/EXTERNAL BLUEPRINT/variants/K006303_17_lane_gembs
BACK
SAMPLE K006303_17_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1081891287 |
483226599 |
44.66 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1081891287 |
100% |
1059701838 |
97.95 % |
22189449 |
2.05 % |
| |
|
|
|
|
|
|
| Passed |
486588755 |
44.98 % |
482063100 |
45.49 % |
4525655 |
0.93 % |
| Filtered |
595302532 |
55.02 % |
577638738 |
54.51 % |
17663794 |
3.63 % |
| |
|
|
|
|
|
|
| q20 |
499072118 |
83.84 % |
493248903 |
85.39 % |
5823215 |
32.97 % |
| q20,qd2 |
61298861 |
10.30 % |
50198923 |
8.69 % |
11099938 |
62.84 % |
| q20,mq40 |
19597211 |
3.29 % |
19412502 |
3.36 % |
184709 |
1.05 % |
| q20,qd2,mq40 |
5376658 |
0.90 % |
5161366 |
0.89 % |
215292 |
1.22 % |
| mq40 |
5196230 |
0.87 % |
4983391 |
0.86 % |
212839 |
1.20 % |
| qd2 |
4663969 |
0.78 % |
4558612 |
0.79 % |
105357 |
0.60 % |
| qd2,mq40 |
86640 |
0.01 % |
75041 |
0.01 % |
11599 |
0.07 % |
| q20,qd2,fs60 |
3141 |
0.00 % |
0 |
0.00 % |
3141 |
0.02 % |
| qd2,fs60 |
2709 |
0.00 % |
0 |
0.00 % |
2709 |
0.02 % |
| fs60 |
1922 |
0.00 % |
0 |
0.00 % |
1922 |
0.01 % |
| qd2,fs60,mq40 |
1673 |
0.00 % |
0 |
0.00 % |
1673 |
0.01 % |
| q20,qd2,fs60,mq40 |
861 |
0.00 % |
0 |
0.00 % |
861 |
0.00 % |
| fs60,mq40 |
536 |
0.00 % |
0 |
0.00 % |
536 |
0.00 % |
| q20,fs60 |
3 |
0.00 % |
0 |
0.00 % |
3 |
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 |
7481086 |
25.93 % |
| Transition |
G>A |
All |
6034166 |
20.92 % |
| Transition |
T>C |
All |
3341924 |
11.58 % |
| Transition |
C>T |
All |
5865243 |
20.33 % |
| Transversion |
A>C |
All |
377326 |
1.31 % |
| Transversion |
C>A |
All |
1039740 |
3.60 % |
| Transversion |
T>G |
All |
865552 |
3.00 % |
| Transversion |
G>T |
All |
807616 |
2.80 % |
| Transversion |
A>T |
All |
994875 |
3.45 % |
| Transversion |
T>A |
All |
1284774 |
4.45 % |
| Transversion |
C>G |
All |
455214 |
1.58 % |
| Transversion |
G>C |
All |
303385 |
1.05 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
349392 |
21.76 % |
| Transition |
G>A |
Passed |
253674 |
15.80 % |
| Transition |
T>C |
Passed |
313841 |
19.54 % |
| Transition |
C>T |
Passed |
255433 |
15.91 % |
| Transversion |
A>C |
Passed |
53876 |
3.36 % |
| Transversion |
C>A |
Passed |
50504 |
3.15 % |
| Transversion |
T>G |
Passed |
60725 |
3.78 % |
| Transversion |
G>T |
Passed |
50492 |
3.14 % |
| Transversion |
A>T |
Passed |
37299 |
2.32 % |
| Transversion |
T>A |
Passed |
37795 |
2.35 % |
| Transversion |
C>G |
Passed |
72316 |
4.50 % |
| Transversion |
G>C |
Passed |
70425 |
4.39 % |
| |
|
|
|
|
| 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 |
3.71 |
22722419 |
6128482 |
| Passed |
2.70 |
1172340 |
433432 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |