/EXTERNAL BLUEPRINT/variants/K006272_11_lane_gembs
BACK
SAMPLE K006272_11_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1130825875 |
704171875 |
62.27 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1130825875 |
100% |
1112116962 |
98.35 % |
18708913 |
1.65 % |
| |
|
|
|
|
|
|
| Passed |
706075915 |
62.44 % |
702695294 |
63.19 % |
3380621 |
0.48 % |
| Filtered |
424749960 |
37.56 % |
409421668 |
36.81 % |
15328292 |
2.17 % |
| |
|
|
|
|
|
|
| q20 |
354704857 |
83.51 % |
352821529 |
86.18 % |
1883328 |
12.29 % |
| q20,qd2 |
43043959 |
10.13 % |
30231762 |
7.38 % |
12812197 |
83.59 % |
| q20,mq40 |
14334947 |
3.37 % |
14222637 |
3.47 % |
112310 |
0.73 % |
| mq40 |
6979214 |
1.64 % |
6784117 |
1.66 % |
195097 |
1.27 % |
| q20,qd2,mq40 |
3202340 |
0.75 % |
3006732 |
0.73 % |
195608 |
1.28 % |
| qd2 |
2389042 |
0.56 % |
2277146 |
0.56 % |
111896 |
0.73 % |
| qd2,mq40 |
88923 |
0.02 % |
77745 |
0.02 % |
11178 |
0.07 % |
| q20,qd2,fs60 |
2162 |
0.00 % |
0 |
0.00 % |
2162 |
0.01 % |
| qd2,fs60,mq40 |
1318 |
0.00 % |
0 |
0.00 % |
1318 |
0.01 % |
| fs60 |
1295 |
0.00 % |
0 |
0.00 % |
1295 |
0.01 % |
| qd2,fs60 |
899 |
0.00 % |
0 |
0.00 % |
899 |
0.01 % |
| fs60,mq40 |
523 |
0.00 % |
0 |
0.00 % |
523 |
0.00 % |
| q20,qd2,fs60,mq40 |
473 |
0.00 % |
0 |
0.00 % |
473 |
0.00 % |
| q20,fs60 |
6 |
0.00 % |
0 |
0.00 % |
6 |
0.00 % |
| q20,fs60,mq40 |
2 |
0.00 % |
0 |
0.00 % |
2 |
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 |
3622748 |
16.28 % |
| Transition |
G>A |
All |
6006968 |
27.00 % |
| Transition |
T>C |
All |
3563114 |
16.02 % |
| Transition |
C>T |
All |
6255520 |
28.12 % |
| Transversion |
A>C |
All |
218698 |
0.98 % |
| Transversion |
C>A |
All |
534353 |
2.40 % |
| Transversion |
T>G |
All |
226855 |
1.02 % |
| Transversion |
G>T |
All |
527177 |
2.37 % |
| Transversion |
A>T |
All |
448460 |
2.02 % |
| Transversion |
T>A |
All |
435842 |
1.96 % |
| Transversion |
C>G |
All |
208458 |
0.94 % |
| Transversion |
G>C |
All |
200054 |
0.90 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
434212 |
19.62 % |
| Transition |
G>A |
Passed |
370393 |
16.74 % |
| Transition |
T>C |
Passed |
410086 |
18.53 % |
| Transition |
C>T |
Passed |
367946 |
16.63 % |
| Transversion |
A>C |
Passed |
83505 |
3.77 % |
| Transversion |
C>A |
Passed |
77925 |
3.52 % |
| Transversion |
T>G |
Passed |
83305 |
3.76 % |
| Transversion |
G>T |
Passed |
77120 |
3.48 % |
| Transversion |
A>T |
Passed |
56200 |
2.54 % |
| Transversion |
T>A |
Passed |
56416 |
2.55 % |
| Transversion |
C>G |
Passed |
98256 |
4.44 % |
| Transversion |
G>C |
Passed |
97843 |
4.42 % |
| |
|
|
|
|
| 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 |
6.95 |
19448350 |
2799897 |
| Passed |
2.51 |
1582637 |
630570 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |