/EXTERNAL McGill EMC/variants/K006156_1_lane_gembs
BACK
SAMPLE K006156_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1141161105 |
154213616 |
13.51 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1141161105 |
100% |
1121358643 |
98.26 % |
19802462 |
1.74 % |
| |
|
|
|
|
|
|
| Passed |
159677052 |
13.99 % |
153066556 |
13.65 % |
6610496 |
4.14 % |
| Filtered |
981484053 |
86.01 % |
968292087 |
86.35 % |
13191966 |
8.26 % |
| |
|
|
|
|
|
|
| q20 |
928706012 |
94.62 % |
925354239 |
95.57 % |
3351773 |
25.41 % |
| q20,qd2 |
28566027 |
2.91 % |
19068763 |
1.97 % |
9497264 |
71.99 % |
| q20,mq40 |
18381885 |
1.87 % |
18281120 |
1.89 % |
100765 |
0.76 % |
| q20,qd2,mq40 |
5442711 |
0.55 % |
5340499 |
0.55 % |
102212 |
0.77 % |
| mq40 |
350283 |
0.04 % |
215198 |
0.02 % |
135085 |
1.02 % |
| qd2 |
24358 |
0.00 % |
22131 |
0.00 % |
2227 |
0.02 % |
| qd2,mq40 |
12588 |
0.00 % |
10137 |
0.00 % |
2451 |
0.02 % |
| qd2,fs60,mq40 |
105 |
0.00 % |
0 |
0.00 % |
105 |
0.00 % |
| fs60,mq40 |
39 |
0.00 % |
0 |
0.00 % |
39 |
0.00 % |
| qd2,fs60 |
26 |
0.00 % |
0 |
0.00 % |
26 |
0.00 % |
| q20,qd2,fs60,mq40 |
11 |
0.00 % |
0 |
0.00 % |
11 |
0.00 % |
| fs60 |
8 |
0.00 % |
0 |
0.00 % |
8 |
0.00 % |
| q20,fs60 |
0 |
0.00 % |
0 |
0.00 % |
0 |
0.00 % |
| q20,qd2,fs60 |
0 |
0.00 % |
0 |
0.00 % |
0 |
0.00 % |
| q20,fs60,mq40 |
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 |
4416504 |
20.35 % |
| Transition |
G>A |
All |
981110 |
4.52 % |
| Transition |
T>C |
All |
4119723 |
18.98 % |
| Transition |
C>T |
All |
987800 |
4.55 % |
| Transversion |
A>C |
All |
312184 |
1.44 % |
| Transversion |
C>A |
All |
4119580 |
18.98 % |
| Transversion |
T>G |
All |
356271 |
1.64 % |
| Transversion |
G>T |
All |
4045370 |
18.64 % |
| Transversion |
A>T |
All |
861753 |
3.97 % |
| Transversion |
T>A |
All |
902864 |
4.16 % |
| Transversion |
C>G |
All |
314083 |
1.45 % |
| Transversion |
G>C |
All |
285223 |
1.31 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
188223 |
14.55 % |
| Transition |
G>A |
Passed |
178840 |
13.83 % |
| Transition |
T>C |
Passed |
188401 |
14.57 % |
| Transition |
C>T |
Passed |
182680 |
14.12 % |
| Transversion |
A>C |
Passed |
67951 |
5.25 % |
| Transversion |
C>A |
Passed |
75598 |
5.85 % |
| Transversion |
T>G |
Passed |
68351 |
5.28 % |
| Transversion |
G>T |
Passed |
76192 |
5.89 % |
| Transversion |
A>T |
Passed |
64110 |
4.96 % |
| Transversion |
T>A |
Passed |
63936 |
4.94 % |
| Transversion |
C>G |
Passed |
69637 |
5.38 % |
| Transversion |
G>C |
Passed |
69427 |
5.37 % |
| |
|
|
|
|
| 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 |
0.94 |
10505137 |
11197328 |
| Passed |
1.33 |
738144 |
555202 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |