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 |
2,321,351 |
G→T |
42.0% |
R209S (CGC→AGC) |
cdh ← |
CDP‑diacylglycerol phosphotidylhydrolase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,321,351 | 0 | G | T | 42.0%
| 44.0
/ 58.4
| 69 | R209S (CGC→AGC) | cdh | CDP‑diacylglycerol phosphotidylhydrolase |
| Reads supporting (aligned to +/- strand): ref base G (33/7); new base T (2/27); total (35/34) |
| Fisher's exact test for biased strand distribution p-value = 1.47e-10 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
TTCGTTGTGTCGCCAGCAATACAAATGAGTTATCACTCTGCCGTACCATCGCCAGCCCGTAGCGTCCCATATGTTCCCGCGCCTCAGGTACTTCTTCTGCCAGCATCATAAATGGGCTGCGTTG > minE/2321288‑2321411
|
ttCGTTGTGTCGCCAGCAATACAAATGAGTTATCACTCTGCCGTACCATCGCCAGCCCGTAGCGTCCCa < 1:2693762/69‑1 (MQ=255)
ttCGTTGTGTCGCCAGCAATACAAATGAGTTATCACTCTGCCGTACCATCGCCAGCCCGTAGCGTCCCa < 1:572660/69‑1 (MQ=255)
cAGCAATACAAATGAGTTATCACTCTGCCGTACCATCGCCAGCCCGTAGCGTCCCATATGTTCCCgcgc < 1:870246/69‑1 (MQ=255)
cAGCAATACAAATGAGTTATCACTCTGCCGTACCATCGCCAGCCCGTAGCGTCCCATATGTTCCCgcgc < 1:2039505/69‑1 (MQ=255)
cAATACAAATGAGTTATCACTCTGCCGTATCATCGCCAGCCCGTAGCTTCCCATATGTTCCCGCGCCTc < 1:3267505/69‑1 (MQ=255)
cAATACAAATGAGTTATCACTCTGCCGTACCATCGCCAGCCCGTAGCTTCCCATATGTTCCCGCGCCTc < 1:3029631/69‑1 (MQ=255)
cAATACAAATGAGTTATCACTCTGCCGTACCATCGCCAGCCCGTAGCTTCCCATATGTTCCCGCGCCTc < 1:2540171/69‑1 (MQ=255)
cAATACAAATGAGTTATCACTCTGCCGTACCATCGCCAGCCCGTAGCTTCCCATATGTTCCCGCGCCTc < 1:2561138/69‑1 (MQ=255)
cAATACAAATGAGTTATCACTCTGCCGTACCATCGCCAGCCCGTAGCTTCCCATATGTTCCCGCGCCTc < 1:2644063/69‑1 (MQ=255)
cAATACAAATGAGTTATCACTCTGCCGTACCATCGCCAGCCCGTAGCTTCCCATATGTTCCCGCGCCTc < 1:2242366/69‑1 (MQ=255)
cAATACAAATGAGTTATCACTCTGCCGTACCATCGCCAGCCCGTAGCTTCCCATATGTTCCCGCGCCTc < 1:2048663/69‑1 (MQ=255)
cAATACAAATGAGTTATCACTCTGCCGTACCATCGCCAGCCCGTAGCTTCCCATATGTTCCCGCGCCTc < 1:2930170/69‑1 (MQ=255)
cAATACAAATGAGTTATCACTCTGCCGTACCATCGCCAGCCCGTAGCTTCCCATATGTTCCCGCGCCTc < 1:1750669/69‑1 (MQ=255)
cAATACAAATGAGTTATCACTCTGCCGTACCATCGCCAGCCCGTAGCTTCCCATATGTTCCCGCGCCTc < 1:173266/69‑1 (MQ=255)
cAATACAAATGAGTTATCACTCTGCCGTACCATCGCCAGCCCGTAGCTTCCCATATGTTCCCGCGCCTc < 1:3015932/69‑1 (MQ=255)
cAATACAAATGAGTTATCACTCTGCCGTACCATCGCCAGCCCGTAGCTTCCCATATGTTCCCGCGCCTc < 1:1628813/69‑1 (MQ=255)
cAATACAAATGAGTTATCACTCTGCCGTACCATCGCCAGCCCGTAGCTTCCCATATGTTCCCGCGCCTc < 1:3226505/69‑1 (MQ=255)
cAATACAAATGAGTTATCACTCTGCCGTACCATCGCCAGCCCGTAGCTTCCCATATGTTCCCGCGCCTc < 1:3432909/69‑1 (MQ=255)
cAATACAAATGAGTTATCACTCTGCCGTACCATCGCCAGCCCGTAGCTTCCCATATGTTCCCGCGCCTc < 1:1432194/69‑1 (MQ=255)
cAATACAAATGAGTTATCACTCTGCCGTACCATCGCCAGCCCGTAGCTTCCCATATGTTCCCGCGCCTc < 1:378572/69‑1 (MQ=255)
cAATACAAATGAGTTATCACTCTGCCGTACCATCGCCAGCCCGTAGCTTCCCATATGTTCCCGCGCCTc < 1:1377461/69‑1 (MQ=255)
cAATACAAATGAGTTATCACTCTGCCGTACCATCGCCAGCCCGTAGCTTCCCATATGTTCCCGCGCCTc < 1:1311930/69‑1 (MQ=255)
cAATACAAATGAGTTATCACTCTGCCGTACCATCGCCAGCCCGTAGCTTCCCATATGTTCCCGCGCCTc < 1:587314/69‑1 (MQ=255)
cAATACAAATGAGTTATCACTCTGCCGTACCATCGCCAGCCCGTAGCTTCCCATATGTTCCCGCGCCTc < 1:1168691/69‑1 (MQ=255)
cAATACAAATGAGTTATCACTCTGCCGTACCATCGCCAGCCCGTAGCTTCCCATATGTTCCCGCGCCTc < 1:1156014/69‑1 (MQ=255)
cAATACAAATGAGTTATCACTCTGCCGTACCATCGCCAGCCCGTAGCTTCCCATATGTTCCCGCGCCTc < 1:1021934/69‑1 (MQ=255)
cAATACAAATGAGTTATCACTCTGCCGTACCATCGCCAGCCCGTAGCTTCCCATATGTTCCCGCGCCTc < 1:1020274/69‑1 (MQ=255)
cAATACAAATGAGTTACCACTCTGCCGTACCATCGCCAGCCCGTAGCTTCCCATATGTTCCCGCGCCTc < 1:2691285/69‑1 (MQ=255)
aaTACAAATGAGTTATCACTCTGCCGTACCATCGGCTGCCCGTAGCTTCCCATATGTTCCCGCGCCTc < 1:2744117/68‑1 (MQ=255)
aCAAATGAGTTATCACTCTGCCGTACCATCGCCAGCCCGTAGCGTCCCATATGTTCCCGCGCCTCAgg > 1:966793/1‑68 (MQ=255)
aCAAATGAGTTATCACTCTGCCGTACCATCGCCAGCCCGTAGCGTCCCATATGTTCCCGCGCCTCAgg > 1:2996238/1‑68 (MQ=255)
aCAAATGAGTTATCACTCTGCCGTACCATCGCCAGCCCGTAGCGTCCCATATGTTCCCGCGCCTCAgg > 1:2320108/1‑68 (MQ=255)
aCAAATGAGTTATCACTCTGCCGTACCATCGCCAGCCCGTAGCGTCCCATATGTTCCCGCGCCTCAGGt > 1:334006/1‑69 (MQ=255)
cAAATGAGTTATCACTCTGCCGTACCATCGCCAGCCCGTAGCGTCCCATATGTTCCCGCGCCTCAGGTa > 1:3156586/1‑69 (MQ=255)
cAAATGAGTTATCACTCTGCCGTACCATCGCCAGCCCGTAGCGTCCCATATGTTCCCGCGCCTCAGGTa > 1:1640833/1‑69 (MQ=255)
cAAATGAGTTATCACTCTGCCGTACCATCGCCAGCCCGTAGCGTCCCATATGTTCCCGCGCCTCAGGTa > 1:2955067/1‑69 (MQ=255)
cAAATGAGTTATCACTCTGCCGTACCATCGCCAGCCCGTAGCGTCCCATATGTTCCCGCGCCTCAGGTa > 1:2011660/1‑69 (MQ=255)
cAAATGAGTTATCACTCTGCCGTACCATCGCCAGCCCGTAGCGTCCCATATGTTCCCGCGCCTCAGGTa > 1:144560/1‑69 (MQ=255)
cAAATGAGTTATCACTCTGCCGTACCATCGCCAGCCCGTAGCGTCCCATATGTTCCCGCGCCTCAGGTa > 1:2565032/1‑69 (MQ=255)
tGAGTTATCACTCTGCCGTACCATCGCCAGCCCGTAGCGTCCCATATGTTCCCGCGCCTc > 1:2349243/1‑60 (MQ=255)
tGAGTTATCACTCTGCCGTACCATCGCCAGCCCGTAGCGTCCCATATGTTCCCGCGCCTCAGGTActtc > 1:1196582/1‑69 (MQ=255)
tGAGTTATCACTCTGCCGTACCATCGCCAGCCCGTAGCGTCCCATATGTTCCCGCGCCTCAGGTActtc > 1:3292916/1‑69 (MQ=255)
tGAGTTATCACTCTGCCGTACCATCGCCAGCCCGTAGCGTCCCATATGTTCCCGCGCCTCAGGTActtc > 1:2357496/1‑69 (MQ=255)
tGAGTTATCACTCTGCCGTACCATCGCCAGCCCGTAGCGTCCCATATGTTCCCGCGCCTCAGGTActtc > 1:167610/1‑69 (MQ=255)
tGAGTTATCACTCTGCCGTACCATCGCCAGCCCGTAGCGTCCCATATGTTCCCGCGCCTCAGGTActt > 1:1559799/1‑68 (MQ=255)
gTTATCACTCTGCCGTACCATCGCCAGCCCGTAGCTTCCCATATGTTCCCGCGCCTc < 1:528970/57‑1 (MQ=255)
ctGCCGTACCATCGCCAGCCCGTAGCGTCCCATATGTTCCCGCGCCTCAGGTACTTCTTCTGCCAGcat < 1:2497268/69‑1 (MQ=255)
ctGCCGTACCATCGCCAGCCCGTAGCGTCCCATATGTTCCCGCGCCTCAGGTACTTCTTCTGCCAGcat < 1:1010635/69‑1 (MQ=255)
ctGCCGTACCATCGCCAGCCCGTAGCGTCCCATATGTTCCCGCGCCTCAGGTACTTCTTCTGCCAGcat < 1:1832501/69‑1 (MQ=255)
ccATCGCCAGCCCGTAGCGTCCCATATGTTCCCGCGCCTCAGGTACTTCTTCTGCCAGCATCATAAAt > 1:1490559/1‑68 (MQ=255)
ccATCGCCAGCCCGTAGCGTCCCATATGTTCCCGCGCCTCAGGTACTTCTTCTGCCAGCATCATAAATg > 1:2674131/1‑69 (MQ=255)
ccATCGCCAGCCCGTAGCGTCCCATATGTTCCCGCGCCTCAGGTACTTCTTCTGCCAGCATCATAAATg > 1:420988/1‑69 (MQ=255)
ccATCGCCAGCCCGTAGCGTCCCATATGTTCCCGCGCCTCAGGTACTTCTTCTGCCAGCATCATAAATg > 1:487657/1‑69 (MQ=255)
aTCGCCAGCCCGTAGCGTCCCATATGTTCCCGCGCCTCAGGTACTTCTTCTGCCAGCATCATAAATggg > 1:633812/1‑69 (MQ=255)
aTCGCCAGCCCGTAGCGTCCCATATGTTCCCGCGCCTCAGGTACTTCTTCTGCCAGCATCATAAATggg > 1:1247582/1‑69 (MQ=255)
gCCAGCCCGTAGCTTCCCATATGTTCCCGCGCCTc < 1:2223971/35‑1 (MQ=255)
cAGCCCGTAGCGTCCCATATGTTCCCGCGCCTCAGGTACTTCTTCTGCCAGCATCATAAATGGGCTGCg > 1:1590753/1‑69 (MQ=255)
cAGCCCGTAGCGTCCCATATGTTCCCGCGCCTCAGGTACTTCTTCTGCCAGCATCATAAATGGGCTGCg > 1:141419/1‑69 (MQ=255)
aGCCCGTAGCTTCCCATATGTTCCCGCGCCTCAGGCACTTCTTCCGCCAGCATCATaaa > 1:2992349/1‑59 (MQ=255)
aGCCCGTAGCTTCCCATATGTTCCCGCGCCTCAGGCACTTCTTCCGCCAGCATCATAAATGGGCTGCGt > 1:2650792/1‑69 (MQ=255)
aGCGTCCCATATGTTCCCGCGCCTCAGGTACTTCTTCTGCCAGCATCATAAATGGGCTGCGtt > 1:885909/1‑63 (MQ=255)
aGCGTCCCATATGTTCCCGCGCCTCAGGTACTTCTTCTGCCAGCATCATAAATGGGCTGCGTTg > 1:2378737/1‑64 (MQ=255)
aGCGTCCCATATGTTCCCGCGCCTCAGGTACTTCTTCTGCCAGCATCATAAATGGGCTGCGTTg > 1:1082960/1‑64 (MQ=255)
aGCGTCCCATATGTTCCCGCGCCTCAGGTACTTCTTCTGCCAGCATCATAAATGGGCTGCGTTg > 1:781128/1‑64 (MQ=255)
aGCGTCCCATATGTTCCCGCGCCTCAGGTACTTCTTCTGCCAGCATCATAAATGGGCTGCGTTg > 1:2673465/1‑64 (MQ=255)
aGCGTCCCATATGTTCCCGCGCCTCAGGTACTTCTTCTGCCAGCATCATAAATGGGCTGCGTTg > 1:3219899/1‑64 (MQ=255)
aGCGTCCCATATGTTCCCGCGCCTCAGGTACTTCTTCTGCCAGCATCATAAATGGGCTGCGTTg > 1:3193586/1‑64 (MQ=255)
aGCGTCCCATATGTTCCCGCGCCTCAGGTACTTCTTCTGCCAGCATCATAAATGGGCTGCGTTg > 1:3087405/1‑64 (MQ=255)
aGCGTCCAATATGTTCCCGCGCCTCAGGTACTTCTTCTGCCAGCATCATAAATGGGCTGCGTTg > 1:3039529/1‑64 (MQ=255)
|
TTCGTTGTGTCGCCAGCAATACAAATGAGTTATCACTCTGCCGTACCATCGCCAGCCCGTAGCGTCCCATATGTTCCCGCGCCTCAGGTACTTCTTCTGCCAGCATCATAAATGGGCTGCGTTG > minE/2321288‑2321411
|
| 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
