/EXTERNAL McGill EMC/variants/K006217_1_lane_gembs
BACK
SAMPLE K006217_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1171682257 |
1096705876 |
93.60 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1171682257 |
100% |
1156348310 |
98.69 % |
15333947 |
1.31 % |
| |
|
|
|
|
|
|
| Passed |
1097383444 |
93.66 % |
1093419917 |
94.56 % |
3963527 |
0.36 % |
| Filtered |
74298813 |
6.34 % |
62928393 |
5.44 % |
11370420 |
1.04 % |
| |
|
|
|
|
|
|
| q20 |
33857024 |
45.57 % |
32980220 |
52.41 % |
876804 |
7.71 % |
| q20,qd2 |
12807886 |
17.24 % |
4289942 |
6.82 % |
8517944 |
74.91 % |
| q20,mq40 |
11556726 |
15.55 % |
11339574 |
18.02 % |
217152 |
1.91 % |
| qd2 |
7248335 |
9.76 % |
6176433 |
9.82 % |
1071902 |
9.43 % |
| mq40 |
5990315 |
8.06 % |
5667661 |
9.01 % |
322654 |
2.84 % |
| q20,qd2,mq40 |
2728350 |
3.67 % |
2383764 |
3.79 % |
344586 |
3.03 % |
| qd2,mq40 |
107650 |
0.14 % |
90799 |
0.14 % |
16851 |
0.15 % |
| qd2,fs60 |
728 |
0.00 % |
0 |
0.00 % |
728 |
0.01 % |
| qd2,fs60,mq40 |
663 |
0.00 % |
0 |
0.00 % |
663 |
0.01 % |
| fs60 |
562 |
0.00 % |
0 |
0.00 % |
562 |
0.00 % |
| fs60,mq40 |
326 |
0.00 % |
0 |
0.00 % |
326 |
0.00 % |
| q20,qd2,fs60 |
175 |
0.00 % |
0 |
0.00 % |
175 |
0.00 % |
| q20,qd2,fs60,mq40 |
71 |
0.00 % |
0 |
0.00 % |
71 |
0.00 % |
| q20,fs60,mq40 |
2 |
0.00 % |
0 |
0.00 % |
2 |
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 |
5777682 |
33.89 % |
| Transition |
G>A |
All |
1034122 |
6.07 % |
| Transition |
T>C |
All |
5577850 |
32.72 % |
| Transition |
C>T |
All |
1043501 |
6.12 % |
| Transversion |
A>C |
All |
305317 |
1.79 % |
| Transversion |
C>A |
All |
679117 |
3.98 % |
| Transversion |
T>G |
All |
311727 |
1.83 % |
| Transversion |
G>T |
All |
678213 |
3.98 % |
| Transversion |
A>T |
All |
540207 |
3.17 % |
| Transversion |
T>A |
All |
542131 |
3.18 % |
| Transversion |
C>G |
All |
280714 |
1.65 % |
| Transversion |
G>C |
All |
278129 |
1.63 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
990530 |
21.73 % |
| Transition |
G>A |
Passed |
632746 |
13.88 % |
| Transition |
T>C |
Passed |
964652 |
21.17 % |
| Transition |
C>T |
Passed |
634366 |
13.92 % |
| Transversion |
A>C |
Passed |
172134 |
3.78 % |
| Transversion |
C>A |
Passed |
172969 |
3.80 % |
| Transversion |
T>G |
Passed |
173117 |
3.80 % |
| Transversion |
G>T |
Passed |
171213 |
3.76 % |
| Transversion |
A>T |
Passed |
153217 |
3.36 % |
| Transversion |
T>A |
Passed |
153651 |
3.37 % |
| Transversion |
C>G |
Passed |
169573 |
3.72 % |
| Transversion |
G>C |
Passed |
169305 |
3.71 % |
| |
|
|
|
|
| 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 |
3.72 |
13433155 |
3615555 |
| Passed |
2.41 |
3222294 |
1335179 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |