/cemt/variants/A54762_3_lane_gembs
BACK
SAMPLE A54762_3_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1164755236 |
541786216 |
46.52 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1164755236 |
100% |
1137057621 |
97.62 % |
27697615 |
2.38 % |
| |
|
|
|
|
|
|
| Passed |
546125060 |
46.89 % |
539998435 |
47.49 % |
6126625 |
1.12 % |
| Filtered |
618630176 |
53.11 % |
597059186 |
52.51 % |
21570990 |
3.95 % |
| |
|
|
|
|
|
|
| q20 |
548967202 |
88.74 % |
542287604 |
90.83 % |
6679598 |
30.97 % |
| q20,qd2 |
37011341 |
5.98 % |
23049497 |
3.86 % |
13961844 |
64.73 % |
| qd2 |
13940762 |
2.25 % |
13730408 |
2.30 % |
210354 |
0.98 % |
| q20,mq40 |
12872485 |
2.08 % |
12609343 |
2.11 % |
263142 |
1.22 % |
| q20,qd2,mq40 |
4131706 |
0.67 % |
3876465 |
0.65 % |
255241 |
1.18 % |
| mq40 |
1609920 |
0.26 % |
1436749 |
0.24 % |
173171 |
0.80 % |
| qd2,mq40 |
81159 |
0.01 % |
69120 |
0.01 % |
12039 |
0.06 % |
| q20,qd2,fs60 |
5137 |
0.00 % |
0 |
0.00 % |
5137 |
0.02 % |
| qd2,fs60 |
4950 |
0.00 % |
0 |
0.00 % |
4950 |
0.02 % |
| fs60 |
3342 |
0.00 % |
0 |
0.00 % |
3342 |
0.02 % |
| qd2,fs60,mq40 |
1469 |
0.00 % |
0 |
0.00 % |
1469 |
0.01 % |
| fs60,mq40 |
429 |
0.00 % |
0 |
0.00 % |
429 |
0.00 % |
| q20,qd2,fs60,mq40 |
266 |
0.00 % |
0 |
0.00 % |
266 |
0.00 % |
| q20,fs60 |
7 |
0.00 % |
0 |
0.00 % |
7 |
0.00 % |
| q20,fs60,mq40 |
1 |
0.00 % |
0 |
0.00 % |
1 |
0.00 % |
Coverage and Quality
| Coverage Variants |
Quality Variants |
 |
 |
Filtering Criteria Distribution
| Phred scale strand bias estimated using Fisher's Exact Test. |
 |
| Allele-specific call confidence normalized by depth of sample reads supporting the allele. Variants. |
Allele-specific call confidence normalized by depth of sample reads supporting the allele. Non-Variants. |
 |
 |
| Root Mean Square of the mapping quality of reads. Variants. |
Root Mean Square of the mapping quality of reads. Non-Variants. |
 |
 |
Mutations
| Type |
Mutation |
Status |
# |
% |
| Transition |
A>G |
All |
8805280 |
28.35 % |
| Transition |
G>A |
All |
2540322 |
8.18 % |
| Transition |
T>C |
All |
7157018 |
23.04 % |
| Transition |
C>T |
All |
2569865 |
8.27 % |
| Transversion |
A>C |
All |
744142 |
2.40 % |
| Transversion |
C>A |
All |
2032529 |
6.54 % |
| Transversion |
T>G |
All |
851631 |
2.74 % |
| Transversion |
G>T |
All |
1932147 |
6.22 % |
| Transversion |
A>T |
All |
1549595 |
4.99 % |
| Transversion |
T>A |
All |
1661286 |
5.35 % |
| Transversion |
C>G |
All |
655295 |
2.11 % |
| Transversion |
G>C |
All |
565479 |
1.82 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
514091 |
20.24 % |
| Transition |
G>A |
Passed |
360569 |
14.20 % |
| Transition |
T>C |
Passed |
467865 |
18.42 % |
| Transition |
C>T |
Passed |
364709 |
14.36 % |
| Transversion |
A>C |
Passed |
102909 |
4.05 % |
| Transversion |
C>A |
Passed |
111545 |
4.39 % |
| Transversion |
T>G |
Passed |
106153 |
4.18 % |
| Transversion |
G>T |
Passed |
110398 |
4.35 % |
| Transversion |
A>T |
Passed |
101960 |
4.02 % |
| Transversion |
T>A |
Passed |
103598 |
4.08 % |
| Transversion |
C>G |
Passed |
98673 |
3.89 % |
| Transversion |
G>C |
Passed |
96977 |
3.82 % |
| |
|
|
|
|
| Transition |
A>G |
dbSNPAll |
0 |
0.00 % |
| Transition |
G>A |
dbSNPAll |
0 |
0.00 % |
| Transition |
T>C |
dbSNPAll |
0 |
0.00 % |
| Transition |
C>T |
dbSNPAll |
0 |
0.00 % |
| Transversion |
A>C |
dbSNPAll |
0 |
0.00 % |
| Transversion |
C>A |
dbSNPAll |
0 |
0.00 % |
| Transversion |
T>G |
dbSNPAll |
0 |
0.00 % |
| Transversion |
G>T |
dbSNPAll |
0 |
0.00 % |
| Transversion |
A>T |
dbSNPAll |
0 |
0.00 % |
| Transversion |
T>A |
dbSNPAll |
0 |
0.00 % |
| Transversion |
C>G |
dbSNPAll |
0 |
0.00 % |
| Transversion |
G>C |
dbSNPAll |
0 |
0.00 % |
| |
|
|
|
|
| Transition |
A>G |
dbSNPPassed |
0 |
0.00 % |
| Transition |
G>A |
dbSNPPassed |
0 |
0.00 % |
| Transition |
T>C |
dbSNPPassed |
0 |
0.00 % |
| Transition |
C>T |
dbSNPPassed |
0 |
0.00 % |
| Transversion |
A>C |
dbSNPPassed |
0 |
0.00 % |
| Transversion |
C>A |
dbSNPPassed |
0 |
0.00 % |
| Transversion |
T>G |
dbSNPPassed |
0 |
0.00 % |
| Transversion |
G>T |
dbSNPPassed |
0 |
0.00 % |
| Transversion |
A>T |
dbSNPPassed |
0 |
0.00 % |
| Transversion |
T>A |
dbSNPPassed |
0 |
0.00 % |
| Transversion |
C>G |
dbSNPPassed |
0 |
0.00 % |
| Transversion |
G>C |
dbSNPPassed |
0 |
0.00 % |
| |
|
|
|
|
Ti/Tv Ratio
| Status |
Ratio |
Transitions |
Transversions |
| All |
2.11 |
21072485 |
9992104 |
| Passed |
2.05 |
1707234 |
832213 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |