/EXTERNAL McGill EMC/variants/K006204_1_lane_gembs
BACK
SAMPLE K006204_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1121967004 |
38123804 |
3.40 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1121967004 |
100% |
1110837396 |
99.01 % |
11129608 |
0.99 % |
| |
|
|
|
|
|
|
| Passed |
42203944 |
3.76 % |
37458260 |
3.37 % |
4745684 |
11.24 % |
| Filtered |
1079763060 |
96.24 % |
1073379136 |
96.63 % |
6383924 |
15.13 % |
| |
|
|
|
|
|
|
| q20 |
1007930774 |
93.35 % |
1005187594 |
93.65 % |
2743180 |
42.97 % |
| q20,qd2 |
50665478 |
4.69 % |
47237441 |
4.40 % |
3428037 |
53.70 % |
| q20,mq40 |
14531565 |
1.35 % |
14458023 |
1.35 % |
73542 |
1.15 % |
| q20,qd2,mq40 |
6446792 |
0.60 % |
6389739 |
0.60 % |
57053 |
0.89 % |
| mq40 |
166684 |
0.02 % |
87859 |
0.01 % |
78825 |
1.23 % |
| qd2 |
12210 |
0.00 % |
11011 |
0.00 % |
1199 |
0.02 % |
| qd2,mq40 |
9446 |
0.00 % |
7469 |
0.00 % |
1977 |
0.03 % |
| qd2,fs60,mq40 |
52 |
0.00 % |
0 |
0.00 % |
52 |
0.00 % |
| fs60,mq40 |
32 |
0.00 % |
0 |
0.00 % |
32 |
0.00 % |
| qd2,fs60 |
17 |
0.00 % |
0 |
0.00 % |
17 |
0.00 % |
| fs60 |
7 |
0.00 % |
0 |
0.00 % |
7 |
0.00 % |
| q20,qd2,fs60,mq40 |
3 |
0.00 % |
0 |
0.00 % |
3 |
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 |
2938996 |
22.15 % |
| Transition |
G>A |
All |
888742 |
6.70 % |
| Transition |
T>C |
All |
2843105 |
21.42 % |
| Transition |
C>T |
All |
898195 |
6.77 % |
| Transversion |
A>C |
All |
274844 |
2.07 % |
| Transversion |
C>A |
All |
1491861 |
11.24 % |
| Transversion |
T>G |
All |
291212 |
2.19 % |
| Transversion |
G>T |
All |
1455401 |
10.97 % |
| Transversion |
A>T |
All |
835474 |
6.30 % |
| Transversion |
T>A |
All |
857146 |
6.46 % |
| Transversion |
C>G |
All |
253427 |
1.91 % |
| Transversion |
G>C |
All |
242349 |
1.83 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
90191 |
12.90 % |
| Transition |
G>A |
Passed |
90431 |
12.94 % |
| Transition |
T>C |
Passed |
92366 |
13.22 % |
| Transition |
C>T |
Passed |
93209 |
13.34 % |
| Transversion |
A>C |
Passed |
41363 |
5.92 % |
| Transversion |
C>A |
Passed |
44352 |
6.35 % |
| Transversion |
T>G |
Passed |
41594 |
5.95 % |
| Transversion |
G>T |
Passed |
44372 |
6.35 % |
| Transversion |
A>T |
Passed |
39233 |
5.61 % |
| Transversion |
T>A |
Passed |
39433 |
5.64 % |
| Transversion |
C>G |
Passed |
41114 |
5.88 % |
| Transversion |
G>C |
Passed |
41267 |
5.90 % |
| |
|
|
|
|
| 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 |
1.33 |
7569038 |
5701714 |
| Passed |
1.10 |
366197 |
332728 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |