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 |
1,986,052 |
C→T |
62.5% |
E170K (GAA→AAA) |
yggM ← |
conserved hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,986,052 | 0 | C | T | 62.5%
| 22.3
/ 28.7
| 48 | E170K (GAA→AAA) | yggM | conserved hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base C (12/6); new base T (17/13); total (29/19) |
| Fisher's exact test for biased strand distribution p-value = 5.54e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
ATATGCATCCGCTGCTTTCTGCGCCGCCACCATTTGCTTATCAAGCGCTTTCACTTCCTTTTCCAGCGCAGGAATCGAGTTCTTCTGGGTATTCAACGCAGATTCAAGCTGACTAAAGCGATAA > minE/1985990‑1986113
|
atatGCATCCGCTGCTTTCTGCGCCGCCACCATTTGCTTATCAAGCGCTTTTACATCCTTTTTCAgtgc < 1:942448/69‑1 (MQ=255)
atatGCATCCGCTGCTTTCTGCGCCGCCACCATTTGCTTATCAAGCGCTTTTACATCCTTTTTCAgtgc < 1:1720083/69‑1 (MQ=255)
atatGCATCCGCTGCTTTCTGCGCCGCCACCATTTGCTTATCAAGCGCTTTTACATCCTTTTTCAgtgc < 1:1830792/69‑1 (MQ=255)
atatGCATCCGCTGCTTTCTGCGCCGCCACCATTTGCTTATCAAGCGCTTTTACATCCTTTTTCAgtgc < 1:2173780/69‑1 (MQ=255)
atatGCATCCGCTGCTTTCTGCGCCGCCACCATTTGCTTATCAAGCGCTTTTACATCCTTTTTCAgtgc < 1:2255670/69‑1 (MQ=255)
atatGCATCCGCTGCTTTCTGCGCCGCCACCATTTGCTTATCAAGCGCTTTTACATCCTTTTTCAgtgc < 1:1460928/69‑1 (MQ=255)
atatGCATCCGCTGCTTTCTGCGCCGCCACCATTTGCTTATCAAGCGCTTTTACATCCTTTTTCAgtgc < 1:2670254/69‑1 (MQ=255)
atatGCATCCGCTGCTTTCTGCGCCGCCACCATTTGCTTATCAAGCGCTTTTACATCCTTTTTCAgtgc < 1:2843065/69‑1 (MQ=255)
atatGCATCCGCTGCTTTCTGCGCCGCCACCATTTGCTTATCAAGCGCTTTTACATCCTTTTTCAgtgc < 1:2887805/69‑1 (MQ=255)
atatGCATCCGCTGCTTTCTGCGCCGCCACCATTTGCTTATCAAGCGCTTTTACATCCTTTTTCAgtgc < 1:1252575/69‑1 (MQ=255)
atatGCATCCGCTGCTTTCTGCGCCGCCACCATTTGCTTATCAAGCGCTTTTACATCCTTTTTCAgtgc < 1:1191917/69‑1 (MQ=255)
atatGCATCCGCTGCTTTCTGCGCCGCCACCATTTGCTTATCAAGCGCTTTTACATCCTTTTTCAgtgc < 1:1104174/69‑1 (MQ=255)
tGCATCCGCTGCTTTCTGCGCCGCCACCATTTGCTTATCAAGCGCTTTCACTTCCTTTTCCAGCGCAgg > 1:2412579/1‑69 (MQ=255)
tGCATCCGCTGCTTTCTGCGCCGCCACCATTTGCTTATCAAGCGCTTTCACTTCCTTTTCCAGCGCAgg > 1:3139981/1‑69 (MQ=255)
tGCATCCGCTGCTTTCTGCGCCGCCACCATTTGCTTATCAAGCGCTTTCACTTCCTTTTCCAGCGCAgg > 1:2245285/1‑69 (MQ=255)
tGCATCCGCTGCTTTCTGCGCCGCCACCATTTGCTTATCAAGCGCTTTCACTTCCTTTTCCAGCGCAgg > 1:599758/1‑69 (MQ=255)
tGCATCCGCTGCTTTCTGCGCCGCCACCATTTGCTTATCAAGCGCTTTCACTTCCTTTTCCAGCGCAgg > 1:974991/1‑69 (MQ=255)
tGCATCCGCTGCTTTCTGCGCCGCCACCATTTGCTTATCAAGCGCTTTCACTTCCTTTTCCAGCGCAgg > 1:1798388/1‑69 (MQ=255)
ctgctTTCTGCGCCGCCACCATTTGCTTATCAAGCGCTTTCACTTCCTTTTCCAGCGCAGGAATCGAg < 1:2915719/68‑1 (MQ=255)
gctTTCTGGGCCGCCACCATTTGCTTATCAAGCGCTTTTACATCCTTTTTCAGTGCAGGAATCGAGtta > 1:780909/1‑68 (MQ=255)
gctTTCTGCGCCGCCACCATTTGCTTATCAAGCGCTTTTACATCCTTTTTCAGTGCAGGAATCGAGtta > 1:774779/1‑68 (MQ=255)
gctTTCTGCGCCGCCACCATTTGCTTATCAAGCGCTTTTACATCCTTTTTCAGTGCAGGAATCGAGtta > 1:2372509/1‑68 (MQ=255)
gctTTCTGCGCCGCCACCATTTGCTTATCAAGCGCTTTTACATCCTTTTTCAGTGCAGGAATCGAGtta > 1:844404/1‑68 (MQ=255)
gctTTCTGCGCCGCCACCATTTGCTTATCAAGCGCTTTTACATCCTTTTTCAGTGCAGGAATCGAGtta > 1:2182394/1‑68 (MQ=255)
gctTTCTGCGCCGCCACCATTTGCTTATCAAGCGCTTTTACATCCTTTTTCAGTGCAGGAATCGAGtta > 1:1087351/1‑68 (MQ=255)
gctTTCTGCGCCGCCACCATTTGCTTATCAAGCGCTTTTACATCCTTTTTCAGTGCAGGAATCGAGtta > 1:1744781/1‑68 (MQ=255)
gctTTCTGCGCCGCCACCATTTGCTTATCAAGCGCTTTTACATCCTTTTTCAGTGAAGGAATCGAGtt > 1:1512934/1‑68 (MQ=255)
ttCTGCGCCGCCACCATTTGCTTATCAAGCGCTTTCACTTCCTTTTCCAGCGCAGGAATCGAGttct < 1:3365149/67‑1 (MQ=255)
ttCTGCGCCGCCACCATTTGCTTATCAAGCGCTTTCACTTCCTTTTCCAGCGCAGGAATCGAGttct < 1:3300885/67‑1 (MQ=255)
ttCTGCGCCGCCACCATTTGCTTATCAAGCGCTTTCACTTCCTTTTCCAGCGCAGGAATCGAGttct < 1:1425576/67‑1 (MQ=255)
aTTTGCTTATCAAGCGCTTTCACTTCCTTTTCCAGCGCAGGAATCGAGTTCTTCTGGGTATTCaa > 1:1742798/1‑65 (MQ=255)
tttGCTTATCAAGCGCTTTTACATCCTTTTTCAgtgc < 1:599951/37‑1 (MQ=25)
gCTTATCAAGCGCTTTTACATCCTTTTTCAGTGCAGGAATCGAGTTATTCTGGTTATTCAACGCAGac > 1:1064625/1‑67 (MQ=255)
gCTTATCAAGCGCTTTTACATCCTTTTTCAGTGCAGGAATCGAGTTATTCTGGTTATTCAACGCAGac > 1:1179797/1‑67 (MQ=255)
gCTTATCAAGCGCTTTTACATCCTTTTTCAGTGCAGGAATCGAGTTATTCTGGTTATTCAACGCAGac > 1:3087762/1‑67 (MQ=255)
gCTTATCAAGCGCTTTTACATCCTTTTTCAGTGCAGGAATCGAGTTATTCTGGTTATTCAACGCAGac > 1:1377346/1‑67 (MQ=255)
gCTTATCAAGCGCTTTTACATCCTTTTTCAGTGCAGGAATCGAGTTATTCTGGTTATTCAACGCAGac > 1:2635548/1‑67 (MQ=255)
gCTTATCAAGCGCTTTTACATCCTTTTTCAGTGCAGGAATCGAGTTATTCTGGTTATTCAACGCAGac > 1:2419848/1‑67 (MQ=255)
gCTTATCAAGCGCTTTTACATCCTTTTTCAGTGCAGGAATCGAGTTATTCTGGTTATTCAACGCAGac > 1:2299802/1‑67 (MQ=255)
gCTTATCAAGCGCTTTTACATCCTTTTTCAGTGCAGGAATCGAGTTATTCTGGTTATTCAACGCAGac > 1:1576701/1‑67 (MQ=255)
gCTTATCAAGCGCTTTTACATCCTTTTTCAGTGCAGGAATCGAGTTATTCTGGTTATTCAACGCAGac > 1:167512/1‑67 (MQ=255)
aTCAAGCGCTTTCACTTCCTTTTCCAGCGCAGGAATCGAGTTCTTCTGGGTATTCAACGCAGATTCAAg > 1:1313111/1‑69 (MQ=255)
aTCAAGCGCTTTCACTTCCTTTTCCAGCGCAGGAATCGAGTTCTTCTGGGTATTCAACGCAGATTCAAg > 1:124685/1‑69 (MQ=255)
gcTTTCACTTCCTTTTCCAGCGCAGGAATCGAGttct < 1:1458607/37‑1 (MQ=255)
ttCCTTTTCCAGCGCAGGAATCGAGTTCTTCTGGGTATTCAACGCAGATTCAAGCTGACTAAAGCGAt < 1:2376246/68‑1 (MQ=255)
ccTTTTCCAGCGCAGGAATCGAGTTCTTCTGGGTATTCAACGCAGATTCAAGCTGAGTAAAGCGATaa > 1:381945/1‑68 (MQ=255)
ccTTTTCCAGCGCAGGAATCGAGTTCTTCTGGGTATTCAACGCAGATTCAAGCTGACTAAAGCGATaa > 1:227032/1‑68 (MQ=255)
ccTTTTCCAGCGCAGGAATCGAGTTCTTCTGGGTATTCAAAGCAGATTCAAGCTGACTAAAGAGATaa > 1:1517979/1‑68 (MQ=255)
|
ATATGCATCCGCTGCTTTCTGCGCCGCCACCATTTGCTTATCAAGCGCTTTCACTTCCTTTTCCAGCGCAGGAATCGAGTTCTTCTGGGTATTCAACGCAGATTCAAGCTGACTAAAGCGATAA > minE/1985990‑1986113
|
| 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
