGCGGAGAGCGCTACGCCACGATg < 1:455576/69‑1 (MQ=255)
cACGCCAGAAGATGCGAGGTCGGAGCGCACCATCCGCTGAACACCGGCGGAGAGCGCTACGCCACGATg < 1:3247734/69‑1 (MQ=255)
cACGCCAGAAGATGCGAGGTCGGAGCGCACCATCCGCTGAACACCGGCGGAGAGCGCTACGCCACGATg < 1:3323777/69‑1 (MQ=255)
cACGCCAGAAGATGCGAGGTCGGAGCGCACCATCCGCTGAACACCGGCGGAGAGCGCTACGCCACGATg < 1:3015331/69‑1 (MQ=255)
cACGCCAGAAGATGCGAGGTCGGAGCGCACCATCCGCTGAACACCGGCGGAGAGCGCTACGCCACGATg < 1:1552701/69‑1 (MQ=255)
cACGCCAGAAGATGCGAGGTCGGAGCGCACCATCCGCTGAACACCGGCGGAGAGCGCTACGCCACGATg < 1:3134574/69‑1 (MQ=255)
cACGCCAGAAGATGCGAGGTCGGAGCGCACCATCCGCTGAACACCGGCGGAGAGCGCTACGCCACGATg < 1:975178/69‑1 (MQ=255)
cACGCCAGAAGATGCGAGGTCGGAGCGCACCATCCGCTGAACACCGGCGGAGAGCGCTACGCCACGATg < 1:987955/69‑1 (MQ=255)
cACGCCAGAAGATGCGAGGTCGGAGCGCACCATCCGCTGAACACCGGCGGAGAGCGCTACGCCACGATg < 1:2276939/69‑1 (MQ=255)
aCGCCAGATGATGCGATGTCAGAGCGCACCATCCGTTGAACACCGGCGGAGAGCGCCACACCACGGTg < 1:825291/68‑1 (MQ=255)
aCGCCAGATGATGCGAGGTCAGAGCGCACCATCCGTTGAACACCGGCGGAGAGCGCCACACCACGGTg < 1:2871786/68‑1 (MQ=255)
tgatgCGAGGTCAGAGCGCACCATCCGTTGAACACCGGCGGAGAGCGCCACACCACGGTGATCGTa < 1:81802/66‑1 (MQ=255)
tgatgCGAGGTCAGAGCGCACCATCCGTTGAACACCGGCGGAGAGCGCCACACCACGGTGATCGTa < 1:779707/66‑1 (MQ=255)
tgatgCGAGGTCAGAGCGCACCATCCGTTGAACACCGGCGGAGAGCGCCACACCACGGTGATCGTa < 1:1772809/66‑1 (MQ=255)
tgatgCGAGGTCAGAGCGCACCATCCGTTGAACACCGGCGGAGAGCGCCACACCACGGTGATCGTa < 1:3339457/66‑1 (MQ=255)
gatgCGAGGTCAGAGCGCACCATCCGTTGAACACCGGCGGAGAGCGCCACACCACGGTGATCGTa < 1:45211/65‑1 (MQ=255)
ggagCGCACCATCCGCTGAACACCGGCGGAGAGCGCTACGCCACGATGGTCGTAACCCTGGTGCacac > 1:405293/2‑68 (MQ=255)
ggagCGCACCATCCGCTGAACACCGGCGGAGAGCGCTACGCCACGATGGTCGTAACCCTGGTGCacac > 1:2274438/2‑68 (MQ=255)
ggagCGCACCATCCGCTGAACACCGGCGGAGAGCGCTACGCCACGATGGTCGTAACCCTGGTGCacac > 1:3324753/2‑68 (MQ=255)
ggagCGCACCATCCGCTGAACACCGGCGGAGAGCGCTACGCCACGATGGTCGTAACCCTGGTGCacac > 1:3044785/2‑68 (MQ=255)
ggagCGCACCATCCGCTGAACACCGGCGGAGAGCGCTACGCCACGATGGTCGTAACCCTGGTGCacac > 1:663800/2‑68 (MQ=255)
ggagCGCACCATCCGCTGAACACCGGCGGAGAGCGCTACGCCACGATGGTCGTAACCCTGGTGCacac > 1:2645514/2‑68 (MQ=255)
ggagCGCACCATCCGCTGAACACCGGCGGAGAGCGCTACGCCACGATGGTCGTAACCCTGGTGCacac > 1:739486/2‑68 (MQ=255)
ggagCGCACCATCCGCTGAACACCGGCGGAGAGCGCTACGCCACGATGGTCGTAACCCTGGTGCacac > 1:2162066/2‑68 (MQ=255)
ggagCGCACCATCCGCTGAACACCGGCGGAGAGCGCTACGCCACGATGGTCGTAACCCTGGTGCacac > 1:1998210/2‑68 (MQ=255)
ggagCGCACCATCCGCTGAACACCGGCGGAGAGCGCTACGCCACGATGGTCGTAACCCTGGTGCacac > 1:1818891/2‑68 (MQ=255)
ggagCGCACCATCCGCTGAACACCGGCGGAGAGCGCTACGCCACGATGGTCGTAACCCTGGTGCacac > 1:1677959/2‑68 (MQ=255)
ggagCGCACCATCCGCTGAACACCGGCGGAGAGCGCTACGCCACGATGGTCGTAACCCTGGTGCacac > 1:84192/2‑68 (MQ=255)
ggagCGCACCATCCGCTGAACACCGGCGGAGAGCGCTACGCCACGATGGTCGTAACCCTGGTGCacac > 1:1621203/2‑68 (MQ=255)
ggagCGCACCATCCGCTGAACACCGGCGGAGAGCGCTACGCCACGATGGTCGTAACCCTGGTGCacac > 1:963935/2‑68 (MQ=255)
ggagCGCACCATCCGCTGAACACCGGCGGAGAGCGCTACGCCACGATGGTCGTAACCCTGGTGCacac > 1:1420057/2‑68 (MQ=255)
ggagCGCACCATCCGCTGAACACCGGCGGAGAGCGCTACGCCACGATGGTCGTAACCCTGGTGCacac > 1:1240889/2‑68 (MQ=255)
ggagCGCACCATCCGCTGAACACCGGCGGAGAGCGCTACGCCACGATGGTCGTAACCCTGGTGCacac > 1:1163883/2‑68 (MQ=255)
cACCATCCGTTGAACACCGGCGGAGAGCGCCACACCACGGTGATCGTAACCCTGGTGCACACGATAaga < 1:465043/69‑1 (MQ=255)
cACCATCCGTTGAACACCGGCGGAGAGCGCCACACCACGGTGATCGTAACCCTGGTGCACACGATAaga < 1:99443/69‑1 (MQ=255)
cACCATCCGTTGAACACCGGCGGAGAGCGCCACACCACGGTGATCGTAACCCTGGTGCACACGATAaga < 1:1087571/69‑1 (MQ=255)
cACCATCCGTTGAACACCGGCGGAGAGCGCCACACCACGGTGATCGTAACCCTGGTGCACACGATAaga < 1:3339911/69‑1 (MQ=255)
cACCATCCGTTGAACACCGGCGGAGAGCGCCACACCACGGTGATCGTAACCCTGGTGCACACGATAaga < 1:1406038/69‑1 (MQ=255)
cACCATCCGTTGAACACCGGCGGAGAGCGCCACACCACGGTGATCGTAACCCTGGTGCACACGATAaga < 1:3311775/69‑1 (MQ=255)
cACCATCCGTTGAACACCGGCGGAGAGCGCCACACCACGGTGATCGTAACCCTGGTGCACACGATAaga < 1:3264014/69‑1 (MQ=255)
cACCATCCGTTGAACACCGGCGGAGAGCGCCACACCACGGTGATCGTAACCCTGGTGCACACGATAaga < 1:1576788/69‑1 (MQ=255)
cACCATCCGTTGAACACCGGCGGAGAGCGCCACACCACGGTGATCGTAACCCTGGTGCACACGATAaga < 1:3004421/69‑1 (MQ=255)
cACCATCCGTTGAACACCGGCGGAGAGCGCCACACCACGGTGATCGTAACCCTGGTGCACACGATAaga < 1:1649152/69‑1 (MQ=255)
cACCATCCGTTGAACACCGGCGGAGAGCGCCACACCACGGTGATCGTAACCCTGGTGCACACGATAaga < 1:220665/69‑1 (MQ=255)
cACCATCCGTTGAACACCGGCGGAGAGCGCCACACCACGGTGATCGTAACCCTGGTGCACACGATAaga < 1:2396964/69‑1 (MQ=255)
cACCATCCGTTGAACACCGGCGGAGAGCGCCACACCACGGTGATCGTAACCCTGGTGCACACGATAaga < 1:2588815/69‑1 (MQ=255)
ccATCCGTTGAACACGGGCGGAGAGCGCCACACCACGGTGATCGTa < 1:2604412/46‑1 (MQ=255)
cGTTGAACACCGGCGGAGAGCGCCACACCACGGTGATCGTAACCCTGGTGCACACGATAAGAGATGgc > 1:3356651/1‑68 (MQ=255)
cGTTGAACACCGGCGGAGAGCGCCACACCACGGTGATCGTAACCCTGGTGCACACGATAAGAGATGgc > 1:50272/1‑68 (MQ=255)
cGTTGAACACCGGCGGAGAGCGCCACACCACGGTGATCGTAACCCTGGTGCACACGATAAGAGATGgc > 1:2963740/1‑68 (MQ=255)
cGTTGAACACCGGCGGAGAGCGCCACACCACGGTGATCGTAACCCTGGTGCACACGATAAGAGATGgc > 1:1634935/1‑68 (MQ=255)
cGTTGAACACCGGCGGAGAGCGCCACACCACGGTGATCGTAACCCTGGTGCACACGATAAGAGATGgc > 1:3220545/1‑68 (MQ=255)
cGTTGAACACCGGCGGAGAGCGCCACACCACGGTGATCGTAACCCTGGTGCACACGATAAGAGATGgc > 1:1460464/1‑68 (MQ=255)
cGTTGAACACCGGCGGAGAGCGCCACACCACGGTGATCGTAACCCTGGTGCACACGATAAGAGATGgc > 1:344422/1‑68 (MQ=255)
cGTTGAACACCGGCGGAGAGCGCCACACCACGGTGATCGTAACCCTGGTGCACACGATAAGAGATGgc > 1:1364511/1‑68 (MQ=255)
ccGGCGGAGAGCGCCACACCACGGTGATCGTAACCCTGGTGCACACGATAAGAGATGGCGCGATCGTTa > 1:288655/1‑69 (MQ=255)
ccGGCGGAGAGCGCCACACCACGGTGATCGTAACCCTGGTGCACACGATAAGAGATGGCGCGATCGTTa > 1:2438896/1‑69 (MQ=255)
ggcggAGAGCGCCACACCACGGTGATCGTAACCCTGGTGCACACGATAAGAGATGGCGCGATCGTTa > 1:2953262/1‑67 (MQ=255)
cacaCCACGGTGATCGTAACCCTGGTGCACACGATAAGAGATGGCGCGATCGTTAAACAGAGAAGCaaa < 1:884200/69‑1 (MQ=255)
|
CATCACGCCAGATGATGCGAGGTCAGAGCGCACCATCCGTTGAACACCGGCGGAGAGCGCCACACCACGGTGATCGTAACCCTGGTGCACACGATAAGAGATGGCGCGATCGTTAAACAGAGAAGCAAA > minE/1114186‑1114314
|
| 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
