/EXTERNAL McGill EMC/variants/K006182_1_lane_gembs
BACK
SAMPLE K006182_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1133341174 |
216467419 |
19.10 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1133341174 |
100% |
1121270129 |
98.93 % |
12071045 |
1.07 % |
| |
|
|
|
|
|
|
| Passed |
220104264 |
19.42 % |
215333901 |
19.20 % |
4770363 |
2.17 % |
| Filtered |
913236910 |
80.58 % |
905936228 |
80.80 % |
7300682 |
3.32 % |
| |
|
|
|
|
|
|
| q20 |
871083171 |
95.38 % |
868285520 |
95.84 % |
2797651 |
38.32 % |
| q20,qd2 |
24499636 |
2.68 % |
20234735 |
2.23 % |
4264901 |
58.42 % |
| q20,mq40 |
13206348 |
1.45 % |
13135556 |
1.45 % |
70792 |
0.97 % |
| q20,qd2,mq40 |
3912122 |
0.43 % |
3854826 |
0.43 % |
57296 |
0.78 % |
| mq40 |
376621 |
0.04 % |
278565 |
0.03 % |
98056 |
1.34 % |
| qd2 |
140384 |
0.02 % |
132296 |
0.01 % |
8088 |
0.11 % |
| qd2,mq40 |
18225 |
0.00 % |
14730 |
0.00 % |
3495 |
0.05 % |
| qd2,fs60,mq40 |
165 |
0.00 % |
0 |
0.00 % |
165 |
0.00 % |
| fs60,mq40 |
101 |
0.00 % |
0 |
0.00 % |
101 |
0.00 % |
| qd2,fs60 |
82 |
0.00 % |
0 |
0.00 % |
82 |
0.00 % |
| fs60 |
27 |
0.00 % |
0 |
0.00 % |
27 |
0.00 % |
| q20,qd2,fs60,mq40 |
24 |
0.00 % |
0 |
0.00 % |
24 |
0.00 % |
| q20,qd2,fs60 |
4 |
0.00 % |
0 |
0.00 % |
4 |
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 |
3437374 |
24.70 % |
| Transition |
G>A |
All |
1340794 |
9.63 % |
| Transition |
T>C |
All |
2971398 |
21.35 % |
| Transition |
C>T |
All |
1364714 |
9.81 % |
| Transversion |
A>C |
All |
427807 |
3.07 % |
| Transversion |
C>A |
All |
943567 |
6.78 % |
| Transversion |
T>G |
All |
499072 |
3.59 % |
| Transversion |
G>T |
All |
907720 |
6.52 % |
| Transversion |
A>T |
All |
703253 |
5.05 % |
| Transversion |
T>A |
All |
757276 |
5.44 % |
| Transversion |
C>G |
All |
302159 |
2.17 % |
| Transversion |
G>C |
All |
261447 |
1.88 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
205444 |
15.20 % |
| Transition |
G>A |
Passed |
202819 |
15.01 % |
| Transition |
T>C |
Passed |
205604 |
15.21 % |
| Transition |
C>T |
Passed |
206337 |
15.27 % |
| Transversion |
A>C |
Passed |
65789 |
4.87 % |
| Transversion |
C>A |
Passed |
70681 |
5.23 % |
| Transversion |
T>G |
Passed |
66539 |
4.92 % |
| Transversion |
G>T |
Passed |
70562 |
5.22 % |
| Transversion |
A>T |
Passed |
62043 |
4.59 % |
| Transversion |
T>A |
Passed |
61994 |
4.59 % |
| Transversion |
C>G |
Passed |
66760 |
4.94 % |
| Transversion |
G>C |
Passed |
67099 |
4.96 % |
| |
|
|
|
|
| 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 |
9114280 |
4802301 |
| Passed |
1.54 |
820204 |
531467 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |