/EXTERNAL BLUEPRINT/variants/K006390_K006403_24_lane_gembs
BACK
SAMPLE K006390_K006403_24_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1152002616 |
1025089405 |
88.98 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1152002616 |
100% |
1140924967 |
99.04 % |
11077649 |
0.96 % |
| |
|
|
|
|
|
|
| Passed |
1026295138 |
89.09 % |
1022699747 |
89.64 % |
3595391 |
0.35 % |
| Filtered |
125707478 |
10.91 % |
118225220 |
10.36 % |
7482258 |
0.73 % |
| |
|
|
|
|
|
|
| q20 |
89746427 |
71.39 % |
88855579 |
75.16 % |
890848 |
11.91 % |
| q20,mq40 |
11451354 |
9.11 % |
11346243 |
9.60 % |
105111 |
1.40 % |
| q20,qd2 |
9228552 |
7.34 % |
3336542 |
2.82 % |
5892010 |
78.75 % |
| mq40 |
7167915 |
5.70 % |
6951785 |
5.88 % |
216130 |
2.89 % |
| qd2 |
5218079 |
4.15 % |
5062971 |
4.28 % |
155108 |
2.07 % |
| q20,qd2,mq40 |
2763494 |
2.20 % |
2570777 |
2.17 % |
192717 |
2.58 % |
| qd2,mq40 |
118833 |
0.09 % |
101323 |
0.09 % |
17510 |
0.23 % |
| fs60 |
3726 |
0.00 % |
0 |
0.00 % |
3726 |
0.05 % |
| qd2,fs60 |
2799 |
0.00 % |
0 |
0.00 % |
2799 |
0.04 % |
| q20,qd2,fs60 |
2756 |
0.00 % |
0 |
0.00 % |
2756 |
0.04 % |
| qd2,fs60,mq40 |
2311 |
0.00 % |
0 |
0.00 % |
2311 |
0.03 % |
| fs60,mq40 |
870 |
0.00 % |
0 |
0.00 % |
870 |
0.01 % |
| q20,qd2,fs60,mq40 |
358 |
0.00 % |
0 |
0.00 % |
358 |
0.00 % |
| q20,fs60 |
3 |
0.00 % |
0 |
0.00 % |
3 |
0.00 % |
| q20,fs60,mq40 |
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 |
4086833 |
31.73 % |
| Transition |
G>A |
All |
1130385 |
8.78 % |
| Transition |
T>C |
All |
4050639 |
31.45 % |
| Transition |
C>T |
All |
1144202 |
8.88 % |
| Transversion |
A>C |
All |
215422 |
1.67 % |
| Transversion |
C>A |
All |
463243 |
3.60 % |
| Transversion |
T>G |
All |
218772 |
1.70 % |
| Transversion |
G>T |
All |
465218 |
3.61 % |
| Transversion |
A>T |
All |
355510 |
2.76 % |
| Transversion |
T>A |
All |
344720 |
2.68 % |
| Transversion |
C>G |
All |
203159 |
1.58 % |
| Transversion |
G>C |
All |
201298 |
1.56 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
607121 |
17.21 % |
| Transition |
G>A |
Passed |
583118 |
16.53 % |
| Transition |
T>C |
Passed |
606590 |
17.20 % |
| Transition |
C>T |
Passed |
587604 |
16.66 % |
| Transversion |
A>C |
Passed |
148230 |
4.20 % |
| Transversion |
C>A |
Passed |
148738 |
4.22 % |
| Transversion |
T>G |
Passed |
147800 |
4.19 % |
| Transversion |
G>T |
Passed |
149810 |
4.25 % |
| Transversion |
A>T |
Passed |
126288 |
3.58 % |
| Transversion |
T>A |
Passed |
126140 |
3.58 % |
| Transversion |
C>G |
Passed |
147967 |
4.19 % |
| Transversion |
G>C |
Passed |
148202 |
4.20 % |
| |
|
|
|
|
| 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 |
4.22 |
10412059 |
2467342 |
| Passed |
2.09 |
2384433 |
1143175 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |