/EXTERNAL BLUEPRINT/variants/K010374_K010526_2_lane_gembs
BACK
SAMPLE K010374_K010526_2_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1123970264 |
246863342 |
21.96 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1123970264 |
100% |
1113243492 |
99.05 % |
10726772 |
0.95 % |
| |
|
|
|
|
|
|
| Passed |
250155051 |
22.26 % |
246050034 |
22.10 % |
4105017 |
1.64 % |
| Filtered |
873815213 |
77.74 % |
867193458 |
77.90 % |
6621755 |
2.65 % |
| |
|
|
|
|
|
|
| q20 |
797795018 |
91.30 % |
795361787 |
91.72 % |
2433231 |
36.75 % |
| q20,qd2 |
51455551 |
5.89 % |
47619562 |
5.49 % |
3835989 |
57.93 % |
| q20,mq40 |
17828521 |
2.04 % |
17722682 |
2.04 % |
105839 |
1.60 % |
| q20,qd2,mq40 |
5144939 |
0.59 % |
5041298 |
0.58 % |
103641 |
1.57 % |
| mq40 |
1134866 |
0.13 % |
1016944 |
0.12 % |
117922 |
1.78 % |
| qd2 |
421381 |
0.05 % |
402949 |
0.05 % |
18432 |
0.28 % |
| qd2,mq40 |
33747 |
0.00 % |
28236 |
0.00 % |
5511 |
0.08 % |
| qd2,fs60,mq40 |
511 |
0.00 % |
0 |
0.00 % |
511 |
0.01 % |
| qd2,fs60 |
224 |
0.00 % |
0 |
0.00 % |
224 |
0.00 % |
| fs60,mq40 |
178 |
0.00 % |
0 |
0.00 % |
178 |
0.00 % |
| q20,qd2,fs60,mq40 |
104 |
0.00 % |
0 |
0.00 % |
104 |
0.00 % |
| fs60 |
101 |
0.00 % |
0 |
0.00 % |
101 |
0.00 % |
| q20,qd2,fs60 |
72 |
0.00 % |
0 |
0.00 % |
72 |
0.00 % |
| q20,fs60 |
0 |
0.00 % |
0 |
0.00 % |
0 |
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 |
3209220 |
24.77 % |
| Transition |
G>A |
All |
804613 |
6.21 % |
| Transition |
T>C |
All |
3143022 |
24.25 % |
| Transition |
C>T |
All |
814528 |
6.29 % |
| Transversion |
A>C |
All |
316754 |
2.44 % |
| Transversion |
C>A |
All |
1139419 |
8.79 % |
| Transversion |
T>G |
All |
324540 |
2.50 % |
| Transversion |
G>T |
All |
1132111 |
8.74 % |
| Transversion |
A>T |
All |
796772 |
6.15 % |
| Transversion |
T>A |
All |
775057 |
5.98 % |
| Transversion |
C>G |
All |
255908 |
1.97 % |
| Transversion |
G>C |
All |
246480 |
1.90 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
172498 |
16.74 % |
| Transition |
G>A |
Passed |
161098 |
15.63 % |
| Transition |
T>C |
Passed |
173435 |
16.83 % |
| Transition |
C>T |
Passed |
161290 |
15.65 % |
| Transversion |
A>C |
Passed |
47611 |
4.62 % |
| Transversion |
C>A |
Passed |
45026 |
4.37 % |
| Transversion |
T>G |
Passed |
47895 |
4.65 % |
| Transversion |
G>T |
Passed |
45132 |
4.38 % |
| Transversion |
A>T |
Passed |
32196 |
3.12 % |
| Transversion |
T>A |
Passed |
32305 |
3.13 % |
| Transversion |
C>G |
Passed |
55791 |
5.41 % |
| Transversion |
G>C |
Passed |
56419 |
5.47 % |
| |
|
|
|
|
| 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 |
1.60 |
7971383 |
4987041 |
| Passed |
1.84 |
668321 |
362375 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |