/EXTERNAL McGill EMC/variants/K006195_1_lane_gembs
BACK
SAMPLE K006195_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1137908021 |
248575790 |
21.84 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1137908021 |
100% |
1126517873 |
99.00 % |
11390148 |
1.00 % |
| |
|
|
|
|
|
|
| Passed |
251867481 |
22.13 % |
247392418 |
21.96 % |
4475063 |
1.78 % |
| Filtered |
886040540 |
77.87 % |
879125455 |
78.04 % |
6915085 |
2.75 % |
| |
|
|
|
|
|
|
| q20 |
843381487 |
95.19 % |
840917010 |
95.65 % |
2464477 |
35.64 % |
| q20,qd2 |
24795172 |
2.80 % |
20583021 |
2.34 % |
4212151 |
60.91 % |
| q20,mq40 |
13246764 |
1.50 % |
13177001 |
1.50 % |
69763 |
1.01 % |
| q20,qd2,mq40 |
3991873 |
0.45 % |
3931970 |
0.45 % |
59903 |
0.87 % |
| mq40 |
413501 |
0.05 % |
318343 |
0.04 % |
95158 |
1.38 % |
| qd2 |
189774 |
0.02 % |
180492 |
0.02 % |
9282 |
0.13 % |
| qd2,mq40 |
21536 |
0.00 % |
17618 |
0.00 % |
3918 |
0.06 % |
| qd2,fs60,mq40 |
209 |
0.00 % |
0 |
0.00 % |
209 |
0.00 % |
| fs60,mq40 |
104 |
0.00 % |
0 |
0.00 % |
104 |
0.00 % |
| qd2,fs60 |
76 |
0.00 % |
0 |
0.00 % |
76 |
0.00 % |
| q20,qd2,fs60,mq40 |
28 |
0.00 % |
0 |
0.00 % |
28 |
0.00 % |
| fs60 |
15 |
0.00 % |
0 |
0.00 % |
15 |
0.00 % |
| q20,qd2,fs60 |
1 |
0.00 % |
0 |
0.00 % |
1 |
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 |
3247001 |
24.55 % |
| Transition |
G>A |
All |
1344116 |
10.16 % |
| Transition |
T>C |
All |
2935450 |
22.19 % |
| Transition |
C>T |
All |
1362951 |
10.30 % |
| Transversion |
A>C |
All |
312141 |
2.36 % |
| Transversion |
C>A |
All |
916074 |
6.93 % |
| Transversion |
T>G |
All |
357815 |
2.71 % |
| Transversion |
G>T |
All |
891508 |
6.74 % |
| Transversion |
A>T |
All |
650553 |
4.92 % |
| Transversion |
T>A |
All |
684222 |
5.17 % |
| Transversion |
C>G |
All |
277364 |
2.10 % |
| Transversion |
G>C |
All |
247814 |
1.87 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
220765 |
15.33 % |
| Transition |
G>A |
Passed |
219124 |
15.21 % |
| Transition |
T>C |
Passed |
221310 |
15.37 % |
| Transition |
C>T |
Passed |
223011 |
15.48 % |
| Transversion |
A>C |
Passed |
69109 |
4.80 % |
| Transversion |
C>A |
Passed |
74566 |
5.18 % |
| Transversion |
T>G |
Passed |
69200 |
4.80 % |
| Transversion |
G>T |
Passed |
74032 |
5.14 % |
| Transversion |
A>T |
Passed |
64319 |
4.47 % |
| Transversion |
T>A |
Passed |
64299 |
4.46 % |
| Transversion |
C>G |
Passed |
70226 |
4.88 % |
| Transversion |
G>C |
Passed |
70351 |
4.88 % |
| |
|
|
|
|
| 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 |
2.05 |
8889518 |
4337491 |
| Passed |
1.59 |
884210 |
556102 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |