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 |
2,283,685 |
C→T |
39.9% |
V71V (GTG→GTA) |
oxyR ← |
DNA‑binding transcriptional dual regulator |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,283,685 | 0 | C | T | 39.9%
| 26.9
/ 38.3
| 60 | V71V (GTG→GTA) | oxyR | DNA‑binding transcriptional dual regulator |
| Reads supporting (aligned to +/- strand): ref base C (8/28); new base T (5/19); total (13/47) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.62e-01 |
TGCAGCGGTCCGGACATCGTCTCGCCCTGCTGGCTTGCCATCTCTTTAAGGACTTTCACCTCACGCAGCACGGTACGCGCCTGATCCACCAGCAGCATTCCCGCCTGGGTGAACAACACTT > minE/2283617‑2283737
|
tgCAGCGGTCCGGACATCGTCTCGCCCTGCTGGCTTGCCATCTCTTTAAGGACTTTCACCTCACgcagc > 1:2622604/1‑69 (MQ=255)
cGGACATCGTCTCGCCCTGCTGGCTTGCCATCTCTTTAAGGACTTTCACCTCACGCAGCACGGTAcgcg < 1:2932874/69‑1 (MQ=255)
cGGACATCGTCTCGCCCTGCTGGCTTGCCATCTCTTTAAGGACTTTCACCTCACGCAGCACGGTAcgcg < 1:2103178/69‑1 (MQ=255)
cGGACATCGTCTCGCCCTGCTGGCTTGCCATCTCTTTAAGGACTTTCACCTCACGCAGCACGGTAcgcg < 1:2033403/69‑1 (MQ=255)
ctgctgGCTTGCCATCTCTTTAAGGACTTTCACCTCACGCAGCACGGTACGCGCCTGATCCACcagcag < 1:297698/69‑1 (MQ=255)
ctgctgGCTTGCCATCTCTTTAAGGACTTTCACCTCACGCAGCACGGTACGCGCCTGATCCACcagcag < 1:795599/69‑1 (MQ=255)
ctgctgGCTTGCCATCTCTTTAAGGACTTTCACCTCACGCAGCACGGTACGCGCCTGATCCACcagcag < 1:2106845/69‑1 (MQ=255)
ctgctgGCTTGCCATCTCTTTAAGGACTTTCACCTCACGCAGCACGGTACGCGCCTGATCCACcagcag < 1:2520813/69‑1 (MQ=255)
ctgctgGCTTGCCATCTCTTTAAGGACTTTCACCTCACGCAGCACGGTACGCGCCTGATCCACcagcag < 1:117805/69‑1 (MQ=255)
ctgctgGCTTGCCATCTCTTTAAGGACTTTCACCTCACGCAGCACGGTACGCGCCTGATCCACcagcag < 1:3069507/69‑1 (MQ=255)
ctgctgGCTTGCCATCTCTTTAAGGACTTTCACCTCACGCAGCACGGTACGCGCCTGATCCACcagcag < 1:2348657/69‑1 (MQ=255)
ctgctgGCTTGCCATCTCTTTAAGGACTTTCACCTCACGCAGCACGGTACGCGCCTGATCCACcagcag < 1:3330831/69‑1 (MQ=255)
ctgctgGCTTGCCATCTCTTTAAGGACTTTCACCTCACGCAGCACGGTACGCGCCTGATCCACcagcag < 1:2310411/69‑1 (MQ=255)
tgctgGCTTGCCATCTCTTTAAGGACTTTCACCTCACGCAGCACGGTACGCGCCTGATCCACcagcag < 1:1372748/68‑1 (MQ=255)
tgctgGCTTGCCATCTCTTTAAGGACTTTCACCTCACGCAGCACGGTACGCGCCTGATCCACcagcag < 1:344696/68‑1 (MQ=255)
tctcTTTAAGGACTTTCACCTCACGCAGTACGGTACGCGCCTGATCCACCAGCAGCATTCCCGCCTgg > 1:1814072/1‑68 (MQ=255)
tctcTTTAAGGACTTTCACCTCACGCAGTACGGTACGCGCCTGATCCACCAGCAGCATTCCCGCCTgg > 1:3403220/1‑68 (MQ=255)
tctcTTTAAGGACTTTCACCTCACGCAGTACGGTACGCGCCTGATCCACCAGCAGCATTCCCGCCTgg > 1:3204230/1‑68 (MQ=255)
tctcTTTAAGGACTTTCACCTCACGCAGTACGGTACGCGCCTGATCCACCAGCAGCATTCCCGCCTgg > 1:2817816/1‑68 (MQ=255)
tctcTTTAAGGACTTTCACCTCACGCAGTACGGTACGCGCCTGATCCACCAGCAGCATTCCCGCCTgg > 1:2394093/1‑68 (MQ=255)
tctTTAAGGACTTTCACCTCACGCAGCACGGTACGCGCCTGATCCACcagcag < 1:2925944/53‑1 (MQ=255)
tctTTAAGGACTTTCACCTCACGCAGCACGGTACGCGCCTGATCCACcagcag < 1:2056018/53‑1 (MQ=255)
tctTTAAGGACTTTCACCTCACGCAGCACGGTACGCGCCTGATCCACcagcag < 1:92435/53‑1 (MQ=255)
tctTTAAGGACTTTCACCTCACGCAGCACGGTACGCGCCTGATCCACcagcag < 1:1963081/53‑1 (MQ=255)
tctTTAAGGACTTTCACCTCACGCAGCACGGTACGCGCCTGATCCACcagcag < 1:1959056/53‑1 (MQ=255)
tctTTAAGGACTTTCACCTCACGCAGCACGGTACGCGCCTGATCCACcagcag < 1:1500984/53‑1 (MQ=255)
tctTTAAGGACTTTCACCTCACGCAGCACGGTACGCGCCTGATCCACcagcag < 1:1179542/53‑1 (MQ=255)
tctTTAAGGACTTTCACCTCACGCAGCACGGTACGCGCCTGATCCACcagcag < 1:907959/53‑1 (MQ=255)
tctTTAAGGACTTTCACCTCACGCAGCACGGTACGCGCCTGATCCACcagcag < 1:1190507/53‑1 (MQ=255)
tctTTAAGGACTTTCACCTCACGCAGCACGGTACGCGCCTGATCCACCAGCAGCATTCCCGCCTgg > 1:318810/1‑66 (MQ=255)
tctTTAAGGACTTTCACCTCACGCAGCACGGTACGCGCCTGATCCACCAGCAGCATTCCCGCCTgg > 1:593982/1‑66 (MQ=255)
tctTTAAGGACTTTCACCTCACGCAGCACGGTACGCGCCTGATCCACCAGCAGCATTCCCGCCTgg > 1:715085/1‑66 (MQ=255)
tctTTAAGGACTTTCACCTCACGCAGCACGGTACGCGCCTGATCCACCAGCAGCATTCCCGCCTgg > 1:2943920/1‑66 (MQ=255)
tctTTAAGGACTTTCACCTCACGCAGCACGGTACGCGCCTGATCCACCAGCAGCATTCCCGCCTg > 1:2780387/1‑65 (MQ=255)
tctTTAAGGACTTTCACCTCACGCAGCACGGTACGCGCCTGATCCACCAGCAGCATTCCCGCCTGGGTg > 1:1566730/1‑69 (MQ=255)
tctTTAAGGACTTTCACCTCACGCAGCACGGTACGCGCCTGATCCACCAGCAGCATTCCCGCCTGGGTg > 1:1426962/1‑69 (MQ=255)
ctTTTAGGACTTTCACCTCACGCAGCACGGTACGCGCCTGATCCACcagcag < 1:2576767/52‑1 (MQ=255)
ctTTAAGGACTTTCACCTCACGCAGCACGGTACGCGCCTGATCCACcagcag < 1:2709955/52‑1 (MQ=255)
aGGACTTTCACCTCACGCAGCACGGTACGCGCCTGATCCACCAGCAGCATTCCCGCCTGGGTGaacaa < 1:3307111/68‑1 (MQ=255)
aCTTTCACCTCACGCAGCACGGTACGCGCCTGATCCACCAGCAGCATTCCCGCCTGGGTGAACAacac > 1:992607/1‑68 (MQ=255)
cTTTCACCTCACGCAGCACGGTACGCGCCTGATCCACCAGCAGCATTCCCGCCTGGGTGAACAACACtt < 1:1125102/69‑1 (MQ=255)
tttCACCTCACGCAGCACGGTACGCGCCTGATCCACCAGCAGCATTCCCGCCTGGGTGAACAACACtt < 1:746590/68‑1 (MQ=255)
cACGCAGTACGGTACGCGCCTGATCCACCAGCAGCATTCCCGCCTGGGTGAACAACACtt < 1:1948974/60‑1 (MQ=255)
cACGCAGTACGGTACGCGCCTGATCCACCAGCAGCATTCCCGCCTGGGTGAACAACACtt < 1:1043412/60‑1 (MQ=255)
cACGCAGTACGGTACGCGCCTGATCCACCAGCAGCATTCCCGCCTGGGTGAACAACACtt < 1:961929/60‑1 (MQ=255)
cACGCAGTACGGTACGCGCCTGATCCACCAGCAGCATTCCCGCCTGGGTGAACAACACtt < 1:1305214/60‑1 (MQ=255)
cACGCAGTACGGTACGCGCCTGATCCACCAGCAGCATTCCCGCCTGGGTGAACAACACtt < 1:1554642/60‑1 (MQ=255)
cACGCAGTACGGTACGCGCCTGATCCACCAGCAGCATTCCCGCCTGGGTGAACAACACtt < 1:676928/60‑1 (MQ=255)
cACGCAGTACGGTACGCGCCTGATCCACCAGCAGCATTCCCGCCTGGGTGAACAACACtt < 1:173817/60‑1 (MQ=255)
cACGCAGTACGGTACGCGCCTGATCCACCAGCAGCATTCCCGCCTGGGTGAACAACACtt < 1:587418/60‑1 (MQ=255)
cACGCAGTACGGTACGCGCCTGATCCACCAGCAGCATTCCCGCCTGGGTGAACAACACtt < 1:2695025/60‑1 (MQ=255)
cACGCAGTACGGTACGCGCCTGATCCACCAGCAGCATTCCCGCCTGGGTGAACAACACtt < 1:1982188/60‑1 (MQ=255)
cACGCAGTACGGTACGCGCCTGATCCACCAGCAGCATTCCCGCCTGGGTGAACAACACtt < 1:1986262/60‑1 (MQ=255)
cACGCAGTACGGTACGCGCCTGATCCACCAGCAGCATTCCCGCCTGGGTGAACAACACtt < 1:2071205/60‑1 (MQ=255)
cACGCAGTACGGTACGCGCCTGATCCACCAGCAGCATTCCCGCCTGGGTGAACAACACtt < 1:2246420/60‑1 (MQ=255)
cACGCAGTACGGTACGCGCCTGATCCACCAGCAGCATTCCCGCCTGGGTGAACAACACtt < 1:2266601/60‑1 (MQ=255)
cACGCAGTACGGTACGCGCCTGATCCACCAGCAGCATTCCCGCCTGGGTGAACAACACtt < 1:3089115/60‑1 (MQ=255)
cACGCAGTACGGTACGCGCCTGATCCACCAGCAGCATTCCCGCCTGGGTGAACAACACtt < 1:2363974/60‑1 (MQ=255)
cACGCAGTACGGTACGCGCCTGATCCACCAGCAGCATTCCCGCCTGGGTGAACAACACtt < 1:2688938/60‑1 (MQ=255)
cACGCAGTACGGTACGCGCCTGATCCACCAGCAGCATTCCCGCCTGGGTGAACAACACtt < 1:2953811/60‑1 (MQ=255)
cACGCAGTACGGTACGCGCCTGATCCACCAGAAGCATTCCCGCCTGGGTGAACAACACtt < 1:1425966/60‑1 (MQ=255)
|
TGCAGCGGTCCGGACATCGTCTCGCCCTGCTGGCTTGCCATCTCTTTAAGGACTTTCACCTCACGCAGCACGGTACGCGCCTGATCCACCAGCAGCATTCCCGCCTGGGTGAACAACACTT > minE/2283617‑2283737
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
