/CEMT/variants/B33199_1_lane_gembs
BACK
SAMPLE B33199_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1170923607 |
947308298 |
80.90 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1170923607 |
100% |
1150658611 |
98.27 % |
20264996 |
1.73 % |
| |
|
|
|
|
|
|
| Passed |
950377410 |
81.16 % |
944353502 |
82.07 % |
6023908 |
0.63 % |
| Filtered |
220546197 |
18.84 % |
206305109 |
17.93 % |
14241088 |
1.50 % |
| |
|
|
|
|
|
|
| q20 |
186609334 |
84.61 % |
184951950 |
89.65 % |
1657384 |
11.64 % |
| q20,qd2 |
16658292 |
7.55 % |
4881689 |
2.37 % |
11776603 |
82.69 % |
| q20,mq40 |
10331033 |
4.68 % |
10205120 |
4.95 % |
125913 |
0.88 % |
| q20,qd2,mq40 |
2586774 |
1.17 % |
2448733 |
1.19 % |
138041 |
0.97 % |
| qd2 |
2403457 |
1.09 % |
2111863 |
1.02 % |
291594 |
2.05 % |
| mq40 |
1913825 |
0.87 % |
1671833 |
0.81 % |
241992 |
1.70 % |
| qd2,mq40 |
41868 |
0.02 % |
33921 |
0.02 % |
7947 |
0.06 % |
| qd2,fs60,mq40 |
757 |
0.00 % |
0 |
0.00 % |
757 |
0.01 % |
| qd2,fs60 |
331 |
0.00 % |
0 |
0.00 % |
331 |
0.00 % |
| fs60,mq40 |
264 |
0.00 % |
0 |
0.00 % |
264 |
0.00 % |
| fs60 |
133 |
0.00 % |
0 |
0.00 % |
133 |
0.00 % |
| q20,qd2,fs60 |
70 |
0.00 % |
0 |
0.00 % |
70 |
0.00 % |
| q20,qd2,fs60,mq40 |
57 |
0.00 % |
0 |
0.00 % |
57 |
0.00 % |
| q20,fs60,mq40 |
2 |
0.00 % |
0 |
0.00 % |
2 |
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 |
8033505 |
36.56 % |
| Transition |
G>A |
All |
1065005 |
4.85 % |
| Transition |
T>C |
All |
8071637 |
36.73 % |
| Transition |
C>T |
All |
1064264 |
4.84 % |
| Transversion |
A>C |
All |
507252 |
2.31 % |
| Transversion |
C>A |
All |
492777 |
2.24 % |
| Transversion |
T>G |
All |
507568 |
2.31 % |
| Transversion |
G>T |
All |
486165 |
2.21 % |
| Transversion |
A>T |
All |
441125 |
2.01 % |
| Transversion |
T>A |
All |
445858 |
2.03 % |
| Transversion |
C>G |
All |
429595 |
1.95 % |
| Transversion |
G>C |
All |
429430 |
1.95 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
772625 |
19.03 % |
| Transition |
G>A |
Passed |
573094 |
14.11 % |
| Transition |
T>C |
Passed |
792197 |
19.51 % |
| Transition |
C>T |
Passed |
572829 |
14.11 % |
| Transversion |
A>C |
Passed |
185728 |
4.57 % |
| Transversion |
C>A |
Passed |
178747 |
4.40 % |
| Transversion |
T>G |
Passed |
186648 |
4.60 % |
| Transversion |
G>T |
Passed |
171449 |
4.22 % |
| Transversion |
A>T |
Passed |
148569 |
3.66 % |
| Transversion |
T>A |
Passed |
150481 |
3.71 % |
| Transversion |
C>G |
Passed |
164259 |
4.04 % |
| Transversion |
G>C |
Passed |
164468 |
4.05 % |
| |
|
|
|
|
| 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 |
4.88 |
18234411 |
3739770 |
| Passed |
2.01 |
2710745 |
1350349 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |