/EXTERNAL BLUEPRINT/variants/K012136_1_lane_gembs
BACK
SAMPLE K012136_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
676789544 |
747721 |
0.11 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
676789544 |
100% |
668768507 |
98.81 % |
8021037 |
1.19 % |
| |
|
|
|
|
|
|
| Passed |
4782618 |
0.71 % |
647279 |
0.10 % |
4135339 |
86.47 % |
| Filtered |
672006926 |
99.29 % |
668121228 |
99.90 % |
3885698 |
81.25 % |
| |
|
|
|
|
|
|
| q20 |
445520054 |
66.30 % |
442463428 |
66.23 % |
3056626 |
78.66 % |
| q20,qd2 |
167870807 |
24.98 % |
167480103 |
25.07 % |
390704 |
10.05 % |
| q20,mq40 |
36995048 |
5.51 % |
36808342 |
5.51 % |
186706 |
4.80 % |
| q20,qd2,mq40 |
21362609 |
3.18 % |
21335112 |
3.19 % |
27497 |
0.71 % |
| mq40 |
257019 |
0.04 % |
33021 |
0.00 % |
223998 |
5.76 % |
| qd2 |
772 |
0.00 % |
701 |
0.00 % |
71 |
0.00 % |
| qd2,mq40 |
605 |
0.00 % |
521 |
0.00 % |
84 |
0.00 % |
| fs60 |
6 |
0.00 % |
0 |
0.00 % |
6 |
0.00 % |
| fs60,mq40 |
2 |
0.00 % |
0 |
0.00 % |
2 |
0.00 % |
| qd2,fs60,mq40 |
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 % |
| 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 |
2851760 |
23.18 % |
| Transition |
G>A |
All |
987043 |
8.02 % |
| Transition |
T>C |
All |
3706742 |
30.13 % |
| Transition |
C>T |
All |
488340 |
3.97 % |
| Transversion |
A>C |
All |
451449 |
3.67 % |
| Transversion |
C>A |
All |
658311 |
5.35 % |
| Transversion |
T>G |
All |
564478 |
4.59 % |
| Transversion |
G>T |
All |
588595 |
4.78 % |
| Transversion |
A>T |
All |
477345 |
3.88 % |
| Transversion |
T>A |
All |
660481 |
5.37 % |
| Transversion |
C>G |
All |
401353 |
3.26 % |
| Transversion |
G>C |
All |
465039 |
3.78 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
14813 |
15.01 % |
| Transition |
G>A |
Passed |
15243 |
15.44 % |
| Transition |
T>C |
Passed |
26948 |
27.30 % |
| Transition |
C>T |
Passed |
7125 |
7.22 % |
| Transversion |
A>C |
Passed |
4206 |
4.26 % |
| Transversion |
C>A |
Passed |
5359 |
5.43 % |
| Transversion |
T>G |
Passed |
4356 |
4.41 % |
| Transversion |
G>T |
Passed |
3097 |
3.14 % |
| Transversion |
A>T |
Passed |
1905 |
1.93 % |
| Transversion |
T>A |
Passed |
4509 |
4.57 % |
| Transversion |
C>G |
Passed |
4465 |
4.52 % |
| Transversion |
G>C |
Passed |
6672 |
6.76 % |
| |
|
|
|
|
| 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 |
8033885 |
4267051 |
| Passed |
1.86 |
64129 |
34569 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |