/EXTERNAL McGill EMC/variants/K006154_1_lane_gembs
BACK
SAMPLE K006154_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1157152441 |
1090875927 |
94.27 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1157152441 |
100% |
1148908028 |
99.29 % |
8244413 |
0.71 % |
| |
|
|
|
|
|
|
| Passed |
1091118218 |
94.29 % |
1086505028 |
94.57 % |
4613190 |
0.42 % |
| Filtered |
66034223 |
5.71 % |
62403000 |
5.43 % |
3631223 |
0.33 % |
| |
|
|
|
|
|
|
| q20 |
35440530 |
53.67 % |
35103967 |
56.25 % |
336563 |
9.27 % |
| q20,mq40 |
13606043 |
20.60 % |
13449431 |
21.55 % |
156612 |
4.31 % |
| mq40 |
5099804 |
7.72 % |
4839792 |
7.76 % |
260012 |
7.16 % |
| q20,qd2 |
5001003 |
7.57 % |
2781712 |
4.46 % |
2219291 |
61.12 % |
| qd2 |
3497793 |
5.30 % |
3059427 |
4.90 % |
438366 |
12.07 % |
| q20,qd2,mq40 |
3314060 |
5.02 % |
3109259 |
4.98 % |
204801 |
5.64 % |
| qd2,mq40 |
73057 |
0.11 % |
59412 |
0.10 % |
13645 |
0.38 % |
| qd2,fs60,mq40 |
1020 |
0.00 % |
0 |
0.00 % |
1020 |
0.03 % |
| fs60,mq40 |
390 |
0.00 % |
0 |
0.00 % |
390 |
0.01 % |
| qd2,fs60 |
252 |
0.00 % |
0 |
0.00 % |
252 |
0.01 % |
| fs60 |
175 |
0.00 % |
0 |
0.00 % |
175 |
0.00 % |
| q20,qd2,fs60,mq40 |
68 |
0.00 % |
0 |
0.00 % |
68 |
0.00 % |
| q20,qd2,fs60 |
27 |
0.00 % |
0 |
0.00 % |
27 |
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 |
1941468 |
21.35 % |
| Transition |
G>A |
All |
1181079 |
12.99 % |
| Transition |
T>C |
All |
1926949 |
21.19 % |
| Transition |
C>T |
All |
1183117 |
13.01 % |
| Transversion |
A>C |
All |
282870 |
3.11 % |
| Transversion |
C>A |
All |
455085 |
5.00 % |
| Transversion |
T>G |
All |
285850 |
3.14 % |
| Transversion |
G>T |
All |
452995 |
4.98 % |
| Transversion |
A>T |
All |
407819 |
4.48 % |
| Transversion |
T>A |
All |
401466 |
4.41 % |
| Transversion |
C>G |
All |
287403 |
3.16 % |
| Transversion |
G>C |
All |
287566 |
3.16 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
789330 |
16.27 % |
| Transition |
G>A |
Passed |
801524 |
16.52 % |
| Transition |
T>C |
Passed |
791662 |
16.32 % |
| Transition |
C>T |
Passed |
803677 |
16.56 % |
| Transversion |
A>C |
Passed |
206162 |
4.25 % |
| Transversion |
C>A |
Passed |
219637 |
4.53 % |
| Transversion |
T>G |
Passed |
206799 |
4.26 % |
| Transversion |
G>T |
Passed |
220245 |
4.54 % |
| Transversion |
A>T |
Passed |
193520 |
3.99 % |
| Transversion |
T>A |
Passed |
192772 |
3.97 % |
| Transversion |
C>G |
Passed |
213075 |
4.39 % |
| Transversion |
G>C |
Passed |
213900 |
4.41 % |
| |
|
|
|
|
| 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 |
2.18 |
6232613 |
2861054 |
| Passed |
1.91 |
3186193 |
1666110 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |