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 |
1,889,568 |
C→T |
45.4% |
A221T (GCA→ACA) |
gudX ← |
predicted glucarate dehydratase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,889,568 | 0 | C | T | 45.4%
| 11.6
/ 51.8
| 66 | A221T (GCA→ACA) | gudX | predicted glucarate dehydratase |
| Reads supporting (aligned to +/- strand): ref base C (17/19); new base T (3/27); total (20/46) |
| Fisher's exact test for biased strand distribution p-value = 1.20e-03 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.20e-01 |
CAAGCAGCCATGCACCGTTGGGATCAACGGTAATCCGCGCATCCGGGAAGCGTTTCTTCAATGCACGAACAGTGTCGATTTCTTGCTCGCCAGGTAACACGCCGCCCTTAAGTTTGAAAT > minE/1889505‑1889624
|
caAGCAGCCAGGCACCATTGGGATCAACGGTAATCCGCGCATCAGGGAAGCGTTTCTTCAATGTACg > 1:579991/1‑67 (MQ=255)
caAGCAGCCAGGCACCATTGGGATCAACGGTAATCCGCGCATCAGGGAAGCGTTTCTTCAATGTACg > 1:429695/1‑67 (MQ=255)
caAGCAGCCAGGCACCATTGGGATCAACGGTAATCCGCGCATCAGGGAAGCGTTTCTTCAATGTACg > 1:1791840/1‑67 (MQ=255)
cATGCACCGTTGGGATCAACGGTAATCCGCGCATCCGGGAAGCGTTTCTTCAATGCACGAACAGTGTCg > 1:3260298/1‑69 (MQ=255)
cATGCACCGTTGGGATCAACGGTAATCCGCGCATCCGGGAAGCGTTTCTTCAATGCACGAACAGTGTCg > 1:597277/1‑69 (MQ=255)
cATGCACCGTTGGGATCAACGGTAATCCGCGCATCCGGGAAGCGTTTCTTCAATGCACGAACAGTGTCg > 1:1194342/1‑69 (MQ=255)
caacGTTGGGATCAACGGTAATCCGCGCATCCGGGAAGCGTTTCTTCAATGCACGAACAGTGTCGAtt > 1:3184319/4‑68 (MQ=255)
cACCGTTGGGATCAACGGTAATCCGCGCATCCGGGAAGCGTTTCTTCAATGCACGAACAGTGTCGAttt > 1:2179592/1‑69 (MQ=255)
cACCGTTGGGATCAACGGTAATCCGCGCATCCGGGAAGCGTTTCTTCAATGCACGAACAGTGTCGAtt > 1:2308972/1‑68 (MQ=255)
cACCGTTGGGATCAACGGTAATCCGCGCATCCGGGAAGCGTTTCTTCAATGCACGAACAGTGTCGAtt > 1:155519/1‑68 (MQ=255)
cACCGTTGGGATCAACGGTAATCCGCGCATCCGGGAAGCGTTTCTTCAATGCACGAACAGTGTCGAtt > 1:1529273/1‑68 (MQ=255)
cACCGTTGGGATCAACGGTAATCCGCGCATCCGGGAAGCGTTTCTTCAATGCACGAACAGTGTCGAtt > 1:342442/1‑68 (MQ=255)
cACCGTTGGGATCAACGGTAATCCGCGCATCCGGGAAGCGTTTCTTCAATGCACGAACAGTGTCGAtt > 1:1093408/1‑68 (MQ=255)
gTTGGGATCAACGGTAATCCGCGCATCCGGGAAGCGTTTCTTCAATGCACGAACAGTGTCGATTTCTTg < 1:1495338/69‑1 (MQ=255)
gTTGGGATCAACGGTAATCCGCGCATCCGGGAAGCGTTTCTTCAATGCACGAACAGTGTCGATTTCTTg < 1:877464/69‑1 (MQ=255)
gTTGGGATCAACGGTAATCCGCGCATCCGGGAAGCGTTTCTTCAATGCACGAACAGTGTCGATTTCTTg < 1:3162330/69‑1 (MQ=255)
gTTGGGATCAACGGTAATCCGCGCATCCGGGAAGCGTTTCTTCAATGCACGAACAGTGTCGATTTCTTg < 1:3199968/69‑1 (MQ=255)
gTTGGGATCAACGGTAATCCGCGCATCCGGGAAGCGTTTCTTCAATGCACGAACAGTGTCGATTTCTTg < 1:3240810/69‑1 (MQ=255)
gTTGGGATCAACGGTAATCCGCGCATCCGGGAAGCGTTTCTTCAATGCACGAACAGTGTCGATTTCTTg < 1:842061/69‑1 (MQ=255)
gTTGGGATCAACGGTAATCCGCGCATCCGGGAAGCGTTTCTTCAATGCACGAACAGTGTCGATTTCTTg < 1:2289798/69‑1 (MQ=255)
gTTGGGATCAACGGTAATCCGCGCATCCGGGAAGCGTTTCTTCAATGCACGAACAGTGTCGATTTCTTg < 1:1181048/69‑1 (MQ=255)
gTTGGGATCAACGGTAATCCGCGCATCCGGGAAGCGTTTCTTCAATGCACGAACAGTGCCGATTTCTTg < 1:1124002/69‑1 (MQ=255)
ttGGGATCAACGGTAATCCGCGCATCCGGGAAGCGTTTCTTCAATGCACGAACAGTGTCGATTTCTTg < 1:2444231/68‑1 (MQ=255)
aaCGGTAATCCGCGCATCCGGGAAGCGTTTCTTCAATGCACGAACAGTGTCGATTTCTTGCTCGc > 1:2179026/1‑65 (MQ=255)
ggTAATCCGCGCATCCGGGAAGCGTTTCTTCAATGCACGAACAGTGTCGATTTCTTGCTCGCCAGGTaa < 1:1528404/69‑1 (MQ=255)
aaTCCGCGCATCCGGGAAGCGTTTCTTCAATGCACGAACAGTGTCGATTTCTTGCTCGCCAGGTAacac > 1:3083030/1‑69 (MQ=255)
aaTCCGCGCATCCGGGAAGCGTTTCTTCAATGCACGAACAGTGTCGATTTCTTGCTCGCCAGGTAacac > 1:1838265/1‑69 (MQ=255)
aaTCCGCGCATCCGGGAAGCGTTTCTTCAATGCACGAACAGTGTCGATTTCTTGCTCGCCAGGTAacac > 1:2218321/1‑69 (MQ=255)
cgcgCATCCGGGAAGCGTTTCTTCAATGCACGAACAGTGTCGATTTCTTGCTCGCCAGGTAACAcgccg > 1:1945194/1‑69 (MQ=255)
cgcgCATCCGGGAAGCGTTTCTTCAATGCACGAACAGTGTCGATTTCTTGCTCGCCAGGTAACAcgccg > 1:2027901/1‑69 (MQ=255)
cgcgCATCCGGGAAGCGTTTCTTCAATGCACGAACAGTGTCGATTTCTTGCTCGCCAGGTAACAcgcc > 1:521059/1‑68 (MQ=255)
cGGGAAGCGTTTCTTCAATGCACGAACAGTGTCGATTTCTTGCTCGCCAGGTAACACGCCGCCCTTAAg < 1:3365871/69‑1 (MQ=255)
cGGGAAGCGTTTCTTCAATGCACGAACAGTGTCGATTTCTTGCTCGCCAGGTAACACGCCGCCCTTAAg < 1:1516/69‑1 (MQ=255)
aGCGTTTCTTCAATGTACGGACAGTGTCGATTTCTTGCTCGCCAGGTAACACGCCACCCTTAAGTTTGa < 1:546929/69‑1 (MQ=255)
aGCGTTTCTTCAATGTACGGACAGTGTCGATTTCTTGCTCGCCAGGTAACACGCCACCCTTAAGTTTGa < 1:1014941/69‑1 (MQ=255)
aGCGTTTCTTCAATGTACGGACAGTGTCGATTTCTTGCTCGCCAGGTAACACGCCACCCTTAAGTTTGa < 1:1265817/69‑1 (MQ=255)
aGCGTTTCTTCAATGTACGGACAGTGTCGATTTCTTGCTCGCCAGGTAACACGCCACCCTTAAGTTTGa < 1:988925/69‑1 (MQ=255)
aGCGTTTCTTCAATGTACGGACAGTGTCGATTTCTTGCTCGCCAGGTAACACGCCACCCTTAAGTTTGa < 1:1690191/69‑1 (MQ=255)
aGCGTTTCTTCAATGTACGGACAGTGTCGATTTCTTGCTCGCCAGGTAACACGCCACCCTTAAGTTTGa < 1:2962003/69‑1 (MQ=255)
aGCGTTTCTTCAATGTACGGACAGTGTCGATTTCTTGCTCGCCAGGTAACACGCCACCCTTAAGTTTGa < 1:3426864/69‑1 (MQ=255)
aGCGTTTCTTCAATGTACGGACAGTGTCGATTTCTTGCTCGCCAGGTAACACGCCACCCTTAAGTTTGa < 1:2746502/69‑1 (MQ=255)
aGCGTTTCTTCAATGTACGGACAGTGTCGATTTCTTGCTCGCCAGGTAACACGCCACCCTTAAGTTTGa < 1:1851409/69‑1 (MQ=255)
aGCGTTTCTTCAATGTACGGACAGTGTCGATTTCTTGCTCGCCAGGTAACACGCCACCCTTAAGTTTGa < 1:2680508/69‑1 (MQ=255)
gCGTTTCTTCAATGTACGGACAGTGTCGATTTCTTGCTCGCCAGGTAACACGCCACCCTTAAGTTTGaa < 1:867925/69‑1 (MQ=255)
gCGTTTCTTCAATGTACGGACAGTGTCGATTTCTTGCTCGCCAGGTAACACGCCACCCTTAAGTTTGaa < 1:455526/69‑1 (MQ=255)
gCGTTTCTTCAATGTACGGACAGTGTCGATTTCTTGCTCGCCAGGTAACACGCCACCCTTAAGTTTGaa < 1:1002739/69‑1 (MQ=255)
gCGTTTCTTCAATGTACGGACAGTGTCGATTTCTTGCTCGCCAGGTAACACGCCACCCTTAAGTTTGaa < 1:75562/69‑1 (MQ=255)
gCGTTTCTTCAATGTACGGACAGTGTCGATTTCTTGCTCGCCAGGTAACACGCCACCCTTAAGTTTGaa < 1:559868/69‑1 (MQ=255)
gCGTTTCTTCAATGTACGGACAGTGTCGATTTCTTGCTCGCCAGGTAACACGCCACCCTTAAGTTTGaa < 1:992880/69‑1 (MQ=255)
gCGTTTCTTCAATGTACGGACAGTGTCGATTTCTTGCTCGCCAGGTAACACGCCACCCTTAAGTTTGaa < 1:1346495/69‑1 (MQ=255)
gCGTTTCTTCAATGTACGGACAGTGTCGATTTCTTGCTCGCCAGGTAACACGCCACCCTTAAGTTTGaa < 1:1496985/69‑1 (MQ=255)
gCGTTTCTTCAATGTACGGACAGTGTCGATTTCTTGCTCGCCAGGTAACACGCCACCCTTAAGTTTGaa < 1:2626143/69‑1 (MQ=255)
gCGTTTCTTCAATGTACGGACAGTGTCGATTTCTTGCTCGCCAGGTAACACGCCACCCTTAAGTTTGaa < 1:2476771/69‑1 (MQ=255)
gCGTTTCTTCAATGTACGGACAGTGTCGATTTCTTGCTCGCCAGGTAACACGCCACCCTTAAGTTTGaa < 1:2274283/69‑1 (MQ=255)
gCGTTTCTTCAATGTACGGACAGTGTCGATTTCTTGCTCGCCAGGTAACACGCCACCCTTAAGTTTGaa < 1:1590900/69‑1 (MQ=255)
gCGTTTCTTCAATGTACGGACAGTGTCGATTTCTTGCTCGCCAGGTAACACGCCACCCTTAAGTTTGaa < 1:167651/69‑1 (MQ=255)
gCGTTTCTTCAATGTACGGACAGTGTCGATTTCTTGCTCGCCAGGTAACACGCCACCCTTAAGTTTGaa < 1:1912205/69‑1 (MQ=255)
gCGTTTCTTCAATGTACGGACAGTGTCGATTTCTTGCTCGCCAGGTAACACGCCACCCTTAAGTTTGa < 1:2880919/68‑1 (MQ=255)
cGTTTCTTCAATGTACGGACAGTGTCGATTTCTTGCTCGCCAGGTAACACGCCACCCTTAAGTTTGaa < 1:3383804/68‑1 (MQ=255)
gTTTCTTCAATGCACGAACAGTGTCGATTTCTTGCTCGCCAGGTAACACGCCGCCCTTAAGTTTGAAAt < 1:2254041/69‑1 (MQ=255)
gTTTCTTCAATGCACGAACAGTGTCGATTTCTTGCTCGCCAGGTAACACGCCGCCCTTAAGTTTGAAAt < 1:96105/69‑1 (MQ=255)
gTTTCTTCAATGCACGAACAGTGTCGATTTCTTGCTCGCCAGGTAACACGCCGCCCTTAAGTTTGAAAt < 1:1986301/69‑1 (MQ=255)
gTTTCTTCAATGCACGAACAGTGTCGATTTCTTGCTCGCCAGGTAACACGCCGCCCTTAAGTTTGAAAt < 1:2547050/69‑1 (MQ=255)
gTTTCTTCAATGCACGAACAGTGTCGATTTCTTGCTCGCCAGGTAACACGCCGCCCTTAAGTTTGAAAt < 1:2693399/69‑1 (MQ=255)
gTTTCTTCAATGCACGAACAGTGTCGATTTCTTGCTCGCCAGGTAACACGCCGCCCTTAAGTTTGAAAt < 1:3173458/69‑1 (MQ=255)
tcttcAATGTACGGACAGTGTCGATTTCTTGCTCGCCAGGTAACACGCCACCCTTAAGTTTGaa < 1:216596/64‑1 (MQ=255)
|
CAAGCAGCCATGCACCGTTGGGATCAACGGTAATCCGCGCATCCGGGAAGCGTTTCTTCAATGCACGAACAGTGTCGATTTCTTGCTCGCCAGGTAACACGCCGCCCTTAAGTTTGAAAT > minE/1889505‑1889624
|
| 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
