/EXTERNAL McGill EMC/variants/K006142_1_lane_gembs
BACK
SAMPLE K006142_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1158379246 |
645543150 |
55.73 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1158379246 |
100% |
1131225611 |
97.66 % |
27153635 |
2.34 % |
| |
|
|
|
|
|
|
| Passed |
649204098 |
56.04 % |
643485261 |
56.88 % |
5718837 |
0.88 % |
| Filtered |
509175148 |
43.96 % |
487740350 |
43.12 % |
21434798 |
3.30 % |
| |
|
|
|
|
|
|
| q20 |
446369432 |
87.67 % |
442916883 |
90.81 % |
3452549 |
16.11 % |
| q20,qd2 |
36245706 |
7.12 % |
18908517 |
3.88 % |
17337189 |
80.88 % |
| q20,mq40 |
18011590 |
3.54 % |
17856780 |
3.66 % |
154810 |
0.72 % |
| q20,qd2,mq40 |
4005000 |
0.79 % |
3747020 |
0.77 % |
257980 |
1.20 % |
| qd2 |
2632197 |
0.52 % |
2596796 |
0.53 % |
35401 |
0.17 % |
| mq40 |
1879871 |
0.37 % |
1688928 |
0.35 % |
190943 |
0.89 % |
| qd2,mq40 |
30772 |
0.01 % |
25426 |
0.01 % |
5346 |
0.02 % |
| qd2,fs60,mq40 |
286 |
0.00 % |
0 |
0.00 % |
286 |
0.00 % |
| fs60,mq40 |
156 |
0.00 % |
0 |
0.00 % |
156 |
0.00 % |
| qd2,fs60 |
102 |
0.00 % |
0 |
0.00 % |
102 |
0.00 % |
| fs60 |
16 |
0.00 % |
0 |
0.00 % |
16 |
0.00 % |
| q20,qd2,fs60,mq40 |
15 |
0.00 % |
0 |
0.00 % |
15 |
0.00 % |
| q20,qd2,fs60 |
4 |
0.00 % |
0 |
0.00 % |
4 |
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 |
7110954 |
24.62 % |
| Transition |
G>A |
All |
1408617 |
4.88 % |
| Transition |
T>C |
All |
6998997 |
24.23 % |
| Transition |
C>T |
All |
1370951 |
4.75 % |
| Transversion |
A>C |
All |
284773 |
0.99 % |
| Transversion |
C>A |
All |
4847966 |
16.78 % |
| Transversion |
T>G |
All |
292790 |
1.01 % |
| Transversion |
G>T |
All |
4819933 |
16.69 % |
| Transversion |
A>T |
All |
549459 |
1.90 % |
| Transversion |
T>A |
All |
551646 |
1.91 % |
| Transversion |
C>G |
All |
329183 |
1.14 % |
| Transversion |
G>C |
All |
320305 |
1.11 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
493304 |
17.73 % |
| Transition |
G>A |
Passed |
414870 |
14.91 % |
| Transition |
T>C |
Passed |
494529 |
17.78 % |
| Transition |
C>T |
Passed |
417943 |
15.03 % |
| Transversion |
A>C |
Passed |
116477 |
4.19 % |
| Transversion |
C>A |
Passed |
130814 |
4.70 % |
| Transversion |
T>G |
Passed |
117204 |
4.21 % |
| Transversion |
G>T |
Passed |
129455 |
4.65 % |
| Transversion |
A>T |
Passed |
107599 |
3.87 % |
| Transversion |
T>A |
Passed |
107335 |
3.86 % |
| Transversion |
C>G |
Passed |
125999 |
4.53 % |
| Transversion |
G>C |
Passed |
126086 |
4.53 % |
| |
|
|
|
|
| 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 |
1.41 |
16889519 |
11996055 |
| Passed |
1.89 |
1820646 |
960969 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |