/EXTERNAL McGill EMC/variants/K006210_1_lane_gembs
BACK
SAMPLE K006210_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1168629040 |
1077242811 |
92.18 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1168629040 |
100% |
1149609576 |
98.37 % |
19019464 |
1.63 % |
| |
|
|
|
|
|
|
| Passed |
1078099286 |
92.25 % |
1073618339 |
93.39 % |
4480947 |
0.42 % |
| Filtered |
90529754 |
7.75 % |
75991237 |
6.61 % |
14538517 |
1.35 % |
| |
|
|
|
|
|
|
| q20 |
45206685 |
49.94 % |
43937307 |
57.82 % |
1269378 |
8.73 % |
| q20,qd2 |
16544815 |
18.28 % |
5537297 |
7.29 % |
11007518 |
75.71 % |
| q20,mq40 |
12576626 |
13.89 % |
12316841 |
16.21 % |
259785 |
1.79 % |
| qd2 |
7382559 |
8.15 % |
6104090 |
8.03 % |
1278469 |
8.79 % |
| mq40 |
5826139 |
6.44 % |
5492678 |
7.23 % |
333461 |
2.29 % |
| q20,qd2,mq40 |
2920460 |
3.23 % |
2543395 |
3.35 % |
377065 |
2.59 % |
| qd2,mq40 |
71467 |
0.08 % |
59629 |
0.08 % |
11838 |
0.08 % |
| qd2,fs60,mq40 |
414 |
0.00 % |
0 |
0.00 % |
414 |
0.00 % |
| qd2,fs60 |
256 |
0.00 % |
0 |
0.00 % |
256 |
0.00 % |
| fs60,mq40 |
145 |
0.00 % |
0 |
0.00 % |
145 |
0.00 % |
| fs60 |
135 |
0.00 % |
0 |
0.00 % |
135 |
0.00 % |
| q20,qd2,fs60,mq40 |
29 |
0.00 % |
0 |
0.00 % |
29 |
0.00 % |
| q20,qd2,fs60 |
21 |
0.00 % |
0 |
0.00 % |
21 |
0.00 % |
| q20,fs60,mq40 |
3 |
0.00 % |
0 |
0.00 % |
3 |
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 |
7219079 |
34.85 % |
| Transition |
G>A |
All |
1099224 |
5.31 % |
| Transition |
T>C |
All |
7022680 |
33.90 % |
| Transition |
C>T |
All |
1107962 |
5.35 % |
| Transversion |
A>C |
All |
363764 |
1.76 % |
| Transversion |
C>A |
All |
818514 |
3.95 % |
| Transversion |
T>G |
All |
369513 |
1.78 % |
| Transversion |
G>T |
All |
825851 |
3.99 % |
| Transversion |
A>T |
All |
630204 |
3.04 % |
| Transversion |
T>A |
All |
627143 |
3.03 % |
| Transversion |
C>G |
All |
317328 |
1.53 % |
| Transversion |
G>C |
All |
313954 |
1.52 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
1136567 |
23.47 % |
| Transition |
G>A |
Passed |
629077 |
12.99 % |
| Transition |
T>C |
Passed |
1099825 |
22.71 % |
| Transition |
C>T |
Passed |
629071 |
12.99 % |
| Transversion |
A>C |
Passed |
177758 |
3.67 % |
| Transversion |
C>A |
Passed |
170806 |
3.53 % |
| Transversion |
T>G |
Passed |
178714 |
3.69 % |
| Transversion |
G>T |
Passed |
170405 |
3.52 % |
| Transversion |
A>T |
Passed |
153579 |
3.17 % |
| Transversion |
T>A |
Passed |
153749 |
3.18 % |
| Transversion |
C>G |
Passed |
171396 |
3.54 % |
| Transversion |
G>C |
Passed |
171062 |
3.53 % |
| |
|
|
|
|
| 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 |
3.86 |
16448945 |
4266271 |
| Passed |
2.59 |
3494540 |
1347469 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |