/EXTERNAL McGill EMC/variants/K006221_1_lane_gembs
BACK
SAMPLE K006221_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1122944816 |
46851227 |
4.17 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1122944816 |
100% |
1110672207 |
98.91 % |
12272609 |
1.09 % |
| |
|
|
|
|
|
|
| Passed |
51438385 |
4.58 % |
46080545 |
4.15 % |
5357840 |
10.42 % |
| Filtered |
1071506431 |
95.42 % |
1064591662 |
95.85 % |
6914769 |
13.44 % |
| |
|
|
|
|
|
|
| q20 |
1006936000 |
93.97 % |
1003992908 |
94.31 % |
2943092 |
42.56 % |
| q20,qd2 |
42837369 |
4.00 % |
39072298 |
3.67 % |
3765071 |
54.45 % |
| q20,mq40 |
15357952 |
1.43 % |
15288723 |
1.44 % |
69229 |
1.00 % |
| q20,qd2,mq40 |
6165958 |
0.58 % |
6117747 |
0.57 % |
48211 |
0.70 % |
| mq40 |
182838 |
0.02 % |
97447 |
0.01 % |
85391 |
1.23 % |
| qd2 |
16228 |
0.00 % |
14661 |
0.00 % |
1567 |
0.02 % |
| qd2,mq40 |
9940 |
0.00 % |
7878 |
0.00 % |
2062 |
0.03 % |
| qd2,fs60,mq40 |
70 |
0.00 % |
0 |
0.00 % |
70 |
0.00 % |
| qd2,fs60 |
33 |
0.00 % |
0 |
0.00 % |
33 |
0.00 % |
| fs60,mq40 |
32 |
0.00 % |
0 |
0.00 % |
32 |
0.00 % |
| q20,qd2,fs60,mq40 |
6 |
0.00 % |
0 |
0.00 % |
6 |
0.00 % |
| fs60 |
5 |
0.00 % |
0 |
0.00 % |
5 |
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 |
3162494 |
22.07 % |
| Transition |
G>A |
All |
806489 |
5.63 % |
| Transition |
T>C |
All |
3059589 |
21.35 % |
| Transition |
C>T |
All |
804131 |
5.61 % |
| Transversion |
A>C |
All |
496853 |
3.47 % |
| Transversion |
C>A |
All |
1540450 |
10.75 % |
| Transversion |
T>G |
All |
514286 |
3.59 % |
| Transversion |
G>T |
All |
1508855 |
10.53 % |
| Transversion |
A>T |
All |
821276 |
5.73 % |
| Transversion |
T>A |
All |
843791 |
5.89 % |
| Transversion |
C>G |
All |
390770 |
2.73 % |
| Transversion |
G>C |
All |
378806 |
2.64 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
106102 |
13.11 % |
| Transition |
G>A |
Passed |
102224 |
12.63 % |
| Transition |
T>C |
Passed |
109312 |
13.50 % |
| Transition |
C>T |
Passed |
105232 |
13.00 % |
| Transversion |
A>C |
Passed |
48105 |
5.94 % |
| Transversion |
C>A |
Passed |
51118 |
6.32 % |
| Transversion |
T>G |
Passed |
48312 |
5.97 % |
| Transversion |
G>T |
Passed |
50921 |
6.29 % |
| Transversion |
A>T |
Passed |
46138 |
5.70 % |
| Transversion |
T>A |
Passed |
46026 |
5.69 % |
| Transversion |
C>G |
Passed |
48255 |
5.96 % |
| Transversion |
G>C |
Passed |
47692 |
5.89 % |
| |
|
|
|
|
| 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 |
1.21 |
7832703 |
6495087 |
| Passed |
1.09 |
422870 |
386567 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |