/EXTERNAL BLUEPRINT/variants/K006368_20_lane_gembs
BACK
SAMPLE K006368_20_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1123331252 |
438225471 |
39.01 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1123331252 |
100% |
1067427165 |
95.02 % |
55904087 |
4.98 % |
| |
|
|
|
|
|
|
| Passed |
446248557 |
39.73 % |
430999689 |
40.38 % |
15248868 |
3.42 % |
| Filtered |
677082695 |
60.27 % |
636427476 |
59.62 % |
40655219 |
9.11 % |
| |
|
|
|
|
|
|
| q20 |
508896044 |
75.16 % |
499812023 |
78.53 % |
9084021 |
22.34 % |
| q20,qd2 |
79987085 |
11.81 % |
60206656 |
9.46 % |
19780429 |
48.65 % |
| q20,mq40 |
31608510 |
4.67 % |
30072006 |
4.73 % |
1536504 |
3.78 % |
| mq40 |
27694918 |
4.09 % |
23435402 |
3.68 % |
4259516 |
10.48 % |
| qd2 |
14757604 |
2.18 % |
12708949 |
2.00 % |
2048655 |
5.04 % |
| q20,qd2,mq40 |
12323519 |
1.82 % |
8772146 |
1.38 % |
3551373 |
8.74 % |
| qd2,mq40 |
1809186 |
0.27 % |
1420294 |
0.22 % |
388892 |
0.96 % |
| qd2,fs60,mq40 |
2220 |
0.00 % |
0 |
0.00 % |
2220 |
0.01 % |
| qd2,fs60 |
857 |
0.00 % |
0 |
0.00 % |
857 |
0.00 % |
| q20,qd2,fs60 |
828 |
0.00 % |
0 |
0.00 % |
828 |
0.00 % |
| fs60 |
810 |
0.00 % |
0 |
0.00 % |
810 |
0.00 % |
| fs60,mq40 |
629 |
0.00 % |
0 |
0.00 % |
629 |
0.00 % |
| q20,qd2,fs60,mq40 |
484 |
0.00 % |
0 |
0.00 % |
484 |
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 |
11954808 |
19.85 % |
| Transition |
G>A |
All |
6847860 |
11.37 % |
| Transition |
T>C |
All |
10883434 |
18.07 % |
| Transition |
C>T |
All |
6457637 |
10.72 % |
| Transversion |
A>C |
All |
1969718 |
3.27 % |
| Transversion |
C>A |
All |
3652007 |
6.06 % |
| Transversion |
T>G |
All |
2059717 |
3.42 % |
| Transversion |
G>T |
All |
3754353 |
6.23 % |
| Transversion |
A>T |
All |
4883828 |
8.11 % |
| Transversion |
T>A |
All |
4718675 |
7.83 % |
| Transversion |
C>G |
All |
1558098 |
2.59 % |
| Transversion |
G>C |
All |
1490506 |
2.47 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
2075643 |
27.47 % |
| Transition |
G>A |
Passed |
848771 |
11.23 % |
| Transition |
T>C |
Passed |
1837553 |
24.32 % |
| Transition |
C>T |
Passed |
764569 |
10.12 % |
| Transversion |
A>C |
Passed |
307695 |
4.07 % |
| Transversion |
C>A |
Passed |
178083 |
2.36 % |
| Transversion |
T>G |
Passed |
324855 |
4.30 % |
| Transversion |
G>T |
Passed |
168149 |
2.23 % |
| Transversion |
A>T |
Passed |
217361 |
2.88 % |
| Transversion |
T>A |
Passed |
230434 |
3.05 % |
| Transversion |
C>G |
Passed |
308660 |
4.08 % |
| Transversion |
G>C |
Passed |
294727 |
3.90 % |
| |
|
|
|
|
| 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 |
1.50 |
36143739 |
24086902 |
| Passed |
2.72 |
5526536 |
2029964 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |