/EXTERNAL BLUEPRINT/variants/K012033_K012040_K012041_K012042_K012043_K012044_K012045_K012046_K012047_K012106_K012107_11_lane_gembs
BACK
SAMPLE K012033_K012040_K012041_K012042_K012043_K012044_K012045_K012046_K012047_K012106_K012107_11_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
926138084 |
7544329 |
0.81 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
926138084 |
100% |
906662211 |
97.90 % |
19475873 |
2.10 % |
| |
|
|
|
|
|
|
| Passed |
18102872 |
1.95 % |
6921872 |
0.76 % |
11181000 |
61.76 % |
| Filtered |
908035212 |
98.05 % |
899740339 |
99.24 % |
8294873 |
45.82 % |
| |
|
|
|
|
|
|
| q20 |
716631711 |
78.92 % |
710929144 |
79.01 % |
5702567 |
68.75 % |
| q20,qd2 |
120245742 |
13.24 % |
118639560 |
13.19 % |
1606182 |
19.36 % |
| q20,mq40 |
51755433 |
5.70 % |
51417594 |
5.71 % |
337839 |
4.07 % |
| q20,qd2,mq40 |
18690901 |
2.06 % |
18599878 |
2.07 % |
91023 |
1.10 % |
| mq40 |
702724 |
0.08 % |
146327 |
0.02 % |
556397 |
6.71 % |
| qd2 |
6707 |
0.00 % |
6301 |
0.00 % |
406 |
0.00 % |
| qd2,mq40 |
1942 |
0.00 % |
1535 |
0.00 % |
407 |
0.00 % |
| qd2,fs60 |
19 |
0.00 % |
0 |
0.00 % |
19 |
0.00 % |
| fs60,mq40 |
15 |
0.00 % |
0 |
0.00 % |
15 |
0.00 % |
| fs60 |
9 |
0.00 % |
0 |
0.00 % |
9 |
0.00 % |
| qd2,fs60,mq40 |
6 |
0.00 % |
0 |
0.00 % |
6 |
0.00 % |
| q20,qd2,fs60,mq40 |
3 |
0.00 % |
0 |
0.00 % |
3 |
0.00 % |
| q20,fs60 |
0 |
0.00 % |
0 |
0.00 % |
0 |
0.00 % |
| q20,qd2,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 |
5377840 |
22.51 % |
| Transition |
G>A |
All |
1960709 |
8.21 % |
| Transition |
T>C |
All |
6949284 |
29.09 % |
| Transition |
C>T |
All |
918170 |
3.84 % |
| Transversion |
A>C |
All |
777188 |
3.25 % |
| Transversion |
C>A |
All |
1483090 |
6.21 % |
| Transversion |
T>G |
All |
910017 |
3.81 % |
| Transversion |
G>T |
All |
1330139 |
5.57 % |
| Transversion |
A>T |
All |
1135197 |
4.75 % |
| Transversion |
T>A |
All |
1554710 |
6.51 % |
| Transversion |
C>G |
All |
677994 |
2.84 % |
| Transversion |
G>C |
All |
818614 |
3.43 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
103723 |
16.77 % |
| Transition |
G>A |
Passed |
81086 |
13.11 % |
| Transition |
T>C |
Passed |
167661 |
27.11 % |
| Transition |
C>T |
Passed |
37177 |
6.01 % |
| Transversion |
A>C |
Passed |
26337 |
4.26 % |
| Transversion |
C>A |
Passed |
37119 |
6.00 % |
| Transversion |
T>G |
Passed |
28481 |
4.61 % |
| Transversion |
G>T |
Passed |
22753 |
3.68 % |
| Transversion |
A>T |
Passed |
15624 |
2.53 % |
| Transversion |
T>A |
Passed |
36188 |
5.85 % |
| Transversion |
C>G |
Passed |
26945 |
4.36 % |
| Transversion |
G>C |
Passed |
35295 |
5.71 % |
| |
|
|
|
|
| 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 |
1.75 |
15206003 |
8686949 |
| Passed |
1.70 |
389647 |
228742 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |