/EXTERNAL Roadmap/variants/K012804_1_lane_gembs
BACK
SAMPLE K012804_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1160442650 |
985763171 |
84.95 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1160442650 |
100% |
1137531799 |
98.03 % |
22910851 |
1.97 % |
| |
|
|
|
|
|
|
| Passed |
987629054 |
85.11 % |
982853840 |
86.40 % |
4775214 |
0.48 % |
| Filtered |
172813596 |
14.89 % |
154677959 |
13.60 % |
18135637 |
1.84 % |
| |
|
|
|
|
|
|
| q20 |
124719809 |
72.17 % |
123018998 |
79.53 % |
1700811 |
9.38 % |
| q20,qd2 |
22625164 |
13.09 % |
7124195 |
4.61 % |
15500969 |
85.47 % |
| q20,mq40 |
15311597 |
8.86 % |
15150797 |
9.80 % |
160800 |
0.89 % |
| mq40 |
3929423 |
2.27 % |
3646870 |
2.36 % |
282553 |
1.56 % |
| q20,qd2,mq40 |
3403211 |
1.97 % |
3196653 |
2.07 % |
206558 |
1.14 % |
| qd2 |
2782772 |
1.61 % |
2508032 |
1.62 % |
274740 |
1.51 % |
| qd2,mq40 |
40782 |
0.02 % |
32414 |
0.02 % |
8368 |
0.05 % |
| qd2,fs60,mq40 |
435 |
0.00 % |
0 |
0.00 % |
435 |
0.00 % |
| fs60,mq40 |
183 |
0.00 % |
0 |
0.00 % |
183 |
0.00 % |
| qd2,fs60 |
132 |
0.00 % |
0 |
0.00 % |
132 |
0.00 % |
| q20,qd2,fs60,mq40 |
44 |
0.00 % |
0 |
0.00 % |
44 |
0.00 % |
| fs60 |
37 |
0.00 % |
0 |
0.00 % |
37 |
0.00 % |
| q20,qd2,fs60 |
7 |
0.00 % |
0 |
0.00 % |
7 |
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 |
9786902 |
39.85 % |
| Transition |
G>A |
All |
1755265 |
7.15 % |
| Transition |
T>C |
All |
7722144 |
31.44 % |
| Transition |
C>T |
All |
1856833 |
7.56 % |
| Transversion |
A>C |
All |
263719 |
1.07 % |
| Transversion |
C>A |
All |
591487 |
2.41 % |
| Transversion |
T>G |
All |
311523 |
1.27 % |
| Transversion |
G>T |
All |
561903 |
2.29 % |
| Transversion |
A>T |
All |
573679 |
2.34 % |
| Transversion |
T>A |
All |
598869 |
2.44 % |
| Transversion |
C>G |
All |
286555 |
1.17 % |
| Transversion |
G>C |
All |
251337 |
1.02 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
887451 |
22.43 % |
| Transition |
G>A |
Passed |
583386 |
14.74 % |
| Transition |
T>C |
Passed |
693985 |
17.54 % |
| Transition |
C>T |
Passed |
591987 |
14.96 % |
| Transversion |
A>C |
Passed |
150751 |
3.81 % |
| Transversion |
C>A |
Passed |
156000 |
3.94 % |
| Transversion |
T>G |
Passed |
154699 |
3.91 % |
| Transversion |
G>T |
Passed |
156130 |
3.95 % |
| Transversion |
A>T |
Passed |
139989 |
3.54 % |
| Transversion |
T>A |
Passed |
139567 |
3.53 % |
| Transversion |
C>G |
Passed |
152659 |
3.86 % |
| Transversion |
G>C |
Passed |
150286 |
3.80 % |
| |
|
|
|
|
| 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 |
6.14 |
21121144 |
3439072 |
| Passed |
2.30 |
2756809 |
1200081 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |