/EXTERNAL McGill EMC/variants/K006179_1_lane_gembs
BACK
SAMPLE K006179_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1152571957 |
961085434 |
83.39 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1152571957 |
100% |
1138369413 |
98.77 % |
14202544 |
1.23 % |
| |
|
|
|
|
|
|
| Passed |
962555907 |
83.51 % |
958677500 |
84.21 % |
3878407 |
0.40 % |
| Filtered |
190016050 |
16.49 % |
179691913 |
15.79 % |
10324137 |
1.07 % |
| |
|
|
|
|
|
|
| q20 |
154610705 |
81.37 % |
153078068 |
85.19 % |
1532637 |
14.85 % |
| q20,qd2 |
13950741 |
7.34 % |
5710244 |
3.18 % |
8240497 |
79.82 % |
| q20,mq40 |
12514092 |
6.59 % |
12403587 |
6.90 % |
110505 |
1.07 % |
| q20,qd2,mq40 |
3097473 |
1.63 % |
2946444 |
1.64 % |
151029 |
1.46 % |
| qd2 |
2964859 |
1.56 % |
2866720 |
1.60 % |
98139 |
0.95 % |
| mq40 |
2835208 |
1.49 % |
2652957 |
1.48 % |
182251 |
1.77 % |
| qd2,mq40 |
41942 |
0.02 % |
33893 |
0.02 % |
8049 |
0.08 % |
| qd2,fs60,mq40 |
505 |
0.00 % |
0 |
0.00 % |
505 |
0.00 % |
| fs60,mq40 |
222 |
0.00 % |
0 |
0.00 % |
222 |
0.00 % |
| qd2,fs60 |
169 |
0.00 % |
0 |
0.00 % |
169 |
0.00 % |
| fs60 |
85 |
0.00 % |
0 |
0.00 % |
85 |
0.00 % |
| q20,qd2,fs60,mq40 |
32 |
0.00 % |
0 |
0.00 % |
32 |
0.00 % |
| q20,qd2,fs60 |
17 |
0.00 % |
0 |
0.00 % |
17 |
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 |
5486932 |
34.60 % |
| Transition |
G>A |
All |
1176499 |
7.42 % |
| Transition |
T>C |
All |
5230005 |
32.98 % |
| Transition |
C>T |
All |
1195839 |
7.54 % |
| Transversion |
A>C |
All |
208592 |
1.32 % |
| Transversion |
C>A |
All |
623994 |
3.94 % |
| Transversion |
T>G |
All |
215941 |
1.36 % |
| Transversion |
G>T |
All |
613020 |
3.87 % |
| Transversion |
A>T |
All |
345665 |
2.18 % |
| Transversion |
T>A |
All |
341319 |
2.15 % |
| Transversion |
C>G |
All |
212143 |
1.34 % |
| Transversion |
G>C |
All |
207408 |
1.31 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
604112 |
17.32 % |
| Transition |
G>A |
Passed |
569798 |
16.33 % |
| Transition |
T>C |
Passed |
599418 |
17.18 % |
| Transition |
C>T |
Passed |
577353 |
16.55 % |
| Transversion |
A>C |
Passed |
142017 |
4.07 % |
| Transversion |
C>A |
Passed |
153322 |
4.39 % |
| Transversion |
T>G |
Passed |
142348 |
4.08 % |
| Transversion |
G>T |
Passed |
152747 |
4.38 % |
| Transversion |
A>T |
Passed |
129269 |
3.71 % |
| Transversion |
T>A |
Passed |
128422 |
3.68 % |
| Transversion |
C>G |
Passed |
144889 |
4.15 % |
| Transversion |
G>C |
Passed |
145035 |
4.16 % |
| |
|
|
|
|
| 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 |
4.73 |
13089275 |
2768082 |
| Passed |
2.07 |
2350681 |
1138049 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |