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 |
333,922 |
C→T |
34.0% |
N180N (AAC→AAT) |
ushA → |
bifunctional UDP‑sugar hydrolase and 5'‑nucleotidase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 333,922 | 0 | C | T | 34.0%
| 31.5
/ 20.9
| 44 | N180N (AAC→AAT) | ushA | bifunctional UDP‑sugar hydrolase and 5'‑nucleotidase |
| Reads supporting (aligned to +/- strand): ref base C (15/14); new base T (7/8); total (22/22) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.04e-01 |
CAGGATCTGAAAATTGCCGTTATTGGGCTGACAACCGATGACACAGCAAAAATTGGTAACCCGGAATACTTCACTGATATCGAATTTCGTAAGCCCGCCGATGAAGCGAAGCTGGTGATT > minE/333863‑333982
|
cAGGATCTGAAAATTGCCGTTATTGGGCTGACAACCGATGACACAGCAAAAATTGGTAACCCGGAATAc < 1:2547042/69‑1 (MQ=255)
cAGGATCTGAAAATTGCCGTTATTGGGCTGACAACCGATGACACAGCAAAAATTGGTAACCCGGAATAc < 1:1483399/69‑1 (MQ=255)
aaaaTTGCCGTTATTGGCCTGACGACGGATGACACAGCCAAAATTGGTAATCCGGAATATTTCACTGat > 1:1762190/1‑69 (MQ=255)
aaaaTTGCCGTTATTGGCCTGACGACGGATGACACAGCCAAAATTGGTAATCCGGAATATTTCACTGat > 1:2558430/1‑69 (MQ=255)
aaaaTTGCCGTTATTGGCCTGACGACGGATGACACAGCCAAAATTGGTAATCCGGAATATTTCACTGat > 1:2729891/1‑69 (MQ=255)
aaaaTTGCCGTTATTGGCCTGACGACGGATGACACAGCCAAAATTGGTAATCCGGAATATTTCACTGat > 1:480439/1‑69 (MQ=255)
aaaaTTGCCGTTATTGGCCTGACGACGGATGACACAGCCAAAATTGGTAATCCGGAATATTTCACTGat > 1:1758389/1‑69 (MQ=255)
aaaaTTGCCGTTATTGGCCTGACGACGGATGACACAGCCAAAATTGGTAATCCGGAATATTTCACTGat > 1:1595216/1‑69 (MQ=255)
aaaaTTGCCGTTATTGGCCTGACGACGGATGACACAGCCAAAATTGGTAATCCGGAATATTTCACTGa > 1:1938558/1‑68 (MQ=255)
aaTTGCCGTTATTGGGCTGACAACCGATGACACAGCAAAAATTGGTAACCCGGAATACTTCACt < 1:1309223/64‑1 (MQ=255)
aTTGGGCTGACAACCGATGACACAGCAAAAATTGGTAACCCGGaa > 1:2851022/1‑45 (MQ=255)
aTTGGGCTGACAACCGATGACACAGCAAAAATTGGTAACCCGGaa > 1:874222/1‑45 (MQ=255)
aTTGGGCTGACAACCGATGACACAGCAAAAATTGGTAACCCGGaa > 1:2416836/1‑45 (MQ=255)
aTTGGGCTGACAACCGATGACACAGCAAAAATTGGTAACCCGGaa > 1:2296041/1‑45 (MQ=255)
aTTGGGCTGACAACCGATGACACAGCAAAAATTGGTAACCCGGaa > 1:2281723/1‑45 (MQ=255)
aTTGGGCTGACAACCGATGACACAGCAAAAATTGGTAACCCGGaa > 1:3217995/1‑45 (MQ=255)
aTTGGGCTGACAACCGATGACACAGCAAAAATTGGTAACCCGGaa > 1:784385/1‑45 (MQ=255)
aTTGGGCTGACAACCGATGACACAGCAAAAATTGGTAACCCGGaa > 1:667390/1‑45 (MQ=255)
aTTGGGCTGACAACCGATGACACAGCAAAAATTGGTAACCCGGaa > 1:1323363/1‑45 (MQ=255)
aTTGGGCTGACAACCGATGACACAGCAAAAATTGGTAACCCGGAATACTTCACTGATATCGAATTTc > 1:1188132/1‑67 (MQ=255)
gggCTGACAACCGATGACACAGCAAAAATTGGTAACCCGGAATACTTCACTGATATCGAATTTCGTaa > 1:609918/1‑68 (MQ=255)
gggCTGACAACCGATGACACAGCAAAAATTGGTAACCCGGAATACTTCACTGATATCGAATTTCGTAAg > 1:1776793/1‑69 (MQ=255)
gggCTGACAACCGATGACACAGCAAAAATTGGTAACCCGGAATACTTCACTGATATCGAATTTCGTAAg > 1:1195916/1‑69 (MQ=255)
cacaGCAAAAATTGGTAACCCGGAATACTTCACTGATATCGAATTTCGTAAGCCCGCCGATgaagcga < 1:2792971/68‑1 (MQ=255)
aGCAAAAATTGGTAACCCGGAATACTTCACTGATATCGAATTTCGTAAGCCCGCCGATGAAGCGAAGCt < 1:3066819/69‑1 (MQ=255)
aGCAAAAATTGGTAACCCGGAATACTTCACTGATATCGAATTTCGTAAGCCCGCCGATGAAGCGAAGCt < 1:1075727/69‑1 (MQ=255)
aGCAAAAATTGGTAACCCGGAATACTTCACTGATATCGAATTTCGTAAGCCCGCCGATGAAGCGAAGCt < 1:43925/69‑1 (MQ=255)
aGCAAAAATTGGTAACCCGGAATACTTCACTGATATCGAATTTCGTAAGCCCGCCGATGAAGCGAAGCt < 1:1212938/69‑1 (MQ=255)
gCAAAAATTGGTAACCCGGAATACTTCACTGATATCGAATTTCGTAAGCCCGCCGATGAAGCGAAGCt > 1:2540587/1‑68 (MQ=255)
gCAAAAATTGGTAACCCGGAATACTTCACTGATATCGAATTTCGTAAGCCCGCCGATGAAGCGAAGCTg > 1:1940635/1‑69 (MQ=255)
aaaaaTTGGTAACCCGGAATACTTCACTGATATCGAATTTCGTAAGCCCGCCGATGAAGCGAAGCTGGt < 1:3123465/69‑1 (MQ=255)
aaaaaTTGGTAACCCGGAATACTTCACTGATATCGAATTTCGTAAGCCCGCCGATGAAGCGAAGCTGGt < 1:1126872/69‑1 (MQ=255)
aaaaaTTGGTAACCCGGAATACTTCACTGATATCGAATTTCGTAAGCCCGCCGATGAAGCGAAGCTGGt < 1:3038500/69‑1 (MQ=255)
aaaaaTTGGTAACCCGGAATACTTCACTGATATCGAATTTCGTAAGCCCGCCGATGAAGCGAAGCTGGt < 1:2481927/69‑1 (MQ=255)
aaaaaTTGGTAACCCGGAATACTTCACTGATATCGAATTTCGTAAGCCCGCCGATGAAGCGAAGCTGGt < 1:2119162/69‑1 (MQ=255)
aaaaaTTGGTAACCCGGAATACTTCACTGATATCGAATTTCGTAAGCCCGCCGATGAAGCGAAGCTGGt < 1:121868/69‑1 (MQ=255)
aTTGGTAATCCGGAATATTTCACTGATATCGAATTTCGTAAGCCCGCTGATGAAGCGAAGCTGGTGAtt < 1:2991566/69‑1 (MQ=255)
aTTGGTAATCCGGAATATTTCACTGATATCGAATTTCGTAAGCCCGCTGATGAAGCGAAGCTGGTGAtt < 1:2586594/69‑1 (MQ=255)
aTTGGTAATCCGGAATATTTCACTGATATCGAATTTCGTAAGCCCGCTGATGAAGCGAAGCTGGTGAtt < 1:195712/69‑1 (MQ=255)
aTTGGTAATCCGGAATATTTCACTGATATCGAATTTCGTAAGCCCGCTGATGAAGCGAAGCTGGTGAtt < 1:1865253/69‑1 (MQ=255)
aTTGGTAATCCGGAATATTTCACTGATATCGAATTTCGTAAGCCCGCTGATGAAGCGAAGCTGGTGAtt < 1:1801350/69‑1 (MQ=255)
aTTGGTAATCCGGAATATTTCACTGATATCGAATTTCGTAAGCCCGCTGATGAAGCGAAGCTGGTGAtt < 1:1153499/69‑1 (MQ=255)
aTTGGTAATCCGGAATATTTCACTGATATCGAATTTCGTAAGCCCGCTGATGAAGCGAAGCTGGTGAtt < 1:1144383/69‑1 (MQ=255)
aTTGGTAATCCGGAATATTTCACTGATATCGAATTTCGTAAGCCCGCTGATGAAGCGAAGCTGGTGAtt < 1:923368/69‑1 (MQ=255)
cccGGAATACTTCACTGATATCGAATTTCGTAAGCCCGCCGATGAAGCGAAGCTGGt < 1:3232371/57‑1 (MQ=255)
|
CAGGATCTGAAAATTGCCGTTATTGGGCTGACAACCGATGACACAGCAAAAATTGGTAACCCGGAATACTTCACTGATATCGAATTTCGTAAGCCCGCCGATGAAGCGAAGCTGGTGATT > minE/333863‑333982
|
| 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
