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 |
2,562,227 |
G→A |
61.9% |
R65R (CGC→CGT) |
lldR ← |
DNA‑binding transcriptional repressor |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,562,227 | 0 | G | A | 61.9%
| 29.0
/ 39.7
| 63 | R65R (CGC→CGT) | lldR | DNA‑binding transcriptional repressor |
| Reads supporting (aligned to +/- strand): ref base G (8/16); new base A (31/8); total (39/24) |
| Fisher's exact test for biased strand distribution p-value = 4.22e-04 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.88e-01 |
TGGACGATGTTTTGCTCCGACCATGTGTCATGACGCCAGCGAATAAACGTCCCGCCGCCGCGTCGACTGAGCAGCACGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAGTGAATTACGTGA > minE/2562168‑2562292
|
tGGACGATGTTTTGCTCCGACCATGTGTCATGACGCCAGCGAATAAACGTCCCGCCGCCGCGTCGACTg < 1:30390/69‑1 (MQ=255)
tgtCATGACGCCAGCGAATAAACGTCCCGCCGCCACGTCGACTGAGCAGCACACCTTCGCTTACCAGtt < 1:669461/69‑1 (MQ=255)
tgtCATGACGCCAGCGAATAAACGTCCCGCCGCCACGTCGACTGAGCAGCACACCTTCGCTTACCAGtt < 1:34374/69‑1 (MQ=255)
tgtCATGACGCCAGCGAATAAACGTCCCGCCGCCACGTCGACTGAGCAGCACACCTTCGCTTACCAGtt < 1:2467631/69‑1 (MQ=255)
tgtCATGACGCCAGCGAATAAACGTCCCGCCGCCACGTCGACTGAGCAGCACACCTTCGCTTACCAGtt < 1:2295830/69‑1 (MQ=255)
tgtCATGACGCCAGCGAATAAACGTCCCGCCGCCACGTCGACTGAGCAGCACACCTTCGCTTACCAGtt < 1:1779858/69‑1 (MQ=255)
tgtCATGACGCCAGCGAATAAACGTCCCGCCGCCACGTCGACTGAGCAGCACACCTTCGCTTACCAGtt < 1:1607866/69‑1 (MQ=255)
gtCATGACGCCAGCGAATAAACGTCCCGCCGCCACGTCGACTGAGCAGCACACCTTCGCTTACCAGtt < 1:842119/68‑1 (MQ=255)
tCATGACGCCAGCGAATAAACGTCCCGCCGCCACGTCGACTGAGCAGCACACCTTCGCTTACCAGtt < 1:1459519/67‑1 (MQ=255)
aCGCCAGCGAATAAACGTCCCGCCGCCGCGTCGACTGAGCAGCACGCCTTCACTCACCAGt < 1:1503534/61‑1 (MQ=255)
aCGCCAGCGAATAAACGTCCCGCCGCCGCGTCGACTGAGCAGCACGCCTTCACTCACCAGTTTTGCCAg > 1:3135761/1‑69 (MQ=255)
aCGCCAGCGAATAAACGTCCCGCCGCCACGTCGACTGAGCAGCACCCCTTCGCTTACCAGTTTCGCCAg > 1:2657803/1‑69 (MQ=255)
aCGCCAGCGAATAAACGTCCCGCCGCCACGTCGACTGAGCAGCACACCtt > 1:1001617/1‑50 (MQ=255)
aCGCCAGCGAATAAACGTCCCGCCGCCACGTCGACTGAGCAGCACACCTtcgct > 1:911853/1‑54 (MQ=255)
aCGCCAGCGAATAAACGTCCCGCCGCCACGTCGACTGAGCAGCACACCTTCGCTTACCAGTTTCGCCa > 1:436689/1‑68 (MQ=255)
aCGCCAGCGAATAAACGTCCCGCCGCCACGTCGACTGAGCAGCACACCTTCGCTTACCAGTTTCGCCa > 1:2210985/1‑68 (MQ=255)
aCGCCAGCGAATAAACGTCCCGCCGCCACGTCGACTGAGCAGCACACCTTCGCTTACCAGTTTCGCCAg > 1:967578/1‑69 (MQ=255)
aCGCCAGCGAATAAACGTCCCGCCGCCACGTCGACTGAGCAGCACACCTTCGCTTACCAGTTTCGCCAg > 1:802202/1‑69 (MQ=255)
aCGCCAGCGAATAAACGTCCCGCCGCCACGTCGACTGAGCAGCACACCTTCGCTTACCAGTTTCGCCAg > 1:514834/1‑69 (MQ=255)
aCGCCAGCGAATAAACGTCCCGCCGCCACGTCGACTGAGCAGCACACCTTCGCTTACCAGTTTCGCCAg > 1:1109741/1‑69 (MQ=255)
aCGCCAGCGAATAAACGTCCCGCCGCCACGTCGACTGAGCAGCACACCTTCGCTTACCAGTTTCGCCAg > 1:3236630/1‑69 (MQ=255)
aCGCCAGCGAATAAACGTCCCGCCGCCACGTCGACTGAGCAGCACACCTTCGCTTACCAGTTTCGCCAg > 1:2815374/1‑69 (MQ=255)
aCGCCAGCGAATAAACGTCCCGCCGCCACGTCGACTGAGCAGCACACCTTCGCTTACCAGTTTCGCCAg > 1:278270/1‑69 (MQ=255)
aCGCCAGCGAATAAACGTCCCGCCGCCACGTCGACTGAGCAGCACACCTTCGCTTACCAGTTTCGCCAg > 1:1958370/1‑69 (MQ=255)
aCGCCAGCGAATAAACGTCCCGCCGCCACGTCGACTGAGCAGCACACCTTCGCTTACCAGTTTCGCCAg > 1:1869038/1‑69 (MQ=255)
aCGCCAGCGAATAAACGTCCCGCCGCCACGTCGACTGAGCAGCACACCTTCGCTTACCAGTTTCGCCAg > 1:1909993/1‑69 (MQ=255)
aCGCCAGCGAATAAACGTCCCGCCGCCACGTCGACTGAGCAGCACACCTTCGCTTACCAGTTTCGCCAg > 1:1592134/1‑69 (MQ=255)
aCGCCAGCGAATAAACGTCCCGCCGCCACGTCGACTGAGCAGCACACCTTCGCTTACCAGTTTCGCCAg > 1:1684566/1‑69 (MQ=255)
aCGCCAGCGAATAAACGTCCCGCCGCCAAGTCGACTGAGCAGCACACCTTCGCTTACCAGTTTCGCCAg > 1:395311/1‑69 (MQ=255)
cGAATAAACGTCCCGCCGCCACGTCGACTGAGCAGCACACCTTCGCTTACCAGTTTCGCCAGCGCCTcg > 1:1591865/1‑69 (MQ=255)
cGAATAAACGTCCCGCCGCCACGTCGACTGAGCAGCACACCTTCGCTTACCAGTTTCGCCAGCGCCTcg > 1:2362737/1‑69 (MQ=255)
cGAATAAACGTCCCGCCGCCACGTCGACTGAGCAGCACACCTTCGCTTACCAGTTTCGCCAGCGCCTcg > 1:3342586/1‑69 (MQ=255)
cGAATAAACGTCCCGCCGCCACGTCGACTGAGCAGCACACCTTCGCTTACCAGTTTCGCCAGCGCCTcg > 1:1345581/1‑69 (MQ=255)
cGAATAAACGTCCCGCCGCCACGTCGACTGAGCAGCACACCTTCGCTTACCAGTTTCGCCAGCGCCTcg > 1:17662/1‑69 (MQ=255)
cGAATAAACGTCCCGCCGCCACGTCGACTGAGCAGCACACCTTCGCTTACCAGTTTCGCCAGCGCCTcg > 1:2536618/1‑69 (MQ=255)
cGAATAAACGTCCCGCCGCCACGTCGACTGAGCAGCACACCTTCGCTTACCAGTTTCGCCAGCGCCTcg > 1:1211911/1‑69 (MQ=255)
cGAATAAACGTCCCGCCGCCACGTCGACTGAGCAGCACACCTTCGCTTACCAGTTTCGCCAGCGCCTcg > 1:480546/1‑69 (MQ=255)
cGAATAAACGTCCCGCCGCCACGTCGACTGAGCAGCACACCTTCGCTTACCAGTTTCGCCAGCGCCTcg > 1:662973/1‑69 (MQ=255)
cGAATAAACGTCCCGCCGCCACGTCGACTGAGCAGCACACCTTCGCTTACCAGTTTCGCCAGCGCCTcg > 1:56595/1‑69 (MQ=255)
cGAATAAACGTCCCGCCGCCACGTCGACTGAGCAGCACACCTTCGCTTACCAGTTTCGCCAGCGCCTcg > 1:1135316/1‑69 (MQ=255)
cGAATAAACGTCCCGCCGCCACGTCGACTGAGCAGCACACCTTCGCTTACCAGTTTCGCCAGCGCCTcg > 1:1114674/1‑69 (MQ=255)
cGAATAAACGTCCCGCCGCCACGTCGACTGAGCAGCACACCTTCGCTTACCAGTTTCGCCAGCGCCTcg > 1:1931601/1‑69 (MQ=255)
aaCGTCCCGCCGCCGCGTCGACTGATCAGCACGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAg > 1:1012729/1‑68 (MQ=255)
aaCGTCCCGCCGCCGCGTCGACTGAGCAGCACGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAg > 1:1640195/1‑68 (MQ=255)
aaCGTCCCGCCGCCGCGTCGACTGAGCAGCACGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAg > 1:1873545/1‑68 (MQ=255)
aaCGTCCCGCCGCCGCGTCGACTGAGCAGCACGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAg > 1:2424141/1‑68 (MQ=255)
aaCGTCCCGCCGCCGCGTCGACTGAGCAGCACGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAg > 1:477900/1‑68 (MQ=255)
aaCGTCCCGCCGCCGCGTCGACTGAGCAGCACGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAg > 1:1879949/1‑68 (MQ=255)
aaCGTCCCGCCGCCGCGTCGACTGAGCAGCACGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAg > 1:784326/1‑68 (MQ=255)
cGTCCCGCCGCCGCGTCGACTGAGCAGCACGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAGTg < 1:835012/68‑1 (MQ=255)
cGTCCCGCCGCCGCGTCGACTGAGCAGCACGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAGTg < 1:756462/68‑1 (MQ=255)
cGTCCCGCCGCCGCGTCGACTGAGCAGCACGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAGTg < 1:1603699/68‑1 (MQ=255)
cGTCCCGCCGCCGCGTCGACTGAGCAGCACGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAGTg < 1:322245/68‑1 (MQ=255)
cGTCCCGCCGCCGCGTCGACTGAGCAGCACGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAGTg < 1:3383000/68‑1 (MQ=255)
cGTCCCGCCGCCGCGTCGACTGAGCAGCACGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAGTg < 1:3350025/68‑1 (MQ=255)
cGTCCCGCCGCCGCGTCGACTGAGCAGCACGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAGTg < 1:3235681/68‑1 (MQ=255)
cGTCCCGCCGCCGCGTCGACTGAGCAGCACGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAGTg < 1:3213057/68‑1 (MQ=255)
cGTCCCGCCGCCGCGTCGACTGAGCAGCACGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAGTg < 1:3181433/68‑1 (MQ=255)
cGTCCCGCCGCCGCGTCGACTGAGCAGCACGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAGTg < 1:302000/68‑1 (MQ=255)
cGTCCCGCCGCCGCGTCGACTGAGCAGCACGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAGTg < 1:2902873/68‑1 (MQ=255)
cGTCCCGCCGCCGCGTCGACTGAGCAGCACGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAGTg < 1:852750/68‑1 (MQ=255)
cGTCCCGCCGCCGCGTCGACTGAGCAGCACGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAGTg < 1:2194821/68‑1 (MQ=255)
cGTCCCGCCGCCGCGTCGACTGAGCAGCACGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAGTg < 1:1936547/68‑1 (MQ=255)
gccgccgcGTCGACTGAGCAGCACGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAGTGAATTACg < 1:837777/69‑1 (MQ=255)
gccgccgcGTCGACTGAGCAGCACGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAGTGAATTACg < 1:993090/69‑1 (MQ=255)
gccgccgcGTCGACTGAGCAGCACGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAGTGAATTACg < 1:401970/69‑1 (MQ=255)
gccgccgcGTCGACTGAGCAGCACGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAGTGAATTACg < 1:248944/69‑1 (MQ=255)
gccgccgcGTCGACTGAGCAGCACGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAGTGAATTACg < 1:1897085/69‑1 (MQ=255)
ccgccgcGTCGACTGAGCAGCACGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAGTGAATTACGt < 1:44940/69‑1 (MQ=255)
gccgcGTCGACTGAGCAGCACGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAGTGAATTACGTGa < 1:494467/69‑1 (MQ=255)
gccgcGTCGACTGAGCAGCACGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAGTGAATTACGTGa < 1:1600278/69‑1 (MQ=255)
gccgcGTCGACTGAGCAGCACGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAGTGAATTACGTGa < 1:1005308/69‑1 (MQ=255)
|
TGGACGATGTTTTGCTCCGACCATGTGTCATGACGCCAGCGAATAAACGTCCCGCCGCCGCGTCGACTGAGCAGCACGCCTTCACTCACCAGTTTTGCCAGCGCCTCGCGCAGTGAATTACGTGA > minE/2562168‑2562292
|
| 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
