/EXTERNAL BLUEPRINT/variants/K012131_1_lane_gembs
BACK
SAMPLE K012131_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
758629521 |
1157976 |
0.15 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
758629521 |
100% |
748143446 |
98.62 % |
10486075 |
1.38 % |
| |
|
|
|
|
|
|
| Passed |
6618922 |
0.87 % |
977083 |
0.13 % |
5641839 |
85.24 % |
| Filtered |
752010599 |
99.13 % |
747166363 |
99.87 % |
4844236 |
73.19 % |
| |
|
|
|
|
|
|
| q20 |
517184724 |
68.77 % |
513474825 |
68.72 % |
3709899 |
76.58 % |
| q20,qd2 |
172500712 |
22.94 % |
171921363 |
23.01 % |
579349 |
11.96 % |
| q20,mq40 |
40273867 |
5.36 % |
40054421 |
5.36 % |
219446 |
4.53 % |
| q20,qd2,mq40 |
21718791 |
2.89 % |
21680338 |
2.90 % |
38453 |
0.79 % |
| mq40 |
328190 |
0.04 % |
31285 |
0.00 % |
296905 |
6.13 % |
| qd2 |
3646 |
0.00 % |
3583 |
0.00 % |
63 |
0.00 % |
| qd2,mq40 |
644 |
0.00 % |
548 |
0.00 % |
96 |
0.00 % |
| qd2,fs60 |
11 |
0.00 % |
0 |
0.00 % |
11 |
0.00 % |
| fs60 |
5 |
0.00 % |
0 |
0.00 % |
5 |
0.00 % |
| fs60,mq40 |
5 |
0.00 % |
0 |
0.00 % |
5 |
0.00 % |
| q20,qd2,fs60,mq40 |
2 |
0.00 % |
0 |
0.00 % |
2 |
0.00 % |
| q20,qd2,fs60 |
1 |
0.00 % |
0 |
0.00 % |
1 |
0.00 % |
| qd2,fs60,mq40 |
1 |
0.00 % |
0 |
0.00 % |
1 |
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 |
3467076 |
23.30 % |
| Transition |
G>A |
All |
1183161 |
7.95 % |
| Transition |
T>C |
All |
4450761 |
29.91 % |
| Transition |
C>T |
All |
583089 |
3.92 % |
| Transversion |
A>C |
All |
505283 |
3.40 % |
| Transversion |
C>A |
All |
845944 |
5.68 % |
| Transversion |
T>G |
All |
625900 |
4.21 % |
| Transversion |
G>T |
All |
763391 |
5.13 % |
| Transversion |
A>T |
All |
606473 |
4.08 % |
| Transversion |
T>A |
All |
834159 |
5.61 % |
| Transversion |
C>G |
All |
468046 |
3.15 % |
| Transversion |
G>C |
All |
547528 |
3.68 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
27854 |
15.67 % |
| Transition |
G>A |
Passed |
25883 |
14.56 % |
| Transition |
T>C |
Passed |
50288 |
28.29 % |
| Transition |
C>T |
Passed |
10904 |
6.14 % |
| Transversion |
A>C |
Passed |
7479 |
4.21 % |
| Transversion |
C>A |
Passed |
9961 |
5.60 % |
| Transversion |
T>G |
Passed |
7694 |
4.33 % |
| Transversion |
G>T |
Passed |
5707 |
3.21 % |
| Transversion |
A>T |
Passed |
3802 |
2.14 % |
| Transversion |
T>A |
Passed |
8989 |
5.06 % |
| Transversion |
C>G |
Passed |
7629 |
4.29 % |
| Transversion |
G>C |
Passed |
11539 |
6.49 % |
| |
|
|
|
|
| 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 |
1.86 |
9684087 |
5196724 |
| Passed |
1.83 |
114929 |
62800 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |