/EXTERNAL McGill EMC/variants/K006136_1_lane_gembs
BACK
SAMPLE K006136_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1143488590 |
537747383 |
47.03 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1143488590 |
100% |
1131332522 |
98.94 % |
12156068 |
1.06 % |
| |
|
|
|
|
|
|
| Passed |
540056501 |
47.23 % |
536042956 |
47.38 % |
4013545 |
0.74 % |
| Filtered |
603432089 |
52.77 % |
595289566 |
52.62 % |
8142523 |
1.51 % |
| |
|
|
|
|
|
|
| q20 |
566026952 |
93.80 % |
564077323 |
94.76 % |
1949629 |
23.94 % |
| q20,qd2 |
16599823 |
2.75 % |
10803999 |
1.81 % |
5795824 |
71.18 % |
| q20,mq40 |
13411402 |
2.22 % |
13322676 |
2.24 % |
88726 |
1.09 % |
| q20,qd2,mq40 |
2761651 |
0.46 % |
2655590 |
0.45 % |
106061 |
1.30 % |
| qd2 |
2531646 |
0.42 % |
2476916 |
0.42 % |
54730 |
0.67 % |
| mq40 |
2050792 |
0.34 % |
1914467 |
0.32 % |
136325 |
1.67 % |
| qd2,mq40 |
46826 |
0.01 % |
38595 |
0.01 % |
8231 |
0.10 % |
| qd2,fs60,mq40 |
1004 |
0.00 % |
0 |
0.00 % |
1004 |
0.01 % |
| qd2,fs60 |
692 |
0.00 % |
0 |
0.00 % |
692 |
0.01 % |
| fs60 |
561 |
0.00 % |
0 |
0.00 % |
561 |
0.01 % |
| fs60,mq40 |
348 |
0.00 % |
0 |
0.00 % |
348 |
0.00 % |
| q20,qd2,fs60 |
268 |
0.00 % |
0 |
0.00 % |
268 |
0.00 % |
| q20,qd2,fs60,mq40 |
123 |
0.00 % |
0 |
0.00 % |
123 |
0.00 % |
| q20,fs60,mq40 |
1 |
0.00 % |
0 |
0.00 % |
1 |
0.00 % |
| q20,fs60 |
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 |
3659695 |
26.24 % |
| Transition |
G>A |
All |
1072011 |
7.69 % |
| Transition |
T>C |
All |
3310801 |
23.74 % |
| Transition |
C>T |
All |
1091551 |
7.83 % |
| Transversion |
A>C |
All |
327027 |
2.34 % |
| Transversion |
C>A |
All |
1404853 |
10.07 % |
| Transversion |
T>G |
All |
348317 |
2.50 % |
| Transversion |
G>T |
All |
1390914 |
9.97 % |
| Transversion |
A>T |
All |
390787 |
2.80 % |
| Transversion |
T>A |
All |
407673 |
2.92 % |
| Transversion |
C>G |
All |
279272 |
2.00 % |
| Transversion |
G>C |
All |
264158 |
1.89 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
384559 |
16.69 % |
| Transition |
G>A |
Passed |
359492 |
15.61 % |
| Transition |
T>C |
Passed |
385080 |
16.72 % |
| Transition |
C>T |
Passed |
364918 |
15.84 % |
| Transversion |
A>C |
Passed |
101281 |
4.40 % |
| Transversion |
C>A |
Passed |
108623 |
4.72 % |
| Transversion |
T>G |
Passed |
101250 |
4.40 % |
| Transversion |
G>T |
Passed |
107003 |
4.65 % |
| Transversion |
A>T |
Passed |
92294 |
4.01 % |
| Transversion |
T>A |
Passed |
92613 |
4.02 % |
| Transversion |
C>G |
Passed |
102847 |
4.46 % |
| Transversion |
G>C |
Passed |
103551 |
4.50 % |
| |
|
|
|
|
| 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 |
1.90 |
9134058 |
4813001 |
| Passed |
1.85 |
1494049 |
809462 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |