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 |
|
A5 F21 I0 R2
|
316 |
65.6 |
5147759 |
97.4% |
5013917 |
60.3 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
3,205,529 |
C→T |
36.4% |
D137D (GAC→GAT) |
ttdA → |
L‑tartrate dehydratase, alpha subunit |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 3,205,529 | 0 | C | T | 36.4%
| 55.0
/ 54.0
| 55 | D137D (GAC→GAT) | ttdA | L‑tartrate dehydratase, alpha subunit |
| Reads supporting (aligned to +/- strand): ref base C (18/17); new base T (8/12); total (26/29) |
| Fisher's exact test for biased strand distribution p-value = 5.75e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.03e-01 |
GTAGAAATTTTTGACGAAGTAAACACCGGCAAAAATACCGGTAGCGGCGTACCGTGGGTCACCTGGGACATCATCCCCGACAATGACGATGCGGAAATCGAAGTTTACATGGCAGGCGGCGGCTGCACGCTACCTG > W3110S.gb/3205461‑3205596
|
gTAGAAATTTTTGACGAAGTAAACACCGGCAAAAATACCGGTAGCGGCGTACCGTGGGTCACCTGGGAcat < 1:812903/71‑1 (MQ=255)
gTAGAAATTTTTGACGAAGTAAACACCGGCAAAAATACCGGTAGCGGCGTACCGTGGGTCACCTGGGAcat < 1:4583563/71‑1 (MQ=255)
gTAGAAATTTTTGACGAAGTAAACACCGGCAAAAATACCGGTAGCGGCGTACCGTGGGTCACCTGGGAcat < 1:1901297/71‑1 (MQ=255)
tAGAAATTTTTGACGAAGTAAACACCGGCAAAAATACCGGTAGCGGCGTACCGTGGGTCACCTGGGatat > 1:2242986/1‑70 (MQ=255)
tAGAAATTTTTGACGAAGTAAACACCGGCAAAAATACCGGTAGCGGCGTACCGTGGGTCACCTGGGAcatc < 1:4414549/71‑1 (MQ=255)
aGAAATTTTTGACGAAGTAAACACCGGCAAAAATACCGGTAGCGGCGTACCGTGGGTCACCTGGGAcatca > 1:15272/1‑71 (MQ=255)
aGAAATTTTTGACGAAGTAAACACCGGCAAAAATACCGGTAGCGGAGTACCGTGGGTCACCTGGGAcatca > 1:4512772/1‑71 (MQ=255)
aTTTTTGACGAAGTAAACACCGGCAAAAATACCGGTAGCGGCGTACCGTGGGTCACCTGGGACATCATccc > 1:3888068/1‑71 (MQ=255)
aTTTTTGACGAAGTAAACACCGGCAAAAATACCGGTAGCGGCGTACCGTGGGTCACCTGGGACATCATccc > 1:3337916/1‑71 (MQ=255)
aCGAAGTAAACACCGGCAAAAATACCGGTAGCGGCGTACCGTGGGTCACCTGGGACATCATCCCCGACAAt < 1:5137036/71‑1 (MQ=255)
cGAAGTAAACACCGGCAAAAATACCGGTAGCGGCGTACCGTGGGTCACCTGGGACATCATCCCCGACAATg < 1:1136345/71‑1 (MQ=255)
aaGTAAACACCGGCAAAAATACCGGTAGCGGCGTACCGTGGGTCACCTGGGACATCATCCCCGACAATGAc < 1:1756974/71‑1 (MQ=255)
aGTAAACACCGGCAAAAATACCGGTAGCGGCGTACCGTGGGTCACCTGGGATATCATCCCCGACAATGAc > 1:1011521/1‑70 (MQ=255)
gTAAACACCGGCAAAAATACCGGTAGCGGCGTACCGTGGGTCACCTGGGACATCATCCCCGACAATGACGa > 1:4943456/1‑71 (MQ=255)
tAAACACCGGCAAAAATACCGGTAGCGGCGTACCGTGGGTCACCTGGGAcat < 1:3532849/52‑1 (MQ=255)
aaaCACCGGCAAAAATACCGGTAGCGGCGTACCGTGGGTCACCTGGGACATCATCCCCGACAATGAc > 1:4304879/1‑67 (MQ=255)
aaCACCGGCAAAAATACCGGTAGCGGCGTACCGTGGGTCACCTGGGACATCATCCCCGACAATGACGATGc > 1:4519878/1‑71 (MQ=255)
acacCGGCAAAAATACCGGTAGCGGCGTACCGTGGGTCACCTGGGATATCATCCCCGACAATGACGATGCg > 1:4338686/1‑71 (MQ=255)
acCGGCAAAAATACCGGTAGCGGCGTACCGTGGGTCACCTGGGACATCATCCCCGACAATGACGATGCgg > 1:4222876/1‑70 (MQ=255)
acCGGCAAAAATACCGGTAGCGGCGTACCGTGGGTCACCTGGGACATCATCCCCGACAATGACGATGCgg > 1:5051416/1‑70 (MQ=255)
acCCGCAAAAATACCGGTAGCGGCGTACCGTGGGTCACCTGGGACATCATCCCCGACAATGACGATGCgg > 1:5027723/1‑70 (MQ=255)
cGGCAAAAATACCGGTAGCGGCGTACCGTGGGTCACCTGGGATATCATCCCCGACAATGACGATGCGGaaa < 1:3252294/71‑1 (MQ=255)
aaTACCGGTAGCGGCGTACCGTGGGTCACCTGGGATATCATCCCCGa > 1:3238567/1‑47 (MQ=255)
aaTACCGGTAGCGGCGTACCGTGGGTCACCTGGGATATCATCCCCGACAATGACGATGCGGAAATCGAAGt > 1:2046670/1‑71 (MQ=255)
aTACCGGTAGCGGCGTACCGTGGGTCACCTGGGACATCATCCCCGACAATGACGATGCGGAAATCGAAGtt < 1:2609965/71‑1 (MQ=255)
aCCGGTAGCGGCGTACCGTGGGTCACCTGGGACATCATCCCCGACAATGACGATGCGGAAATCGAAGTTTa > 1:3323404/1‑71 (MQ=255)
ccGGTAGCGGCGTACCGTGGGTCACCTGGGATATCATCCCCGACAATGACGATGCGGAAATCGAAGTTTa < 1:3955588/70‑1 (MQ=255)
ccGGTAGCGGCGTACCGTGGGTCACCTGGGATATCATCCCCGACAATGACGATGCGGAAATCGAAGTTTa < 1:2981493/70‑1 (MQ=255)
ccGGTAGCGGCGTACCGTGGGTCACCTGGGACATCATCCCCGACAATGACGATGCGGAAATCGAAGTTTa > 1:2919799/1‑70 (MQ=255)
ccGGTAGCGGCGTACCGTGGGTCACCTGGGACATCATCCCCGACAATGACGATGCGGAAATCGAAGTTTAc < 1:3835093/71‑1 (MQ=255)
cGGTAGCGGCGTACCGTGGGTCACCTGGGACATCATCCCCGACAATGACGATGCGGAAATCGAAGTTTa < 1:3648517/69‑1 (MQ=255)
gTAGCGGCGTACCGTGGGTCACCTGGGATATCATCCCCGACAATGACGATGCGGaaa > 1:1337376/1‑57 (MQ=255)
tAGCGGCGTACCGTGGGTCACCTGGGATATCATCCCCGACAATGACGATGCGGAAATCGAAGTTTACAttg > 1:5071003/1‑69 (MQ=255)
tAGCGGCGTACCGTGGGTCACCTGGGACATCATCCCCGACAATGACGATGCGGAAATCGAAGTTTACa > 1:660248/1‑68 (MQ=255)
tAGCGGCGTACCGTGGGTCACCTGGGACATCATCCCCGACAATGACGATGCGGAAATCGAAGTTTACa > 1:4593763/1‑68 (MQ=255)
gcggcgTACCGTGGGTCACCTGGGACATCATCCCCGACAATGACGATGCGGAAATCGAAGTTTACATGGc < 1:3217897/70‑1 (MQ=255)
gcggcgTACCGTGGGTCACCTGGGACATCATCCCCGACAATGACGATGCGGAAATCGAAGTTTACATGGCa < 1:3588687/71‑1 (MQ=255)
gcggcgTACCGTGGGTCACCTGGGACATCATCCCCGACAATGACGATGCGGAAATCGAAGTTTACATGGCa < 1:4327156/71‑1 (MQ=255)
gcggcgTACCGTGGGTCACCTGGGACATCATCCCCGACAATGACGATGCGGAAATCGAAGTTTACATGGCa < 1:1621175/71‑1 (MQ=255)
gcggcgTACCGTGGGTCACCTGGGACATCATCCCCGACAATGACGATGCGGAAATCGAAGTTTACATGGCa < 1:1488700/71‑1 (MQ=255)
ggcgTACCGTGGGTCACCTGGGACATCATCCCCGACAATGACGATGCGGAAATCGAAGTTTACATGGCAgg > 1:1258016/1‑71 (MQ=255)
gcgTACCGTGGGTCACCTGGGATATCATCCCCGAc < 1:4961040/35‑1 (MQ=255)
gcgTACCGTGGGTCACCTGGGATATCATCCCCGAc < 1:257998/35‑1 (MQ=255)
gcgTACCGTGGGTCACCTGGGATATCATCCCCGAc < 1:683423/35‑1 (MQ=255)
gcgTACCGTGGGTCACCTGGGATATCATCCCCGACAATGACGATGCGGAAATCGAAGTTTACATGGCAggc < 1:3021870/71‑1 (MQ=255)
gTACCGTGGGTCACCTGGGATATCATCCCCGACaa > 1:4594016/1‑35 (MQ=255)
tACCGTGGGTCACCTGGGACATCATCCCCGACAATGAc < 1:2397160/38‑1 (MQ=255)
tACCGTGGGTCACCTGGGACATCATCCCCGACAATGAc < 1:4910949/38‑1 (MQ=255)
tACCGTGGGTCACCTGGGACATCATCCCCGACAATGACGATGCGGAAATCGAAGTTTACATGGCAggcggc < 1:2584693/71‑1 (MQ=255)
ccGTGGGTCACCTGGGATATCATCCCCGACAATGACGATGCGGAAATCGAAGTTTa < 1:1047854/56‑1 (MQ=255)
ccGTGGGTCACCTGGGATATCATCCCCGACAATGACGATGCGGAAATCGAAGTTTa < 1:4747775/56‑1 (MQ=255)
ccGTGGGTCACCTGGGATATCATCCCCGACAATGACGATGCGGAAATCGAAGTTTa < 1:4421898/56‑1 (MQ=255)
ccGTGGGTCACCTGGGATATCATCCCCGACAATGACGATGCGGAAATCGAAGTTTa < 1:3209808/56‑1 (MQ=255)
tGGGTCACCTGGGATATCATCCCCGACAATGACGATGCGGAAATCGAAGTTTACATGGCAGGCGGCGGCTg > 1:1373261/1‑71 (MQ=255)
tGGGTCACCTGGGACATCATCCCCGACAATGACGATGCGGAAATCg < 1:2161501/46‑1 (MQ=255)
ggTCACCTGGGACATCATCCCCGACAATGACGATGCGGAAATCGaa > 1:3442703/1‑46 (MQ=255)
gTCACCTGGGATATCATCCCCGACAATGACGATGCGGAAATCGAAGTTTACATGGCAgg < 1:2706830/59‑1 (MQ=255)
cTGGGACATCATCCCCGACAATGACGATGCGGAAATCGAAGtt < 1:4559152/43‑1 (MQ=255)
gggACATCATCCCCGACAATGACGATGCGGAAATCGAAGTTTACa > 1:3758760/1‑45 (MQ=255)
gggACATCATCCCCGACAATGACGATGCGGAAATCGAAGTTTACATGGCAGGCGGCGGCTGCACGCTACCt > 1:77203/1‑71 (MQ=255)
gggACATCATCCCCGACAATGACGATGCGGAAATCGAAGTTTACATGGCAGGCGGCGGCTGCACGATAc > 1:2296214/1‑69 (MQ=255)
gACATCATCCCCGACAATGACGATGCGGAAATCGAAGTTTACATGGCAGGCGGCGGCTGCACGCTACCTg > 1:1949057/1‑70 (MQ=255)
aCATCATCCCCGACAATGACGATGCGGAAATCGAAGTTTACATGGCAggcggcgg < 1:3456980/55‑1 (MQ=255)
|
GTAGAAATTTTTGACGAAGTAAACACCGGCAAAAATACCGGTAGCGGCGTACCGTGGGTCACCTGGGACATCATCCCCGACAATGACGATGCGGAAATCGAAGTTTACATGGCAGGCGGCGGCTGCACGCTACCTG > W3110S.gb/3205461‑3205596
|
| 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
