/EXTERNAL McGill EMC/variants/K006219_1_lane_gembs
BACK
SAMPLE K006219_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1160909829 |
855602624 |
73.70 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1160909829 |
100% |
1139382420 |
98.15 % |
21527409 |
1.85 % |
| |
|
|
|
|
|
|
| Passed |
857965393 |
73.90 % |
851735750 |
74.75 % |
6229643 |
0.73 % |
| Filtered |
302944436 |
26.10 % |
287646670 |
25.25 % |
15297766 |
1.78 % |
| |
|
|
|
|
|
|
| q20 |
257851922 |
85.12 % |
255588077 |
88.85 % |
2263845 |
14.80 % |
| q20,qd2 |
21587842 |
7.13 % |
9243633 |
3.21 % |
12344209 |
80.69 % |
| q20,mq40 |
15229153 |
5.03 % |
15109852 |
5.25 % |
119301 |
0.78 % |
| q20,qd2,mq40 |
3199503 |
1.06 % |
3006505 |
1.05 % |
192998 |
1.26 % |
| qd2 |
2547234 |
0.84 % |
2390972 |
0.83 % |
156262 |
1.02 % |
| mq40 |
2502472 |
0.83 % |
2286809 |
0.80 % |
215663 |
1.41 % |
| qd2,mq40 |
25614 |
0.01 % |
20822 |
0.01 % |
4792 |
0.03 % |
| qd2,fs60,mq40 |
332 |
0.00 % |
0 |
0.00 % |
332 |
0.00 % |
| qd2,fs60 |
157 |
0.00 % |
0 |
0.00 % |
157 |
0.00 % |
| fs60,mq40 |
125 |
0.00 % |
0 |
0.00 % |
125 |
0.00 % |
| fs60 |
42 |
0.00 % |
0 |
0.00 % |
42 |
0.00 % |
| q20,qd2,fs60,mq40 |
22 |
0.00 % |
0 |
0.00 % |
22 |
0.00 % |
| q20,qd2,fs60 |
17 |
0.00 % |
0 |
0.00 % |
17 |
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 |
7463833 |
33.23 % |
| Transition |
G>A |
All |
1349092 |
6.01 % |
| Transition |
T>C |
All |
7377372 |
32.85 % |
| Transition |
C>T |
All |
1350033 |
6.01 % |
| Transversion |
A>C |
All |
269987 |
1.20 % |
| Transversion |
C>A |
All |
1414303 |
6.30 % |
| Transversion |
T>G |
All |
272808 |
1.21 % |
| Transversion |
G>T |
All |
1408813 |
6.27 % |
| Transversion |
A>T |
All |
488369 |
2.17 % |
| Transversion |
T>A |
All |
474979 |
2.11 % |
| Transversion |
C>G |
All |
296733 |
1.32 % |
| Transversion |
G>C |
All |
293591 |
1.31 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
735219 |
16.99 % |
| Transition |
G>A |
Passed |
673379 |
15.56 % |
| Transition |
T>C |
Passed |
736607 |
17.03 % |
| Transition |
C>T |
Passed |
678889 |
15.69 % |
| Transversion |
A>C |
Passed |
185543 |
4.29 % |
| Transversion |
C>A |
Passed |
200055 |
4.62 % |
| Transversion |
T>G |
Passed |
185060 |
4.28 % |
| Transversion |
G>T |
Passed |
200984 |
4.65 % |
| Transversion |
A>T |
Passed |
174784 |
4.04 % |
| Transversion |
T>A |
Passed |
174076 |
4.02 % |
| Transversion |
C>G |
Passed |
190716 |
4.41 % |
| Transversion |
G>C |
Passed |
191244 |
4.42 % |
| |
|
|
|
|
| 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 |
3.57 |
17540330 |
4919583 |
| Passed |
1.88 |
2824094 |
1502462 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |