/EXTERNAL McGill EMC/variants/K006186_1_lane_gembs
BACK
SAMPLE K006186_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1150104778 |
711077932 |
61.83 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1150104778 |
100% |
1140162052 |
99.14 % |
9942726 |
0.86 % |
| |
|
|
|
|
|
|
| Passed |
712634009 |
61.96 % |
709036204 |
62.19 % |
3597805 |
0.50 % |
| Filtered |
437470769 |
38.04 % |
431125848 |
37.81 % |
6344921 |
0.89 % |
| |
|
|
|
|
|
|
| q20 |
408484290 |
93.37 % |
407070647 |
94.42 % |
1413643 |
22.28 % |
| q20,qd2 |
12784695 |
2.92 % |
8202610 |
1.90 % |
4582085 |
72.22 % |
| q20,mq40 |
10672698 |
2.44 % |
10599400 |
2.46 % |
73298 |
1.16 % |
| q20,qd2,mq40 |
2993139 |
0.68 % |
2910484 |
0.68 % |
82655 |
1.30 % |
| qd2 |
1282345 |
0.29 % |
1219754 |
0.28 % |
62591 |
0.99 % |
| mq40 |
1212239 |
0.28 % |
1090584 |
0.25 % |
121655 |
1.92 % |
| qd2,mq40 |
39756 |
0.01 % |
32369 |
0.01 % |
7387 |
0.12 % |
| qd2,fs60,mq40 |
763 |
0.00 % |
0 |
0.00 % |
763 |
0.01 % |
| fs60 |
300 |
0.00 % |
0 |
0.00 % |
300 |
0.00 % |
| qd2,fs60 |
236 |
0.00 % |
0 |
0.00 % |
236 |
0.00 % |
| fs60,mq40 |
223 |
0.00 % |
0 |
0.00 % |
223 |
0.00 % |
| q20,qd2,fs60 |
47 |
0.00 % |
0 |
0.00 % |
47 |
0.00 % |
| q20,qd2,fs60,mq40 |
38 |
0.00 % |
0 |
0.00 % |
38 |
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 |
3513831 |
30.20 % |
| Transition |
G>A |
All |
1003180 |
8.62 % |
| Transition |
T>C |
All |
3126211 |
26.86 % |
| Transition |
C>T |
All |
1045469 |
8.98 % |
| Transversion |
A>C |
All |
217423 |
1.87 % |
| Transversion |
C>A |
All |
662734 |
5.70 % |
| Transversion |
T>G |
All |
241863 |
2.08 % |
| Transversion |
G>T |
All |
636377 |
5.47 % |
| Transversion |
A>T |
All |
362098 |
3.11 % |
| Transversion |
T>A |
All |
372072 |
3.20 % |
| Transversion |
C>G |
All |
237671 |
2.04 % |
| Transversion |
G>C |
All |
218123 |
1.87 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
473492 |
16.41 % |
| Transition |
G>A |
Passed |
468554 |
16.24 % |
| Transition |
T>C |
Passed |
474415 |
16.44 % |
| Transition |
C>T |
Passed |
476801 |
16.52 % |
| Transversion |
A>C |
Passed |
122321 |
4.24 % |
| Transversion |
C>A |
Passed |
134414 |
4.66 % |
| Transversion |
T>G |
Passed |
122667 |
4.25 % |
| Transversion |
G>T |
Passed |
133624 |
4.63 % |
| Transversion |
A>T |
Passed |
117915 |
4.09 % |
| Transversion |
T>A |
Passed |
117385 |
4.07 % |
| Transversion |
C>G |
Passed |
121949 |
4.23 % |
| Transversion |
G>C |
Passed |
122295 |
4.24 % |
| |
|
|
|
|
| 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 |
2.95 |
8688691 |
2948361 |
| Passed |
1.91 |
1893262 |
992570 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |