/cemt/variants/A34406_3_lane_gembs
BACK
SAMPLE A34406_3_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1157441811 |
615546588 |
53.18 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1157441811 |
100% |
1134228170 |
97.99 % |
23213641 |
2.01 % |
| |
|
|
|
|
|
|
| Passed |
618731912 |
53.46 % |
612392060 |
53.99 % |
6339852 |
1.02 % |
| Filtered |
538709899 |
46.54 % |
521836110 |
46.01 % |
16873789 |
2.73 % |
| |
|
|
|
|
|
|
| q20 |
473538082 |
87.90 % |
468723886 |
89.82 % |
4814196 |
28.53 % |
| q20,qd2 |
31380740 |
5.83 % |
20463625 |
3.92 % |
10917115 |
64.70 % |
| qd2 |
16461015 |
3.06 % |
15987963 |
3.06 % |
473052 |
2.80 % |
| q20,mq40 |
11808815 |
2.19 % |
11577296 |
2.22 % |
231519 |
1.37 % |
| q20,qd2,mq40 |
3585257 |
0.67 % |
3343815 |
0.64 % |
241442 |
1.43 % |
| mq40 |
1851011 |
0.34 % |
1681352 |
0.32 % |
169659 |
1.01 % |
| qd2,mq40 |
68719 |
0.01 % |
58173 |
0.01 % |
10546 |
0.06 % |
| q20,qd2,fs60 |
5794 |
0.00 % |
0 |
0.00 % |
5794 |
0.03 % |
| fs60 |
4060 |
0.00 % |
0 |
0.00 % |
4060 |
0.02 % |
| qd2,fs60 |
4032 |
0.00 % |
0 |
0.00 % |
4032 |
0.02 % |
| qd2,fs60,mq40 |
1716 |
0.00 % |
0 |
0.00 % |
1716 |
0.01 % |
| fs60,mq40 |
369 |
0.00 % |
0 |
0.00 % |
369 |
0.00 % |
| q20,qd2,fs60,mq40 |
275 |
0.00 % |
0 |
0.00 % |
275 |
0.00 % |
| q20,fs60 |
13 |
0.00 % |
0 |
0.00 % |
13 |
0.00 % |
| q20,fs60,mq40 |
1 |
0.00 % |
0 |
0.00 % |
1 |
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 |
6298482 |
24.49 % |
| Transition |
G>A |
All |
2807621 |
10.92 % |
| Transition |
T>C |
All |
6079850 |
23.64 % |
| Transition |
C>T |
All |
2773818 |
10.78 % |
| Transversion |
A>C |
All |
565460 |
2.20 % |
| Transversion |
C>A |
All |
1397135 |
5.43 % |
| Transversion |
T>G |
All |
578403 |
2.25 % |
| Transversion |
G>T |
All |
1395231 |
5.42 % |
| Transversion |
A>T |
All |
1442944 |
5.61 % |
| Transversion |
T>A |
All |
1461457 |
5.68 % |
| Transversion |
C>G |
All |
464366 |
1.81 % |
| Transversion |
G>C |
All |
455261 |
1.77 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
609338 |
17.75 % |
| Transition |
G>A |
Passed |
530611 |
15.46 % |
| Transition |
T>C |
Passed |
608975 |
17.74 % |
| Transition |
C>T |
Passed |
533844 |
15.55 % |
| Transversion |
A>C |
Passed |
141219 |
4.11 % |
| Transversion |
C>A |
Passed |
154183 |
4.49 % |
| Transversion |
T>G |
Passed |
141766 |
4.13 % |
| Transversion |
G>T |
Passed |
154520 |
4.50 % |
| Transversion |
A>T |
Passed |
139459 |
4.06 % |
| Transversion |
T>A |
Passed |
140426 |
4.09 % |
| Transversion |
C>G |
Passed |
138369 |
4.03 % |
| Transversion |
G>C |
Passed |
139375 |
4.06 % |
| |
|
|
|
|
| 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 |
2.31 |
17959771 |
7760257 |
| Passed |
1.99 |
2282768 |
1149317 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |