/EXTERNAL McGill EMC/variants/K006144_1_lane_gembs
BACK
SAMPLE K006144_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1127823921 |
55004253 |
4.88 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1127823921 |
100% |
1115797891 |
98.93 % |
12026030 |
1.07 % |
| |
|
|
|
|
|
|
| Passed |
59715869 |
5.29 % |
54242691 |
4.86 % |
5473178 |
9.17 % |
| Filtered |
1068108052 |
94.71 % |
1061555200 |
95.14 % |
6552852 |
10.97 % |
| |
|
|
|
|
|
|
| q20 |
1011190501 |
94.67 % |
1007893825 |
94.95 % |
3296676 |
50.31 % |
| q20,qd2 |
36184722 |
3.39 % |
33133819 |
3.12 % |
3050903 |
46.56 % |
| q20,mq40 |
14872762 |
1.39 % |
14807109 |
1.39 % |
65653 |
1.00 % |
| q20,qd2,mq40 |
5624970 |
0.53 % |
5579548 |
0.53 % |
45422 |
0.69 % |
| mq40 |
204619 |
0.02 % |
115174 |
0.01 % |
89445 |
1.36 % |
| qd2 |
18509 |
0.00 % |
16169 |
0.00 % |
2340 |
0.04 % |
| qd2,mq40 |
11818 |
0.00 % |
9556 |
0.00 % |
2262 |
0.03 % |
| qd2,fs60,mq40 |
62 |
0.00 % |
0 |
0.00 % |
62 |
0.00 % |
| qd2,fs60 |
40 |
0.00 % |
0 |
0.00 % |
40 |
0.00 % |
| fs60,mq40 |
36 |
0.00 % |
0 |
0.00 % |
36 |
0.00 % |
| q20,qd2,fs60,mq40 |
8 |
0.00 % |
0 |
0.00 % |
8 |
0.00 % |
| fs60 |
4 |
0.00 % |
0 |
0.00 % |
4 |
0.00 % |
| q20,qd2,fs60 |
1 |
0.00 % |
0 |
0.00 % |
1 |
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 |
3622944 |
25.77 % |
| Transition |
G>A |
All |
818210 |
5.82 % |
| Transition |
T>C |
All |
3131675 |
22.28 % |
| Transition |
C>T |
All |
837246 |
5.96 % |
| Transversion |
A>C |
All |
609614 |
4.34 % |
| Transversion |
C>A |
All |
877057 |
6.24 % |
| Transversion |
T>G |
All |
667110 |
4.75 % |
| Transversion |
G>T |
All |
823716 |
5.86 % |
| Transversion |
A>T |
All |
821176 |
5.84 % |
| Transversion |
T>A |
All |
891862 |
6.34 % |
| Transversion |
C>G |
All |
496805 |
3.53 % |
| Transversion |
G>C |
All |
461295 |
3.28 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
120968 |
15.05 % |
| Transition |
G>A |
Passed |
103433 |
12.87 % |
| Transition |
T>C |
Passed |
119949 |
14.92 % |
| Transition |
C>T |
Passed |
104418 |
12.99 % |
| Transversion |
A>C |
Passed |
44674 |
5.56 % |
| Transversion |
C>A |
Passed |
46278 |
5.76 % |
| Transversion |
T>G |
Passed |
44865 |
5.58 % |
| Transversion |
G>T |
Passed |
46225 |
5.75 % |
| Transversion |
A>T |
Passed |
39846 |
4.96 % |
| Transversion |
T>A |
Passed |
40089 |
4.99 % |
| Transversion |
C>G |
Passed |
46916 |
5.84 % |
| Transversion |
G>C |
Passed |
46324 |
5.76 % |
| |
|
|
|
|
| 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 |
1.49 |
8410075 |
5648635 |
| Passed |
1.26 |
448768 |
355217 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |