/EXTERNAL BLUEPRINT/variants/K006422_14_lane_gembs
BACK
SAMPLE K006422_14_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1157541648 |
1031622215 |
89.12 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1157541648 |
100% |
1144260204 |
98.85 % |
13281444 |
1.15 % |
| |
|
|
|
|
|
|
| Passed |
1032761539 |
89.22 % |
1029218721 |
89.95 % |
3542818 |
0.34 % |
| Filtered |
124780109 |
10.78 % |
115041483 |
10.05 % |
9738626 |
0.94 % |
| |
|
|
|
|
|
|
| q20 |
88224552 |
70.70 % |
87374139 |
75.95 % |
850413 |
8.73 % |
| q20,mq40 |
13425634 |
10.76 % |
13304885 |
11.57 % |
120749 |
1.24 % |
| q20,qd2 |
13147886 |
10.54 % |
4958494 |
4.31 % |
8189392 |
84.09 % |
| mq40 |
4402135 |
3.53 % |
4180035 |
3.63 % |
222100 |
2.28 % |
| q20,qd2,mq40 |
3103891 |
2.49 % |
2886442 |
2.51 % |
217449 |
2.23 % |
| qd2 |
2427787 |
1.95 % |
2298921 |
2.00 % |
128866 |
1.32 % |
| qd2,mq40 |
46882 |
0.04 % |
38567 |
0.03 % |
8315 |
0.09 % |
| qd2,fs60,mq40 |
601 |
0.00 % |
0 |
0.00 % |
601 |
0.01 % |
| fs60,mq40 |
328 |
0.00 % |
0 |
0.00 % |
328 |
0.00 % |
| qd2,fs60 |
178 |
0.00 % |
0 |
0.00 % |
178 |
0.00 % |
| fs60 |
137 |
0.00 % |
0 |
0.00 % |
137 |
0.00 % |
| q20,qd2,fs60,mq40 |
73 |
0.00 % |
0 |
0.00 % |
73 |
0.00 % |
| q20,qd2,fs60 |
23 |
0.00 % |
0 |
0.00 % |
23 |
0.00 % |
| q20,fs60,mq40 |
2 |
0.00 % |
0 |
0.00 % |
2 |
0.00 % |
| q20,fs60 |
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 |
4927478 |
32.87 % |
| Transition |
G>A |
All |
1068274 |
7.13 % |
| Transition |
T>C |
All |
4875861 |
32.53 % |
| Transition |
C>T |
All |
1068856 |
7.13 % |
| Transversion |
A>C |
All |
223564 |
1.49 % |
| Transversion |
C>A |
All |
626534 |
4.18 % |
| Transversion |
T>G |
All |
225840 |
1.51 % |
| Transversion |
G>T |
All |
621022 |
4.14 % |
| Transversion |
A>T |
All |
468799 |
3.13 % |
| Transversion |
T>A |
All |
464960 |
3.10 % |
| Transversion |
C>G |
All |
209292 |
1.40 % |
| Transversion |
G>C |
All |
209038 |
1.39 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
623821 |
17.34 % |
| Transition |
G>A |
Passed |
582137 |
16.18 % |
| Transition |
T>C |
Passed |
625112 |
17.38 % |
| Transition |
C>T |
Passed |
585729 |
16.28 % |
| Transversion |
A>C |
Passed |
150753 |
4.19 % |
| Transversion |
C>A |
Passed |
156354 |
4.35 % |
| Transversion |
T>G |
Passed |
151368 |
4.21 % |
| Transversion |
G>T |
Passed |
156392 |
4.35 % |
| Transversion |
A>T |
Passed |
133258 |
3.70 % |
| Transversion |
T>A |
Passed |
133123 |
3.70 % |
| Transversion |
C>G |
Passed |
149512 |
4.16 % |
| Transversion |
G>C |
Passed |
149416 |
4.15 % |
| |
|
|
|
|
| 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 |
3.92 |
11940469 |
3049049 |
| Passed |
2.05 |
2416799 |
1180176 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |