/EXTERNAL BLUEPRINT/variants/K012137_1_lane_gembs
BACK
SAMPLE K012137_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
704358375 |
900925 |
0.13 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
704358375 |
100% |
696058440 |
98.82 % |
8299935 |
1.18 % |
| |
|
|
|
|
|
|
| Passed |
5147223 |
0.73 % |
758790 |
0.11 % |
4388433 |
85.26 % |
| Filtered |
699211152 |
99.27 % |
695299650 |
99.89 % |
3911502 |
75.99 % |
| |
|
|
|
|
|
|
| q20 |
470146590 |
67.24 % |
467121540 |
67.18 % |
3025050 |
77.34 % |
| q20,qd2 |
170784407 |
24.43 % |
170352128 |
24.50 % |
432279 |
11.05 % |
| q20,mq40 |
37280339 |
5.33 % |
37095439 |
5.34 % |
184900 |
4.73 % |
| q20,qd2,mq40 |
20727391 |
2.96 % |
20696172 |
2.98 % |
31219 |
0.80 % |
| mq40 |
271230 |
0.04 % |
33352 |
0.00 % |
237878 |
6.08 % |
| qd2 |
603 |
0.00 % |
531 |
0.00 % |
72 |
0.00 % |
| qd2,mq40 |
579 |
0.00 % |
488 |
0.00 % |
91 |
0.00 % |
| fs60,mq40 |
6 |
0.00 % |
0 |
0.00 % |
6 |
0.00 % |
| q20,qd2,fs60,mq40 |
3 |
0.00 % |
0 |
0.00 % |
3 |
0.00 % |
| fs60 |
2 |
0.00 % |
0 |
0.00 % |
2 |
0.00 % |
| qd2,fs60 |
1 |
0.00 % |
0 |
0.00 % |
1 |
0.00 % |
| q20,qd2,fs60 |
1 |
0.00 % |
0 |
0.00 % |
1 |
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 % |
| qd2,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 |
2874934 |
22.98 % |
| Transition |
G>A |
All |
1014254 |
8.11 % |
| Transition |
T>C |
All |
3774992 |
30.18 % |
| Transition |
C>T |
All |
503774 |
4.03 % |
| Transversion |
A>C |
All |
424218 |
3.39 % |
| Transversion |
C>A |
All |
704283 |
5.63 % |
| Transversion |
T>G |
All |
525787 |
4.20 % |
| Transversion |
G>T |
All |
639845 |
5.12 % |
| Transversion |
A>T |
All |
507763 |
4.06 % |
| Transversion |
T>A |
All |
690870 |
5.52 % |
| Transversion |
C>G |
All |
388172 |
3.10 % |
| Transversion |
G>C |
All |
459367 |
3.67 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
22190 |
15.89 % |
| Transition |
G>A |
Passed |
21510 |
15.40 % |
| Transition |
T>C |
Passed |
37858 |
27.11 % |
| Transition |
C>T |
Passed |
8618 |
6.17 % |
| Transversion |
A>C |
Passed |
5666 |
4.06 % |
| Transversion |
C>A |
Passed |
8347 |
5.98 % |
| Transversion |
T>G |
Passed |
5830 |
4.17 % |
| Transversion |
G>T |
Passed |
4564 |
3.27 % |
| Transversion |
A>T |
Passed |
2693 |
1.93 % |
| Transversion |
T>A |
Passed |
6722 |
4.81 % |
| Transversion |
C>G |
Passed |
6244 |
4.47 % |
| Transversion |
G>C |
Passed |
9427 |
6.75 % |
| |
|
|
|
|
| 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 |
1.88 |
8167954 |
4340305 |
| Passed |
1.82 |
90176 |
49493 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |