/EXTERNAL McGill EMC/variants/K006130_1_lane_gembs
BACK
SAMPLE K006130_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1147920996 |
686708197 |
59.82 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1147920996 |
100% |
1132579604 |
98.66 % |
15341392 |
1.34 % |
| |
|
|
|
|
|
|
| Passed |
689126124 |
60.03 % |
684697419 |
60.45 % |
4428705 |
0.64 % |
| Filtered |
458794872 |
39.97 % |
447882185 |
39.55 % |
10912687 |
1.58 % |
| |
|
|
|
|
|
|
| q20 |
424158261 |
92.45 % |
421837205 |
94.18 % |
2321056 |
21.27 % |
| q20,qd2 |
16423375 |
3.58 % |
8179540 |
1.83 % |
8243835 |
75.54 % |
| q20,mq40 |
13067255 |
2.85 % |
12982376 |
2.90 % |
84879 |
0.78 % |
| q20,qd2,mq40 |
3408527 |
0.74 % |
3308298 |
0.74 % |
100229 |
0.92 % |
| mq40 |
1019600 |
0.22 % |
886301 |
0.20 % |
133299 |
1.22 % |
| qd2 |
692024 |
0.15 % |
668133 |
0.15 % |
23891 |
0.22 % |
| qd2,mq40 |
25227 |
0.01 % |
20332 |
0.00 % |
4895 |
0.04 % |
| qd2,fs60,mq40 |
272 |
0.00 % |
0 |
0.00 % |
272 |
0.00 % |
| fs60,mq40 |
130 |
0.00 % |
0 |
0.00 % |
130 |
0.00 % |
| qd2,fs60 |
129 |
0.00 % |
0 |
0.00 % |
129 |
0.00 % |
| q20,qd2,fs60,mq40 |
37 |
0.00 % |
0 |
0.00 % |
37 |
0.00 % |
| fs60 |
24 |
0.00 % |
0 |
0.00 % |
24 |
0.00 % |
| q20,qd2,fs60 |
10 |
0.00 % |
0 |
0.00 % |
10 |
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 |
5264273 |
30.97 % |
| Transition |
G>A |
All |
1226157 |
7.21 % |
| Transition |
T>C |
All |
4953115 |
29.14 % |
| Transition |
C>T |
All |
1242261 |
7.31 % |
| Transversion |
A>C |
All |
236219 |
1.39 % |
| Transversion |
C>A |
All |
1205094 |
7.09 % |
| Transversion |
T>G |
All |
254914 |
1.50 % |
| Transversion |
G>T |
All |
1159692 |
6.82 % |
| Transversion |
A>T |
All |
481886 |
2.83 % |
| Transversion |
T>A |
All |
493626 |
2.90 % |
| Transversion |
C>G |
All |
247523 |
1.46 % |
| Transversion |
G>C |
All |
235474 |
1.39 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
462240 |
16.89 % |
| Transition |
G>A |
Passed |
430916 |
15.75 % |
| Transition |
T>C |
Passed |
468311 |
17.11 % |
| Transition |
C>T |
Passed |
438790 |
16.04 % |
| Transversion |
A>C |
Passed |
117656 |
4.30 % |
| Transversion |
C>A |
Passed |
122852 |
4.49 % |
| Transversion |
T>G |
Passed |
117265 |
4.29 % |
| Transversion |
G>T |
Passed |
123883 |
4.53 % |
| Transversion |
A>T |
Passed |
105724 |
3.86 % |
| Transversion |
T>A |
Passed |
104903 |
3.83 % |
| Transversion |
C>G |
Passed |
121806 |
4.45 % |
| Transversion |
G>C |
Passed |
122001 |
4.46 % |
| |
|
|
|
|
| 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 |
2.94 |
12685806 |
4314428 |
| Passed |
1.92 |
1800257 |
936090 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |