/EXTERNAL McGill EMC/variants/K006169_1_lane_gembs
BACK
SAMPLE K006169_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1123483385 |
253251181 |
22.54 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1123483385 |
100% |
1107658716 |
98.59 % |
15824669 |
1.41 % |
| |
|
|
|
|
|
|
| Passed |
256393815 |
22.82 % |
251651230 |
22.72 % |
4742585 |
1.85 % |
| Filtered |
867089570 |
77.18 % |
856007486 |
77.28 % |
11082084 |
4.32 % |
| |
|
|
|
|
|
|
| q20 |
804398344 |
92.77 % |
801394565 |
93.62 % |
3003779 |
27.10 % |
| q20,qd2 |
42423717 |
4.89 % |
34730263 |
4.06 % |
7693454 |
69.42 % |
| q20,mq40 |
14441827 |
1.67 % |
14327700 |
1.67 % |
114127 |
1.03 % |
| q20,qd2,mq40 |
4907817 |
0.57 % |
4795700 |
0.56 % |
112117 |
1.01 % |
| mq40 |
490867 |
0.06 % |
369075 |
0.04 % |
121792 |
1.10 % |
| qd2 |
408457 |
0.05 % |
375938 |
0.04 % |
32519 |
0.29 % |
| qd2,mq40 |
18028 |
0.00 % |
14245 |
0.00 % |
3783 |
0.03 % |
| qd2,fs60,mq40 |
285 |
0.00 % |
0 |
0.00 % |
285 |
0.00 % |
| fs60,mq40 |
103 |
0.00 % |
0 |
0.00 % |
103 |
0.00 % |
| qd2,fs60 |
75 |
0.00 % |
0 |
0.00 % |
75 |
0.00 % |
| fs60 |
30 |
0.00 % |
0 |
0.00 % |
30 |
0.00 % |
| q20,qd2,fs60,mq40 |
14 |
0.00 % |
0 |
0.00 % |
14 |
0.00 % |
| q20,qd2,fs60 |
6 |
0.00 % |
0 |
0.00 % |
6 |
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 |
3490130 |
19.62 % |
| Transition |
G>A |
All |
1647520 |
9.26 % |
| Transition |
T>C |
All |
2962927 |
16.66 % |
| Transition |
C>T |
All |
1426849 |
8.02 % |
| Transversion |
A>C |
All |
296829 |
1.67 % |
| Transversion |
C>A |
All |
2871962 |
16.15 % |
| Transversion |
T>G |
All |
350548 |
1.97 % |
| Transversion |
G>T |
All |
2801812 |
15.75 % |
| Transversion |
A>T |
All |
656293 |
3.69 % |
| Transversion |
T>A |
All |
701979 |
3.95 % |
| Transversion |
C>G |
All |
306324 |
1.72 % |
| Transversion |
G>C |
All |
271338 |
1.53 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
333477 |
17.70 % |
| Transition |
G>A |
Passed |
252098 |
13.38 % |
| Transition |
T>C |
Passed |
435208 |
23.10 % |
| Transition |
C>T |
Passed |
269023 |
14.28 % |
| Transversion |
A>C |
Passed |
72213 |
3.83 % |
| Transversion |
C>A |
Passed |
78435 |
4.16 % |
| Transversion |
T>G |
Passed |
71710 |
3.81 % |
| Transversion |
G>T |
Passed |
80644 |
4.28 % |
| Transversion |
A>T |
Passed |
80091 |
4.25 % |
| Transversion |
T>A |
Passed |
74765 |
3.97 % |
| Transversion |
C>G |
Passed |
67622 |
3.59 % |
| Transversion |
G>C |
Passed |
68355 |
3.63 % |
| |
|
|
|
|
| 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 |
1.15 |
9527426 |
8257085 |
| Passed |
2.17 |
1289806 |
593835 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |