/EXTERNAL McGill EMC/variants/K006168_1_lane_gembs
BACK
SAMPLE K006168_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
843023887 |
29535446 |
3.50 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
843023887 |
100% |
806413471 |
95.66 % |
36610416 |
4.34 % |
| |
|
|
|
|
|
|
| Passed |
39170784 |
4.65 % |
28050454 |
3.48 % |
11120330 |
28.39 % |
| Filtered |
803853103 |
95.35 % |
778363017 |
96.52 % |
25490086 |
65.07 % |
| |
|
|
|
|
|
|
| q20 |
542977638 |
67.55 % |
537248644 |
69.02 % |
5728994 |
22.48 % |
| q20,qd2 |
135477490 |
16.85 % |
128470360 |
16.51 % |
7007130 |
27.49 % |
| q20,mq40 |
86562965 |
10.77 % |
84099441 |
10.80 % |
2463524 |
9.66 % |
| q20,qd2,mq40 |
24954816 |
3.10 % |
21826688 |
2.80 % |
3128128 |
12.27 % |
| mq40 |
13546733 |
1.69 % |
6425024 |
0.83 % |
7121709 |
27.94 % |
| qd2 |
276595 |
0.03 % |
248627 |
0.03 % |
27968 |
0.11 % |
| qd2,mq40 |
56100 |
0.01 % |
44233 |
0.01 % |
11867 |
0.05 % |
| qd2,fs60,mq40 |
389 |
0.00 % |
0 |
0.00 % |
389 |
0.00 % |
| fs60,mq40 |
163 |
0.00 % |
0 |
0.00 % |
163 |
0.00 % |
| qd2,fs60 |
71 |
0.00 % |
0 |
0.00 % |
71 |
0.00 % |
| fs60 |
50 |
0.00 % |
0 |
0.00 % |
50 |
0.00 % |
| q20,qd2,fs60,mq40 |
50 |
0.00 % |
0 |
0.00 % |
50 |
0.00 % |
| q20,qd2,fs60 |
43 |
0.00 % |
0 |
0.00 % |
43 |
0.00 % |
| q20,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 |
6669284 |
15.94 % |
| Transition |
G>A |
All |
4821866 |
11.53 % |
| Transition |
T>C |
All |
6131350 |
14.66 % |
| Transition |
C>T |
All |
4293661 |
10.26 % |
| Transversion |
A>C |
All |
1365883 |
3.27 % |
| Transversion |
C>A |
All |
3382634 |
8.09 % |
| Transversion |
T>G |
All |
1544306 |
3.69 % |
| Transversion |
G>T |
All |
3547639 |
8.48 % |
| Transversion |
A>T |
All |
3725194 |
8.91 % |
| Transversion |
T>A |
All |
3528874 |
8.44 % |
| Transversion |
C>G |
All |
1481367 |
3.54 % |
| Transversion |
G>C |
All |
1338905 |
3.20 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
330089 |
22.07 % |
| Transition |
G>A |
Passed |
177909 |
11.90 % |
| Transition |
T>C |
Passed |
275443 |
18.42 % |
| Transition |
C>T |
Passed |
144916 |
9.69 % |
| Transversion |
A>C |
Passed |
79466 |
5.31 % |
| Transversion |
C>A |
Passed |
55162 |
3.69 % |
| Transversion |
T>G |
Passed |
86812 |
5.81 % |
| Transversion |
G>T |
Passed |
50314 |
3.36 % |
| Transversion |
A>T |
Passed |
55618 |
3.72 % |
| Transversion |
T>A |
Passed |
62212 |
4.16 % |
| Transversion |
C>G |
Passed |
92090 |
6.16 % |
| Transversion |
G>C |
Passed |
85393 |
5.71 % |
| |
|
|
|
|
| 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 |
1.10 |
21916161 |
19914802 |
| Passed |
1.64 |
928357 |
567067 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |