/EXTERNAL McGill EMC/variants/K006157_1_lane_gembs
BACK
SAMPLE K006157_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1142794804 |
488166601 |
42.72 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1142794804 |
100% |
1130161215 |
98.89 % |
12633589 |
1.11 % |
| |
|
|
|
|
|
|
| Passed |
490741692 |
42.94 % |
486547949 |
43.05 % |
4193743 |
0.85 % |
| Filtered |
652053112 |
57.06 % |
643613266 |
56.95 % |
8439846 |
1.72 % |
| |
|
|
|
|
|
|
| q20 |
617351481 |
94.68 % |
614843981 |
95.53 % |
2507500 |
29.71 % |
| q20,qd2 |
15519159 |
2.38 % |
9909612 |
1.54 % |
5609547 |
66.47 % |
| q20,mq40 |
14040281 |
2.15 % |
13946199 |
2.17 % |
94082 |
1.11 % |
| q20,qd2,mq40 |
3759294 |
0.58 % |
3675727 |
0.57 % |
83567 |
0.99 % |
| mq40 |
793894 |
0.12 % |
670808 |
0.10 % |
123086 |
1.46 % |
| qd2 |
560981 |
0.09 % |
544729 |
0.08 % |
16252 |
0.19 % |
| qd2,mq40 |
27424 |
0.00 % |
22210 |
0.00 % |
5214 |
0.06 % |
| qd2,fs60,mq40 |
292 |
0.00 % |
0 |
0.00 % |
292 |
0.00 % |
| fs60,mq40 |
151 |
0.00 % |
0 |
0.00 % |
151 |
0.00 % |
| qd2,fs60 |
95 |
0.00 % |
0 |
0.00 % |
95 |
0.00 % |
| q20,qd2,fs60,mq40 |
36 |
0.00 % |
0 |
0.00 % |
36 |
0.00 % |
| fs60 |
15 |
0.00 % |
0 |
0.00 % |
15 |
0.00 % |
| q20,qd2,fs60 |
9 |
0.00 % |
0 |
0.00 % |
9 |
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 |
4348656 |
30.25 % |
| Transition |
G>A |
All |
1166048 |
8.11 % |
| Transition |
T>C |
All |
3707999 |
25.79 % |
| Transition |
C>T |
All |
1200036 |
8.35 % |
| Transversion |
A>C |
All |
331258 |
2.30 % |
| Transversion |
C>A |
All |
787357 |
5.48 % |
| Transversion |
T>G |
All |
386885 |
2.69 % |
| Transversion |
G>T |
All |
753388 |
5.24 % |
| Transversion |
A>T |
All |
515619 |
3.59 % |
| Transversion |
T>A |
All |
567795 |
3.95 % |
| Transversion |
C>G |
All |
323480 |
2.25 % |
| Transversion |
G>C |
All |
287930 |
2.00 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
348951 |
16.31 % |
| Transition |
G>A |
Passed |
331824 |
15.51 % |
| Transition |
T>C |
Passed |
346302 |
16.18 % |
| Transition |
C>T |
Passed |
336815 |
15.74 % |
| Transversion |
A>C |
Passed |
97789 |
4.57 % |
| Transversion |
C>A |
Passed |
101287 |
4.73 % |
| Transversion |
T>G |
Passed |
98343 |
4.60 % |
| Transversion |
G>T |
Passed |
101892 |
4.76 % |
| Transversion |
A>T |
Passed |
88560 |
4.14 % |
| Transversion |
T>A |
Passed |
88253 |
4.12 % |
| Transversion |
C>G |
Passed |
99634 |
4.66 % |
| Transversion |
G>C |
Passed |
100020 |
4.67 % |
| |
|
|
|
|
| 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 |
2.64 |
10422739 |
3953712 |
| Passed |
1.76 |
1363892 |
775778 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |