/EXTERNAL McGill EMC/variants/K006203_1_lane_gembs
BACK
SAMPLE K006203_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1158021052 |
1070229997 |
92.42 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1158021052 |
100% |
1146322994 |
98.99 % |
11698058 |
1.01 % |
| |
|
|
|
|
|
|
| Passed |
1070765599 |
92.47 % |
1065498376 |
92.95 % |
5267223 |
0.49 % |
| Filtered |
87255453 |
7.53 % |
80824618 |
7.05 % |
6430835 |
0.60 % |
| |
|
|
|
|
|
|
| q20 |
55307305 |
63.39 % |
54755634 |
67.75 % |
551671 |
8.58 % |
| q20,mq40 |
12134179 |
13.91 % |
12017669 |
14.87 % |
116510 |
1.81 % |
| q20,qd2 |
8250063 |
9.46 % |
3541395 |
4.38 % |
4708668 |
73.22 % |
| mq40 |
5480371 |
6.28 % |
5222874 |
6.46 % |
257497 |
4.00 % |
| qd2 |
3295510 |
3.78 % |
2734352 |
3.38 % |
561158 |
8.73 % |
| q20,qd2,mq40 |
2725469 |
3.12 % |
2502331 |
3.10 % |
223138 |
3.47 % |
| qd2,mq40 |
60616 |
0.07 % |
50363 |
0.06 % |
10253 |
0.16 % |
| qd2,fs60,mq40 |
779 |
0.00 % |
0 |
0.00 % |
779 |
0.01 % |
| qd2,fs60 |
380 |
0.00 % |
0 |
0.00 % |
380 |
0.01 % |
| fs60 |
336 |
0.00 % |
0 |
0.00 % |
336 |
0.01 % |
| fs60,mq40 |
274 |
0.00 % |
0 |
0.00 % |
274 |
0.00 % |
| q20,qd2,fs60 |
116 |
0.00 % |
0 |
0.00 % |
116 |
0.00 % |
| q20,qd2,fs60,mq40 |
54 |
0.00 % |
0 |
0.00 % |
54 |
0.00 % |
| q20,fs60,mq40 |
1 |
0.00 % |
0 |
0.00 % |
1 |
0.00 % |
| q20,fs60 |
0 |
0.00 % |
0 |
0.00 % |
0 |
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 |
3392070 |
27.32 % |
| Transition |
G>A |
All |
1273868 |
10.26 % |
| Transition |
T>C |
All |
3329622 |
26.81 % |
| Transition |
C>T |
All |
1278808 |
10.30 % |
| Transversion |
A>C |
All |
288030 |
2.32 % |
| Transversion |
C>A |
All |
586131 |
4.72 % |
| Transversion |
T>G |
All |
289652 |
2.33 % |
| Transversion |
G>T |
All |
580017 |
4.67 % |
| Transversion |
A>T |
All |
409902 |
3.30 % |
| Transversion |
T>A |
All |
398021 |
3.21 % |
| Transversion |
C>G |
All |
296056 |
2.38 % |
| Transversion |
G>C |
All |
296126 |
2.38 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
856992 |
16.68 % |
| Transition |
G>A |
Passed |
834256 |
16.24 % |
| Transition |
T>C |
Passed |
857554 |
16.70 % |
| Transition |
C>T |
Passed |
840062 |
16.36 % |
| Transversion |
A>C |
Passed |
214797 |
4.18 % |
| Transversion |
C>A |
Passed |
234253 |
4.56 % |
| Transversion |
T>G |
Passed |
214692 |
4.18 % |
| Transversion |
G>T |
Passed |
234693 |
4.57 % |
| Transversion |
A>T |
Passed |
202637 |
3.95 % |
| Transversion |
T>A |
Passed |
201666 |
3.93 % |
| Transversion |
C>G |
Passed |
222103 |
4.32 % |
| Transversion |
G>C |
Passed |
222623 |
4.33 % |
| |
|
|
|
|
| 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 |
2.95 |
9274368 |
3143935 |
| Passed |
1.94 |
3388864 |
1747464 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |