/EXTERNAL McGill EMC/variants/K006184_1_lane_gembs
BACK
SAMPLE K006184_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1139092284 |
408409406 |
35.85 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1139092284 |
100% |
1126418619 |
98.89 % |
12673665 |
1.11 % |
| |
|
|
|
|
|
|
| Passed |
411050182 |
36.09 % |
406889262 |
36.12 % |
4160920 |
1.01 % |
| Filtered |
728042102 |
63.91 % |
719529357 |
63.88 % |
8512745 |
2.07 % |
| |
|
|
|
|
|
|
| q20 |
689159726 |
94.66 % |
686681287 |
95.43 % |
2478439 |
29.11 % |
| q20,qd2 |
20305322 |
2.79 % |
14567050 |
2.02 % |
5738272 |
67.41 % |
| q20,mq40 |
13401582 |
1.84 % |
13316010 |
1.85 % |
85572 |
1.01 % |
| q20,qd2,mq40 |
4066605 |
0.56 % |
3987072 |
0.55 % |
79533 |
0.93 % |
| mq40 |
565611 |
0.08 % |
454419 |
0.06 % |
111192 |
1.31 % |
| qd2 |
520081 |
0.07 % |
505384 |
0.07 % |
14697 |
0.17 % |
| qd2,mq40 |
22682 |
0.00 % |
18135 |
0.00 % |
4547 |
0.05 % |
| qd2,fs60,mq40 |
256 |
0.00 % |
0 |
0.00 % |
256 |
0.00 % |
| fs60,mq40 |
131 |
0.00 % |
0 |
0.00 % |
131 |
0.00 % |
| qd2,fs60 |
69 |
0.00 % |
0 |
0.00 % |
69 |
0.00 % |
| q20,qd2,fs60,mq40 |
21 |
0.00 % |
0 |
0.00 % |
21 |
0.00 % |
| fs60 |
14 |
0.00 % |
0 |
0.00 % |
14 |
0.00 % |
| q20,qd2,fs60 |
2 |
0.00 % |
0 |
0.00 % |
2 |
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 |
3971787 |
27.50 % |
| Transition |
G>A |
All |
1171428 |
8.11 % |
| Transition |
T>C |
All |
3453865 |
23.91 % |
| Transition |
C>T |
All |
1200833 |
8.31 % |
| Transversion |
A>C |
All |
305351 |
2.11 % |
| Transversion |
C>A |
All |
1128498 |
7.81 % |
| Transversion |
T>G |
All |
357855 |
2.48 % |
| Transversion |
G>T |
All |
1085071 |
7.51 % |
| Transversion |
A>T |
All |
570073 |
3.95 % |
| Transversion |
T>A |
All |
621188 |
4.30 % |
| Transversion |
C>G |
All |
306881 |
2.12 % |
| Transversion |
G>C |
All |
270726 |
1.87 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
315851 |
15.95 % |
| Transition |
G>A |
Passed |
303923 |
15.35 % |
| Transition |
T>C |
Passed |
314552 |
15.88 % |
| Transition |
C>T |
Passed |
310388 |
15.67 % |
| Transversion |
A>C |
Passed |
91774 |
4.63 % |
| Transversion |
C>A |
Passed |
97252 |
4.91 % |
| Transversion |
T>G |
Passed |
91944 |
4.64 % |
| Transversion |
G>T |
Passed |
98016 |
4.95 % |
| Transversion |
A>T |
Passed |
87634 |
4.43 % |
| Transversion |
T>A |
Passed |
87349 |
4.41 % |
| Transversion |
C>G |
Passed |
90836 |
4.59 % |
| Transversion |
G>C |
Passed |
90702 |
4.58 % |
| |
|
|
|
|
| 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 |
2.11 |
9797913 |
4645643 |
| Passed |
1.69 |
1244714 |
735507 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |