/EXTERNAL BLUEPRINT/variants/K006306_K006316_21_lane_gembs
BACK
SAMPLE K006306_K006316_21_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1052692149 |
496717902 |
47.19 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1052692149 |
100% |
1033829659 |
98.21 % |
18862490 |
1.79 % |
| |
|
|
|
|
|
|
| Passed |
498800553 |
47.38 % |
495662577 |
47.94 % |
3137976 |
0.63 % |
| Filtered |
553891596 |
52.62 % |
538167082 |
52.06 % |
15724514 |
3.15 % |
| |
|
|
|
|
|
|
| q20 |
450234236 |
81.29 % |
447851520 |
83.22 % |
2382716 |
15.15 % |
| q20,qd2 |
67372199 |
12.16 % |
54592925 |
10.14 % |
12779274 |
81.27 % |
| q20,mq40 |
15909551 |
2.87 % |
15809851 |
2.94 % |
99700 |
0.63 % |
| qd2 |
9745923 |
1.76 % |
9645857 |
1.79 % |
100066 |
0.64 % |
| mq40 |
6819928 |
1.23 % |
6649497 |
1.24 % |
170431 |
1.08 % |
| q20,qd2,mq40 |
3707537 |
0.67 % |
3540162 |
0.66 % |
167375 |
1.06 % |
| qd2,mq40 |
89355 |
0.02 % |
77270 |
0.01 % |
12085 |
0.08 % |
| q20,qd2,fs60 |
3837 |
0.00 % |
0 |
0.00 % |
3837 |
0.02 % |
| qd2,fs60 |
3600 |
0.00 % |
0 |
0.00 % |
3600 |
0.02 % |
| fs60 |
2146 |
0.00 % |
0 |
0.00 % |
2146 |
0.01 % |
| qd2,fs60,mq40 |
1907 |
0.00 % |
0 |
0.00 % |
1907 |
0.01 % |
| q20,qd2,fs60,mq40 |
760 |
0.00 % |
0 |
0.00 % |
760 |
0.00 % |
| fs60,mq40 |
612 |
0.00 % |
0 |
0.00 % |
612 |
0.00 % |
| q20,fs60,mq40 |
4 |
0.00 % |
0 |
0.00 % |
4 |
0.00 % |
| q20,fs60 |
1 |
0.00 % |
0 |
0.00 % |
1 |
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 |
3785619 |
12.29 % |
| Transition |
G>A |
All |
10604495 |
34.43 % |
| Transition |
T>C |
All |
3033770 |
9.85 % |
| Transition |
C>T |
All |
10402732 |
33.78 % |
| Transversion |
A>C |
All |
222776 |
0.72 % |
| Transversion |
C>A |
All |
574740 |
1.87 % |
| Transversion |
T>G |
All |
293161 |
0.95 % |
| Transversion |
G>T |
All |
534772 |
1.74 % |
| Transversion |
A>T |
All |
436078 |
1.42 % |
| Transversion |
T>A |
All |
481695 |
1.56 % |
| Transversion |
C>G |
All |
229543 |
0.75 % |
| Transversion |
G>C |
All |
198428 |
0.64 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
305885 |
20.08 % |
| Transition |
G>A |
Passed |
259899 |
17.06 % |
| Transition |
T>C |
Passed |
302236 |
19.84 % |
| Transition |
C>T |
Passed |
260596 |
17.11 % |
| Transversion |
A>C |
Passed |
52093 |
3.42 % |
| Transversion |
C>A |
Passed |
46566 |
3.06 % |
| Transversion |
T>G |
Passed |
51947 |
3.41 % |
| Transversion |
G>T |
Passed |
46831 |
3.07 % |
| Transversion |
A>T |
Passed |
29009 |
1.90 % |
| Transversion |
T>A |
Passed |
29054 |
1.91 % |
| Transversion |
C>G |
Passed |
69441 |
4.56 % |
| Transversion |
G>C |
Passed |
69467 |
4.56 % |
| |
|
|
|
|
| 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 |
9.37 |
27826616 |
2971193 |
| Passed |
2.86 |
1128616 |
394408 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |