/EXTERNAL BLUEPRINT/variants/K012129_1_lane_gembs
BACK
SAMPLE K012129_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
619609867 |
167133 |
0.03 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
619609867 |
100% |
612821365 |
98.90 % |
6788502 |
1.10 % |
| |
|
|
|
|
|
|
| Passed |
3222114 |
0.52 % |
118756 |
0.02 % |
3103358 |
96.31 % |
| Filtered |
616387753 |
99.48 % |
612702609 |
99.98 % |
3685144 |
114.37 % |
| |
|
|
|
|
|
|
| q20 |
386497798 |
62.70 % |
383492878 |
62.59 % |
3004920 |
81.54 % |
| q20,qd2 |
168540960 |
27.34 % |
168285690 |
27.47 % |
255270 |
6.93 % |
| q20,mq40 |
37945168 |
6.16 % |
37732344 |
6.16 % |
212824 |
5.78 % |
| q20,qd2,mq40 |
23193045 |
3.76 % |
23171071 |
3.78 % |
21974 |
0.60 % |
| mq40 |
207801 |
0.03 % |
17766 |
0.00 % |
190035 |
5.16 % |
| qd2 |
2495 |
0.00 % |
2454 |
0.00 % |
41 |
0.00 % |
| qd2,mq40 |
470 |
0.00 % |
406 |
0.00 % |
64 |
0.00 % |
| qd2,fs60 |
8 |
0.00 % |
0 |
0.00 % |
8 |
0.00 % |
| fs60 |
4 |
0.00 % |
0 |
0.00 % |
4 |
0.00 % |
| fs60,mq40 |
3 |
0.00 % |
0 |
0.00 % |
3 |
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 % |
| q20,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 |
2737347 |
23.21 % |
| Transition |
G>A |
All |
837261 |
7.10 % |
| Transition |
T>C |
All |
3443635 |
29.20 % |
| Transition |
C>T |
All |
402003 |
3.41 % |
| Transversion |
A>C |
All |
583396 |
4.95 % |
| Transversion |
C>A |
All |
593392 |
5.03 % |
| Transversion |
T>G |
All |
703157 |
5.96 % |
| Transversion |
G>T |
All |
533332 |
4.52 % |
| Transversion |
A>T |
All |
429416 |
3.64 % |
| Transversion |
T>A |
All |
601039 |
5.10 % |
| Transversion |
C>G |
All |
441863 |
3.75 % |
| Transversion |
G>C |
All |
487418 |
4.13 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
6936 |
14.64 % |
| Transition |
G>A |
Passed |
7026 |
14.83 % |
| Transition |
T>C |
Passed |
11979 |
25.29 % |
| Transition |
C>T |
Passed |
3043 |
6.42 % |
| Transversion |
A>C |
Passed |
2243 |
4.73 % |
| Transversion |
C>A |
Passed |
2881 |
6.08 % |
| Transversion |
T>G |
Passed |
2236 |
4.72 % |
| Transversion |
G>T |
Passed |
1702 |
3.59 % |
| Transversion |
A>T |
Passed |
1017 |
2.15 % |
| Transversion |
T>A |
Passed |
2459 |
5.19 % |
| Transversion |
C>G |
Passed |
2365 |
4.99 % |
| Transversion |
G>C |
Passed |
3484 |
7.35 % |
| |
|
|
|
|
| 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 |
1.70 |
7420246 |
4373013 |
| Passed |
1.58 |
28984 |
18387 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |