/EXTERNAL McGill EMC/variants/K006197_1_lane_gembs
BACK
SAMPLE K006197_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1169105536 |
1074103760 |
91.87 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1169105536 |
100% |
1149008660 |
98.28 % |
20096876 |
1.72 % |
| |
|
|
|
|
|
|
| Passed |
1074979786 |
91.95 % |
1070238330 |
93.14 % |
4741456 |
0.44 % |
| Filtered |
94125750 |
8.05 % |
78770330 |
6.86 % |
15355420 |
1.43 % |
| |
|
|
|
|
|
|
| q20 |
47697565 |
50.67 % |
46368558 |
58.87 % |
1329007 |
8.65 % |
| q20,qd2 |
17427893 |
18.52 % |
5854716 |
7.43 % |
11573177 |
75.37 % |
| q20,mq40 |
12456830 |
13.23 % |
12202873 |
15.49 % |
253957 |
1.65 % |
| qd2 |
7853323 |
8.34 % |
6355549 |
8.07 % |
1497774 |
9.75 % |
| mq40 |
5731984 |
6.09 % |
5410876 |
6.87 % |
321108 |
2.09 % |
| q20,qd2,mq40 |
2889247 |
3.07 % |
2521377 |
3.20 % |
367870 |
2.40 % |
| qd2,mq40 |
67910 |
0.07 % |
56381 |
0.07 % |
11529 |
0.08 % |
| qd2,fs60,mq40 |
407 |
0.00 % |
0 |
0.00 % |
407 |
0.00 % |
| qd2,fs60 |
277 |
0.00 % |
0 |
0.00 % |
277 |
0.00 % |
| fs60,mq40 |
151 |
0.00 % |
0 |
0.00 % |
151 |
0.00 % |
| fs60 |
118 |
0.00 % |
0 |
0.00 % |
118 |
0.00 % |
| q20,qd2,fs60,mq40 |
23 |
0.00 % |
0 |
0.00 % |
23 |
0.00 % |
| q20,qd2,fs60 |
21 |
0.00 % |
0 |
0.00 % |
21 |
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 |
7716956 |
35.42 % |
| Transition |
G>A |
All |
1132342 |
5.20 % |
| Transition |
T>C |
All |
7428066 |
34.09 % |
| Transition |
C>T |
All |
1144041 |
5.25 % |
| Transversion |
A>C |
All |
367054 |
1.68 % |
| Transversion |
C>A |
All |
855359 |
3.93 % |
| Transversion |
T>G |
All |
375933 |
1.73 % |
| Transversion |
G>T |
All |
854515 |
3.92 % |
| Transversion |
A>T |
All |
624140 |
2.86 % |
| Transversion |
T>A |
All |
627401 |
2.88 % |
| Transversion |
C>G |
All |
333958 |
1.53 % |
| Transversion |
G>C |
All |
327106 |
1.50 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
1245684 |
24.54 % |
| Transition |
G>A |
Passed |
630373 |
12.42 % |
| Transition |
T>C |
Passed |
1199903 |
23.64 % |
| Transition |
C>T |
Passed |
630572 |
12.42 % |
| Transversion |
A>C |
Passed |
179409 |
3.53 % |
| Transversion |
C>A |
Passed |
175492 |
3.46 % |
| Transversion |
T>G |
Passed |
180135 |
3.55 % |
| Transversion |
G>T |
Passed |
174603 |
3.44 % |
| Transversion |
A>T |
Passed |
156907 |
3.09 % |
| Transversion |
T>A |
Passed |
157294 |
3.10 % |
| Transversion |
C>G |
Passed |
172987 |
3.41 % |
| Transversion |
G>C |
Passed |
172442 |
3.40 % |
| |
|
|
|
|
| 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 |
3.99 |
17421405 |
4365466 |
| Passed |
2.71 |
3706532 |
1369269 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |