/EXTERNAL BLUEPRINT/variants/K006268_10_lane_gembs
BACK
SAMPLE K006268_10_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1143341463 |
800916475 |
70.05 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1143341463 |
100% |
1126371805 |
98.52 % |
16969658 |
1.48 % |
| |
|
|
|
|
|
|
| Passed |
802022593 |
70.15 % |
799199834 |
70.95 % |
2822759 |
0.35 % |
| Filtered |
341318870 |
29.85 % |
327171971 |
29.05 % |
14146899 |
1.76 % |
| |
|
|
|
|
|
|
| q20 |
208712935 |
61.15 % |
206456041 |
63.10 % |
2256894 |
15.95 % |
| qd2 |
78062635 |
22.87 % |
77773041 |
23.77 % |
289594 |
2.05 % |
| q20,qd2 |
27797572 |
8.14 % |
16869756 |
5.16 % |
10927816 |
77.25 % |
| q20,mq40 |
11996425 |
3.51 % |
11877489 |
3.63 % |
118936 |
0.84 % |
| mq40 |
11772973 |
3.45 % |
11549689 |
3.53 % |
223284 |
1.58 % |
| q20,qd2,mq40 |
2739592 |
0.80 % |
2468617 |
0.75 % |
270975 |
1.92 % |
| qd2,mq40 |
200726 |
0.06 % |
177338 |
0.05 % |
23388 |
0.17 % |
| q20,qd2,fs60 |
16061 |
0.00 % |
0 |
0.00 % |
16061 |
0.11 % |
| qd2,fs60 |
7244 |
0.00 % |
0 |
0.00 % |
7244 |
0.05 % |
| fs60 |
5945 |
0.00 % |
0 |
0.00 % |
5945 |
0.04 % |
| qd2,fs60,mq40 |
3884 |
0.00 % |
0 |
0.00 % |
3884 |
0.03 % |
| fs60,mq40 |
1475 |
0.00 % |
0 |
0.00 % |
1475 |
0.01 % |
| q20,qd2,fs60,mq40 |
1365 |
0.00 % |
0 |
0.00 % |
1365 |
0.01 % |
| q20,fs60 |
27 |
0.00 % |
0 |
0.00 % |
27 |
0.00 % |
| q20,fs60,mq40 |
11 |
0.00 % |
0 |
0.00 % |
11 |
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 |
2944840 |
6.89 % |
| Transition |
G>A |
All |
17373202 |
40.66 % |
| Transition |
T>C |
All |
2802855 |
6.56 % |
| Transition |
C>T |
All |
17390212 |
40.70 % |
| Transversion |
A>C |
All |
201049 |
0.47 % |
| Transversion |
C>A |
All |
396225 |
0.93 % |
| Transversion |
T>G |
All |
211291 |
0.49 % |
| Transversion |
G>T |
All |
389946 |
0.91 % |
| Transversion |
A>T |
All |
324386 |
0.76 % |
| Transversion |
T>A |
All |
317124 |
0.74 % |
| Transversion |
C>G |
All |
191880 |
0.45 % |
| Transversion |
G>C |
All |
185205 |
0.43 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
492021 |
18.90 % |
| Transition |
G>A |
Passed |
431361 |
16.57 % |
| Transition |
T>C |
Passed |
491584 |
18.88 % |
| Transition |
C>T |
Passed |
430633 |
16.54 % |
| Transversion |
A>C |
Passed |
99433 |
3.82 % |
| Transversion |
C>A |
Passed |
94736 |
3.64 % |
| Transversion |
T>G |
Passed |
99774 |
3.83 % |
| Transversion |
G>T |
Passed |
94082 |
3.61 % |
| Transversion |
A>T |
Passed |
73015 |
2.80 % |
| Transversion |
T>A |
Passed |
73210 |
2.81 % |
| Transversion |
C>G |
Passed |
111351 |
4.28 % |
| Transversion |
G>C |
Passed |
111953 |
4.30 % |
| |
|
|
|
|
| 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 |
18.27 |
40511109 |
2217106 |
| Passed |
2.44 |
1845599 |
757554 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |