/EXTERNAL BLUEPRINT/variants/K011726_1_lane_gembs
BACK
SAMPLE K011726_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
693095114 |
586603 |
0.08 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
693095114 |
100% |
685096926 |
98.85 % |
7998188 |
1.15 % |
| |
|
|
|
|
|
|
| Passed |
4690185 |
0.68 % |
467198 |
0.07 % |
4222987 |
90.04 % |
| Filtered |
688404929 |
99.32 % |
684629728 |
99.93 % |
3775201 |
80.49 % |
| |
|
|
|
|
|
|
| q20 |
456563242 |
66.32 % |
453634848 |
66.26 % |
2928394 |
77.57 % |
| q20,qd2 |
172139922 |
25.01 % |
171747398 |
25.09 % |
392524 |
10.40 % |
| q20,mq40 |
38010881 |
5.52 % |
37823864 |
5.52 % |
187017 |
4.95 % |
| q20,qd2,mq40 |
21422084 |
3.11 % |
21392489 |
3.12 % |
29595 |
0.78 % |
| mq40 |
264252 |
0.04 % |
26732 |
0.00 % |
237520 |
6.29 % |
| qd2 |
3989 |
0.00 % |
3940 |
0.00 % |
49 |
0.00 % |
| qd2,mq40 |
530 |
0.00 % |
457 |
0.00 % |
73 |
0.00 % |
| qd2,fs60 |
17 |
0.00 % |
0 |
0.00 % |
17 |
0.00 % |
| fs60 |
4 |
0.00 % |
0 |
0.00 % |
4 |
0.00 % |
| fs60,mq40 |
4 |
0.00 % |
0 |
0.00 % |
4 |
0.00 % |
| qd2,fs60,mq40 |
2 |
0.00 % |
0 |
0.00 % |
2 |
0.00 % |
| q20,qd2,fs60,mq40 |
2 |
0.00 % |
0 |
0.00 % |
2 |
0.00 % |
| q20,fs60 |
0 |
0.00 % |
0 |
0.00 % |
0 |
0.00 % |
| q20,qd2,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 |
2839271 |
22.96 % |
| Transition |
G>A |
All |
988223 |
7.99 % |
| Transition |
T>C |
All |
3700026 |
29.92 % |
| Transition |
C>T |
All |
486100 |
3.93 % |
| Transversion |
A>C |
All |
440008 |
3.56 % |
| Transversion |
C>A |
All |
690808 |
5.59 % |
| Transversion |
T>G |
All |
545212 |
4.41 % |
| Transversion |
G>T |
All |
632083 |
5.11 % |
| Transversion |
A>T |
All |
502912 |
4.07 % |
| Transversion |
T>A |
All |
687183 |
5.56 % |
| Transversion |
C>G |
All |
390598 |
3.16 % |
| Transversion |
G>C |
All |
465888 |
3.77 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
18359 |
15.67 % |
| Transition |
G>A |
Passed |
17066 |
14.57 % |
| Transition |
T>C |
Passed |
31779 |
27.12 % |
| Transition |
C>T |
Passed |
7366 |
6.29 % |
| Transversion |
A>C |
Passed |
4967 |
4.24 % |
| Transversion |
C>A |
Passed |
6783 |
5.79 % |
| Transversion |
T>G |
Passed |
5117 |
4.37 % |
| Transversion |
G>T |
Passed |
4223 |
3.60 % |
| Transversion |
A>T |
Passed |
2567 |
2.19 % |
| Transversion |
T>A |
Passed |
5602 |
4.78 % |
| Transversion |
C>G |
Passed |
5393 |
4.60 % |
| Transversion |
G>C |
Passed |
7940 |
6.78 % |
| |
|
|
|
|
| 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 |
1.84 |
8013620 |
4354692 |
| Passed |
1.75 |
74570 |
42592 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |