/EXTERNAL McGill EMC/variants/K006199_1_lane_gembs
BACK
SAMPLE K006199_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1139119937 |
180493398 |
15.84 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1139119937 |
100% |
1125350020 |
98.79 % |
13769917 |
1.21 % |
| |
|
|
|
|
|
|
| Passed |
184263609 |
16.18 % |
179311451 |
15.93 % |
4952158 |
2.69 % |
| Filtered |
954856328 |
83.82 % |
946038569 |
84.07 % |
8817759 |
4.79 % |
| |
|
|
|
|
|
|
| q20 |
907410041 |
95.03 % |
904234219 |
95.58 % |
3175822 |
36.02 % |
| q20,qd2 |
26018035 |
2.72 % |
20673378 |
2.19 % |
5344657 |
60.61 % |
| q20,mq40 |
15742262 |
1.65 % |
15643570 |
1.65 % |
98692 |
1.12 % |
| q20,qd2,mq40 |
5309927 |
0.56 % |
5221762 |
0.55 % |
88165 |
1.00 % |
| mq40 |
312041 |
0.03 % |
208371 |
0.02 % |
103670 |
1.18 % |
| qd2 |
47312 |
0.00 % |
44026 |
0.00 % |
3286 |
0.04 % |
| qd2,mq40 |
16466 |
0.00 % |
13243 |
0.00 % |
3223 |
0.04 % |
| qd2,fs60,mq40 |
124 |
0.00 % |
0 |
0.00 % |
124 |
0.00 % |
| fs60,mq40 |
69 |
0.00 % |
0 |
0.00 % |
69 |
0.00 % |
| qd2,fs60 |
34 |
0.00 % |
0 |
0.00 % |
34 |
0.00 % |
| q20,qd2,fs60,mq40 |
9 |
0.00 % |
0 |
0.00 % |
9 |
0.00 % |
| fs60 |
7 |
0.00 % |
0 |
0.00 % |
7 |
0.00 % |
| q20,qd2,fs60 |
1 |
0.00 % |
0 |
0.00 % |
1 |
0.00 % |
| q20,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 |
3845535 |
24.53 % |
| Transition |
G>A |
All |
1178664 |
7.52 % |
| Transition |
T>C |
All |
3677109 |
23.46 % |
| Transition |
C>T |
All |
1177727 |
7.51 % |
| Transversion |
A>C |
All |
238229 |
1.52 % |
| Transversion |
C>A |
All |
1695415 |
10.82 % |
| Transversion |
T>G |
All |
262920 |
1.68 % |
| Transversion |
G>T |
All |
1643791 |
10.49 % |
| Transversion |
A>T |
All |
733629 |
4.68 % |
| Transversion |
T>A |
All |
758485 |
4.84 % |
| Transversion |
C>G |
All |
239997 |
1.53 % |
| Transversion |
G>C |
All |
223578 |
1.43 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
198396 |
14.50 % |
| Transition |
G>A |
Passed |
200180 |
14.64 % |
| Transition |
T>C |
Passed |
204317 |
14.94 % |
| Transition |
C>T |
Passed |
205390 |
15.02 % |
| Transversion |
A>C |
Passed |
69026 |
5.05 % |
| Transversion |
C>A |
Passed |
75250 |
5.50 % |
| Transversion |
T>G |
Passed |
68483 |
5.01 % |
| Transversion |
G>T |
Passed |
76175 |
5.57 % |
| Transversion |
A>T |
Passed |
66935 |
4.89 % |
| Transversion |
T>A |
Passed |
66462 |
4.86 % |
| Transversion |
C>G |
Passed |
68339 |
5.00 % |
| Transversion |
G>C |
Passed |
68839 |
5.03 % |
| |
|
|
|
|
| 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 |
1.70 |
9879035 |
5796044 |
| Passed |
1.44 |
808283 |
559509 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |