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 |
|
A6 F1 I0 R1
|
2892 |
75.3 |
5698161 |
66.1% |
3766484 |
59.5 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
910,940 |
T→C |
21.3% |
D60D (GAT→GAC) |
ycjV → |
predicted sugar transporter subunit |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 910,940 | 0 | T | C | 21.3%
| 154.4
/ 34.9
| 75 | D60D (GAT→GAC) | ycjV | predicted sugar transporter subunit |
| Reads supporting (aligned to +/- strand): ref base T (38/21); new base C (4/12); total (42/33) |
| Fisher's exact test for biased strand distribution p-value = 9.17e-03 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.93e-01 |
CCGTCGGGCTGCGGTAAGTCGACCACCCTGCGCATGATTGCCGGGCTTGAGGAGATCAGCGGCGGCGATC‑TGTTGATCGACGGCAAACGAATGAATGACGTTCCAGCCAAAGCACGCAATATAGCGATGGTGTTC > minE/910872‑911006
|
ccGTCTGGCTGCGGTAAATCGACTTTACTGCGCATGATTGCCGGGCTTGAGACGATCACCAGCGGCGACC‑t > 1:216732/1‑71 (MQ=2)
cGTCTGGCTGCGGTAAATCGACTTTACTGCGCATGATTGCCGGGCTTGAGACGATCACCAGCGGCGACC‑Tg < 1:120551/71‑1 (MQ=9)
cGTCTGGCTGCGGTAAATCGACTTTACTGCGCATGATTGCCGGGCTTGAGACGATCACCAGCGGCGACC‑Tg < 1:127381/71‑1 (MQ=9)
cGTCTGGCTGCGGTAAATCGACTTTACTGCGCATGATTGCCGGGCTTGAGACGATCACCAGCGGCGACC‑Tg < 1:1656270/71‑1 (MQ=9)
tctggCTGCGGTAAATCGACTTTACTGCGCATGATTGCCGGGCTTGAGACGATCACCAGCGGCGACC‑TGtt < 1:281672/68‑1 (MQ=9)
tCGGGCTGCGGTAAGTCGACCACCCTGCGCATGATTGCCGGGCTTGAGGAGATCAGCGGCGGCGATC‑TGtt > 1:5202624/1‑71 (MQ=255)
tCGGGCTGCGGTAAGTCGACCACCCTGCGCATGATTGCCGGGCTTGAGGAGATCAGCGGCGGCGATC‑TGtt > 1:4159067/1‑71 (MQ=255)
tggCTGCGGTAAATCGACTTTACTGCGCATGATTGCCGGGCTTGAGACGATCACCAGCGGCGACC‑TGttca > 1:389365/2‑69 (MQ=16)
gggCTGCGGTAAGTCGACCACCCTGCGCATGATTGCCGGGCTTGAGGAGATCAGCGGCGGCGATC‑TGt > 1:1951081/1‑68 (MQ=255)
gggCTGCGGTAAGTCGACCACCCTGCGCATGATTGCCGGGCTTGAGGAGATCAGCGGCGGCGATC‑TGTTg > 1:811305/1‑70 (MQ=255)
gggCTGCGGTAAGTCGACCACCCTGCGCATGATTGCCGGGCTTGAGGAGATCAGCGGCGGCGATC‑TGTTg < 1:5055415/70‑1 (MQ=255)
gggCTGCGGTAAGTCGACCACCCTGCGCATGATTGCCGGGCTTGAGGAGATCAGCGGCGGCGATC‑TGTTGa > 1:1129392/1‑71 (MQ=255)
gggCTGCGGTAAGTCGACCACCCTGCGCATGATTGCCGGGCTTGAGGAGATCAGCGGCGGCGATC‑TGTTGa > 1:2278525/1‑71 (MQ=255)
gCTGCGGTAAATCGACTTTACTGCGCATGATTGCCGGGCTTGAGACGATCACCAGCGGCGACC‑TGttca < 1:1958908/69‑3 (MQ=16)
cTGCGGTAAATCGACTTTACTGCGCATGATTGCCGGGCTTGAGACGATCACCAGCGGCGACC‑TGTTCATCg > 1:19106/1‑71 (MQ=255)
cGGTAAATCGACTTTACTGCGCATGATTGCCGGGCTTGAGACGATCACCAGCGGCGACC‑TGTTCATCggt < 1:245155/70‑3 (MQ=255)
tAAGTCGACCACCCTGCGCATGATTGCCGGGCTTGAGGAGATCAGCGGCGGCGATC‑TGTTGATCGACGGCa < 1:3368712/71‑1 (MQ=255)
aaGTCGACCACCCTGCGCATGATTGCCGGGCTTGAGGAGATCAGCGGCGGCGATC‑TGTTGATCGACGGCa > 1:747362/1‑70 (MQ=255)
aGTCGACCACCCTGCGCATGATTGCCGGGCTTGAGGAGATCAGCGGCGGCGATC‑TGTTGATCGACGGCaaa > 1:3327204/1‑71 (MQ=255)
gACCACCCTGCGCATGATTGCCGGGCTTGAGGAGATCAGCGGCGGCGATC‑TGTTGATCGACGGCAAACgaa > 1:1960426/1‑71 (MQ=255)
gACCACCCTGCGCATGATTGCCGGGCTTGAGGAGATCAGCGGCGGCGATC‑TGTTGATCGACGGCAAACgaa > 1:4028421/1‑71 (MQ=255)
accaccCTGCGCATGATTGCCGGGCTTGAGGAGATCAGCGGCGGCGATC‑TGTTg < 1:315964/54‑1 (MQ=255)
caccCTGCGCATGATTGCCGGGCTTGAGGAGATCAGCGGCGGCGATC‑TGTTGATCGACGGCAAACgaatg > 1:2835923/1‑70 (MQ=255)
tacTGCGCATGATTGCCGGGCTTGAGACGATCACCAGCGGCGACC‑TGTTCATCGGTGAGAAACggatgaat > 1:4872102/3‑71 (MQ=255)
acTGCGCATGATTGCCGGGCTTGAGACGATCACCAGCGGCGACC‑TGTTCATCGGTGAGAAACggatgaat < 1:617487/69‑1 (MQ=255)
cTGCGCATGATTGCCGGGCTTGAGGAGATCAGCGGCGGCGATC‑TGt > 1:5182558/1‑46 (MQ=255)
cTGCGCATGATTGCCGGGCTTGAGGAGATCAGCGGCGGCGATC‑TGt > 1:2493386/1‑46 (MQ=255)
cTGCGCATGATTGCCGGGCTTGAGGAGATCAGCGGCGGCGATC‑TGTTGAt > 1:3697615/1‑50 (MQ=255)
cTGCGCATGATTGCCGGGCTTGAGACGATCACCAGCGGCGACC‑TGTTCATCGGTGAGAAACggatgaat < 1:4600486/69‑1 (MQ=255)
cTGCGCATGATTGCCGGGCTTGAGACGATCACCAGCGGCGACC‑TGTTCATCGGTGAGAAACGGatgaatga < 1:357269/71‑1 (MQ=255)
tGCGCATGATTGCCGGGCTTGAGGAGATCAGCGGCGGCGATC‑TGTTGATCGa > 1:4735850/1‑52 (MQ=255)
tGCGCATGATTGCCGGGCTTGAGGAGATCAGCGGCGGCGATC‑TGTTGATCGa > 1:5325610/1‑52 (MQ=255)
tGCGCATGATTGCCGGGCTTGAGGAGATCAGCGGCGGCGATC‑TGTTGATCGa > 1:4463217/1‑52 (MQ=255)
tGCGCATGATTGCCGGGCTTGAGGAGATCAGCGGCGGCGATC‑TGTTGATCGACGGCaaa > 1:1088077/1‑59 (MQ=255)
cgcATGATTGCCGGGCTTGAGGAGATCAGCGGCGGCGATC‑TGTTGATCGACGGCAAACGAATGAATGACGt > 1:3574296/1‑71 (MQ=255)
cgcATGATTGCCGGGCTTGAGACGATCACCAGCGGCGACC‑TGTTCATCGGTGAGAAACGGatgaatga < 1:2731504/68‑1 (MQ=255)
gcATGATTGCCGGGCTTGAGGAGATCAGCGGAGGCGATC‑TGTTGATCGACGGCAAACgaatgaat < 1:233013/65‑1 (MQ=255)
aTGATTGCCGGGCTTGAGACGATCACCAGCGGCGACA‑TGtt < 1:1951221/41‑1 (MQ=12)
gATTGCCGGGCTTGAGGAGATCAGCGGCGGCGATC‑TGTTGATCGACGGCAAACGAATGAATGACGTTCCAg > 1:4874606/1‑71 (MQ=255)
gATTGCCGGGCTTGAGGAGATCAGCGGCGGCGATC‑TGTTGATCGACGGCAAACGAATGAATGACGTTCCAg > 1:2038626/1‑71 (MQ=255)
gATTGCCGGGCTTGAGACGATCACCAGCGGCGACC‑TTTTCATCggt < 1:2110753/46‑3 (MQ=255)
aTTGCCGGGCTTGAGGAGATCAGCGGCGGCGATC‑TGTTGATCGACGGCAAACGAATGAATGACGTTCCAGc > 1:2111343/1‑71 (MQ=255)
aTTGCCGGGCTTGAGGAGATCAGCGGCGGCGATC‑TGTTGATCGACGGCAAACGAATGAATGACGTTCCAGc > 1:5464613/1‑71 (MQ=255)
ttGCCGGGCTTGAGGAGATCAGCGGCGGCGATC‑TGTTGATCGACGGCAAACGAATGAATGACGTTCCAGc > 1:3299400/1‑70 (MQ=255)
ttGCCGGGCTTGAGGAGATCAGCGGCGGCGATC‑TGTTGATCGACGGCAAACGAATGAATGACGTTCCAGc > 1:5085129/1‑70 (MQ=255)
tGCCGGGCTTGAGGAGATCAGCGGCGGCGATC‑TGTTGATCGACGGCAAACgaa > 1:2537131/1‑53 (MQ=255)
tGCCGGGCTTGAGGAGATCAGCGGCGGCGATC‑TGTTGATCGACGGCAAACGAATGAATGACGTTCCAGcc > 1:3391508/1‑70 (MQ=255)
tGCCGGGCTTGAGGAGATCAGCGGCGGCGATC‑TGTTGATCGACGGCAAACGAATGAATGACGTTCCAGcc > 1:3397989/1‑70 (MQ=255)
tGCCGGGCTTGAGGAGATCAGCGGCGGCGATC‑TGTTGATCGACGGCAAACGAATGAATGACGTTCCAGcc > 1:5360278/1‑70 (MQ=255)
gCCGGGCTTGAGGAGATCAGCGGCGGCGATC‑TGTTGATCGACGGCAAACgaatg < 1:2574722/54‑1 (MQ=255)
ggCTTGAGGAGATCAGCGGCGGCGATC‑TGTTGATCGACGGCAAACgaatgaat > 1:3226819/1‑53 (MQ=255)
ggCTTGAGGAGATCAGCGGCGGCGATC‑TGTTGATCGACGGCAAACgaatgaat > 1:4148776/1‑53 (MQ=255)
ggCTTGAGGAGATCAGCGGCGGCGATC‑TGTTGATCGACGGCAAACGAATGAATGACGTTCCAGCCa < 1:3291440/66‑1 (MQ=255)
ggCTTGAGGAGATCAGCGGCGGCGATC‑TGTTGATCGACGGCAAACGAATGAATGACGTTCCAGCCa < 1:5373925/66‑1 (MQ=255)
ggCTTGAGGAGATCAGCGGCGGCGATC‑TGTTGATCGACGGCAAACGAATGAATGACGTTCCAGCCAAAGCa > 1:1218710/1‑71 (MQ=255)
ttGAGGAGATCAGCGGCGGCGATC‑TGTTGATCGACGGCAAACg < 1:2853669/43‑1 (MQ=255)
ttGAGGAGATCAGCGGCGGCGATC‑TGTTGATCGACGGCAAACg < 1:446288/43‑1 (MQ=255)
tGAGGAGATCAGCGGCGGCGATC‑TGTTGATCGACGGCAAACGAATGAATGACGTTCCAGCCAAAGCACGc > 1:4399760/1‑70 (MQ=255)
aggagATCAGCGGCGGCGATC‑TGTTGATCGACTGCAAACGAATGAATGACGTTCCAGCCAAAGCACGCaa < 1:1740306/70‑1 (MQ=255)
aggagATCAGCGGCGGCGATC‑TGTTGATCGACGGCAAACGAATGAATGACGTTCCa > 1:2164008/1‑56 (MQ=255)
aggagATCAGCGGCGGCGATC‑TGTTGATCGACGGCAAACGAATGAATGACGTTCCa > 1:2190602/1‑56 (MQ=255)
gagaTCAGCGGCGGCGATC‑TGTTGATCGACGGCAAACGAATGAATGACGTTc < 1:2626302/52‑1 (MQ=255)
gagaTCAGCGGCGGCGATC‑TGTTGATCGACGGCAAACGAATGAATGACGTTc < 1:4989657/52‑1 (MQ=255)
aTCAGCGGCGGCGATC‑TGTTGATCGACGGCAAACGAATGAATGACGTTCCAGCCAAAg < 1:5521638/58‑1 (MQ=255)
aGCGGCGGCGATC‑TGTTGATCGACGGCAAACGAATGAATGACGTTCCAGCCAAAGCACGCAATATAGCGa < 1:3411660/70‑1 (MQ=255)
ggcggcgATC‑TGTTGATCGACGGCAAACGAATGAATGACGTTCCAGCCAAAGCACGCAATATAGCGa < 1:3307363/67‑1 (MQ=255)
ggcggcgATC‑TGTTGATCGACGGCAAACGAATGAATGACGTTCCAGCCAAAGCACGCAATATAGCGa < 1:2257622/67‑1 (MQ=255)
ggcgATC‑TGTTGATCGACGGCAAACGAATGAATGACGTTCCAGCCAAAGCACg > 1:4398509/1‑53 (MQ=255)
ggcgATC‑TGTTGATCGACGGCAAACGAATGAATGACGTTCCAGCCAAAGCACGCAATATAGCGATGGTGtt > 1:4005116/1‑71 (MQ=255)
gcgATC‑TGTTGATCGACGGCAAACGAATGAATGACGTTCCAGCCAAAGCACGCaa < 1:3359202/55‑1 (MQ=255)
gcgATC‑TGTTGATCGACGGCAAACGAATGAATGACGTTCCAGCCAAAGCACGCaa < 1:1407766/55‑1 (MQ=255)
gcgATC‑TGTTGATCGACGGCAAACGAATGAATGACGTTCCAGCCAAAGCACGCaa < 1:3354471/55‑1 (MQ=255)
gcgATC‑TGTTGATCGACGGCAAACGAATGAATGACGTTCCAGCCAAAGCACGCAATATAGCGATGGTGTTc < 1:158861/71‑1 (MQ=255)
ccgATCTTGTTGATCGACGGCAAACGAATGAATGACGTTCCAGCCAAAg > 1:2699680/2‑49 (MQ=255)
aTC‑TGTTGATCGACGGCAAACGAATGAATGACGTTCCAGCCAAAGCACGCa < 1:2900474/51‑1 (MQ=255)
|
CCGTCGGGCTGCGGTAAGTCGACCACCCTGCGCATGATTGCCGGGCTTGAGGAGATCAGCGGCGGCGATC‑TGTTGATCGACGGCAAACGAATGAATGACGTTCCAGCCAAAGCACGCAATATAGCGATGGTGTTC > minE/910872‑911006
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
