/EXTERNAL McGill EMC/variants/K006196_1_lane_gembs
BACK
SAMPLE K006196_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1129310909 |
205422142 |
18.19 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1129310909 |
100% |
1117582050 |
98.96 % |
11728859 |
1.04 % |
| |
|
|
|
|
|
|
| Passed |
208290521 |
18.44 % |
204248107 |
18.28 % |
4042414 |
1.94 % |
| Filtered |
921020388 |
81.56 % |
913333943 |
81.72 % |
7686445 |
3.69 % |
| |
|
|
|
|
|
|
| q20 |
873797366 |
94.87 % |
871067272 |
95.37 % |
2730094 |
35.52 % |
| q20,qd2 |
29588944 |
3.21 % |
24882398 |
2.72 % |
4706546 |
61.23 % |
| q20,mq40 |
12950017 |
1.41 % |
12874592 |
1.41 % |
75425 |
0.98 % |
| q20,qd2,mq40 |
4082757 |
0.44 % |
4022448 |
0.44 % |
60309 |
0.78 % |
| mq40 |
345793 |
0.04 % |
247370 |
0.03 % |
98423 |
1.28 % |
| qd2 |
233847 |
0.03 % |
223177 |
0.02 % |
10670 |
0.14 % |
| qd2,mq40 |
21131 |
0.00 % |
16686 |
0.00 % |
4445 |
0.06 % |
| qd2,fs60,mq40 |
249 |
0.00 % |
0 |
0.00 % |
249 |
0.00 % |
| fs60,mq40 |
171 |
0.00 % |
0 |
0.00 % |
171 |
0.00 % |
| qd2,fs60 |
68 |
0.00 % |
0 |
0.00 % |
68 |
0.00 % |
| q20,qd2,fs60,mq40 |
24 |
0.00 % |
0 |
0.00 % |
24 |
0.00 % |
| fs60 |
19 |
0.00 % |
0 |
0.00 % |
19 |
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 |
2640149 |
19.44 % |
| Transition |
G>A |
All |
1447307 |
10.66 % |
| Transition |
T>C |
All |
2475441 |
18.23 % |
| Transition |
C>T |
All |
1462514 |
10.77 % |
| Transversion |
A>C |
All |
377277 |
2.78 % |
| Transversion |
C>A |
All |
1370161 |
10.09 % |
| Transversion |
T>G |
All |
399359 |
2.94 % |
| Transversion |
G>T |
All |
1353763 |
9.97 % |
| Transversion |
A>T |
All |
699943 |
5.15 % |
| Transversion |
T>A |
All |
713036 |
5.25 % |
| Transversion |
C>G |
All |
327284 |
2.41 % |
| Transversion |
G>C |
All |
313857 |
2.31 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
207978 |
14.88 % |
| Transition |
G>A |
Passed |
206524 |
14.77 % |
| Transition |
T>C |
Passed |
211278 |
15.11 % |
| Transition |
C>T |
Passed |
210927 |
15.09 % |
| Transversion |
A>C |
Passed |
68959 |
4.93 % |
| Transversion |
C>A |
Passed |
75474 |
5.40 % |
| Transversion |
T>G |
Passed |
69289 |
4.96 % |
| Transversion |
G>T |
Passed |
75467 |
5.40 % |
| Transversion |
A>T |
Passed |
68855 |
4.93 % |
| Transversion |
T>A |
Passed |
69202 |
4.95 % |
| Transversion |
C>G |
Passed |
66744 |
4.77 % |
| Transversion |
G>C |
Passed |
67182 |
4.81 % |
| |
|
|
|
|
| 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 |
1.44 |
8025411 |
5554680 |
| Passed |
1.49 |
836707 |
561172 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |