/EXTERNAL BLUEPRINT/variants/K006364_20_lane_gembs
BACK
SAMPLE K006364_20_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1141479797 |
669634745 |
58.66 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1141479797 |
100% |
1122198916 |
98.31 % |
19280881 |
1.69 % |
| |
|
|
|
|
|
|
| Passed |
671618421 |
58.84 % |
668178226 |
59.54 % |
3440195 |
0.51 % |
| Filtered |
469861376 |
41.16 % |
454020690 |
40.46 % |
15840686 |
2.36 % |
| |
|
|
|
|
|
|
| q20 |
400103775 |
85.15 % |
396784599 |
87.39 % |
3319176 |
20.95 % |
| q20,qd2 |
41423150 |
8.82 % |
29634242 |
6.53 % |
11788908 |
74.42 % |
| q20,mq40 |
14493069 |
3.08 % |
14319903 |
3.15 % |
173166 |
1.09 % |
| mq40 |
6803515 |
1.45 % |
6632731 |
1.46 % |
170784 |
1.08 % |
| q20,qd2,mq40 |
3671492 |
0.78 % |
3412435 |
0.75 % |
259057 |
1.64 % |
| qd2 |
3261807 |
0.69 % |
3152835 |
0.69 % |
108972 |
0.69 % |
| qd2,mq40 |
96330 |
0.02 % |
83945 |
0.02 % |
12385 |
0.08 % |
| q20,qd2,fs60 |
2636 |
0.00 % |
0 |
0.00 % |
2636 |
0.02 % |
| fs60 |
1764 |
0.00 % |
0 |
0.00 % |
1764 |
0.01 % |
| qd2,fs60 |
1489 |
0.00 % |
0 |
0.00 % |
1489 |
0.01 % |
| qd2,fs60,mq40 |
1312 |
0.00 % |
0 |
0.00 % |
1312 |
0.01 % |
| fs60,mq40 |
562 |
0.00 % |
0 |
0.00 % |
562 |
0.00 % |
| q20,qd2,fs60,mq40 |
474 |
0.00 % |
0 |
0.00 % |
474 |
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 |
3630705 |
14.93 % |
| Transition |
G>A |
All |
5647708 |
23.22 % |
| Transition |
T>C |
All |
3551751 |
14.60 % |
| Transition |
C>T |
All |
5607555 |
23.05 % |
| Transversion |
A>C |
All |
418630 |
1.72 % |
| Transversion |
C>A |
All |
1085150 |
4.46 % |
| Transversion |
T>G |
All |
421282 |
1.73 % |
| Transversion |
G>T |
All |
1108048 |
4.56 % |
| Transversion |
A>T |
All |
1168719 |
4.80 % |
| Transversion |
T>A |
All |
1121088 |
4.61 % |
| Transversion |
C>G |
All |
285083 |
1.17 % |
| Transversion |
G>C |
All |
278583 |
1.15 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
389885 |
18.20 % |
| Transition |
G>A |
Passed |
361654 |
16.89 % |
| Transition |
T>C |
Passed |
389586 |
18.19 % |
| Transition |
C>T |
Passed |
362043 |
16.90 % |
| Transversion |
A>C |
Passed |
85463 |
3.99 % |
| Transversion |
C>A |
Passed |
79107 |
3.69 % |
| Transversion |
T>G |
Passed |
85358 |
3.99 % |
| Transversion |
G>T |
Passed |
79166 |
3.70 % |
| Transversion |
A>T |
Passed |
57172 |
2.67 % |
| Transversion |
T>A |
Passed |
56763 |
2.65 % |
| Transversion |
C>G |
Passed |
97523 |
4.55 % |
| Transversion |
G>C |
Passed |
98127 |
4.58 % |
| |
|
|
|
|
| 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 |
3.13 |
18437719 |
5886583 |
| Passed |
2.35 |
1503168 |
638679 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |