/EXTERNAL BLUEPRINT/variants/K011728_K011737_K011738_K011739_K011740_K011741_K011742_K011743_K011744_K011768_K011769_11_lane_gembs
BACK
SAMPLE K011728_K011737_K011738_K011739_K011740_K011741_K011742_K011743_K011744_K011768_K011769_11_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
954233167 |
11484929 |
1.20 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
954233167 |
100% |
931228120 |
97.59 % |
23005047 |
2.41 % |
| |
|
|
|
|
|
|
| Passed |
21311762 |
2.23 % |
10747081 |
1.15 % |
10564681 |
49.57 % |
| Filtered |
932921405 |
97.77 % |
920481039 |
98.85 % |
12440366 |
58.37 % |
| |
|
|
|
|
|
|
| q20 |
728340130 |
78.07 % |
719665522 |
78.18 % |
8674608 |
69.73 % |
| q20,qd2 |
118951663 |
12.75 % |
116527063 |
12.66 % |
2424600 |
19.49 % |
| q20,mq40 |
61561612 |
6.60 % |
60977909 |
6.62 % |
583703 |
4.69 % |
| q20,qd2,mq40 |
23233735 |
2.49 % |
23095717 |
2.51 % |
138018 |
1.11 % |
| mq40 |
825417 |
0.09 % |
206920 |
0.02 % |
618497 |
4.97 % |
| qd2 |
6652 |
0.00 % |
6199 |
0.00 % |
453 |
0.00 % |
| qd2,mq40 |
2150 |
0.00 % |
1709 |
0.00 % |
441 |
0.00 % |
| fs60,mq40 |
23 |
0.00 % |
0 |
0.00 % |
23 |
0.00 % |
| qd2,fs60 |
9 |
0.00 % |
0 |
0.00 % |
9 |
0.00 % |
| fs60 |
7 |
0.00 % |
0 |
0.00 % |
7 |
0.00 % |
| q20,qd2,fs60 |
3 |
0.00 % |
0 |
0.00 % |
3 |
0.00 % |
| qd2,fs60,mq40 |
2 |
0.00 % |
0 |
0.00 % |
2 |
0.00 % |
| q20,qd2,fs60,mq40 |
2 |
0.00 % |
0 |
0.00 % |
2 |
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 % |
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 |
6142008 |
22.44 % |
| Transition |
G>A |
All |
2149421 |
7.85 % |
| Transition |
T>C |
All |
7708512 |
28.17 % |
| Transition |
C>T |
All |
977154 |
3.57 % |
| Transversion |
A>C |
All |
985302 |
3.60 % |
| Transversion |
C>A |
All |
1753698 |
6.41 % |
| Transversion |
T>G |
All |
1197493 |
4.38 % |
| Transversion |
G>T |
All |
1577547 |
5.76 % |
| Transversion |
A>T |
All |
1226863 |
4.48 % |
| Transversion |
T>A |
All |
1695298 |
6.20 % |
| Transversion |
C>G |
All |
900690 |
3.29 % |
| Transversion |
G>C |
All |
1051334 |
3.84 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
132081 |
17.93 % |
| Transition |
G>A |
Passed |
97015 |
13.17 % |
| Transition |
T>C |
Passed |
218807 |
29.71 % |
| Transition |
C>T |
Passed |
38542 |
5.23 % |
| Transversion |
A>C |
Passed |
28247 |
3.84 % |
| Transversion |
C>A |
Passed |
41499 |
5.64 % |
| Transversion |
T>G |
Passed |
31637 |
4.30 % |
| Transversion |
G>T |
Passed |
23258 |
3.16 % |
| Transversion |
A>T |
Passed |
14352 |
1.95 % |
| Transversion |
T>A |
Passed |
39097 |
5.31 % |
| Transversion |
C>G |
Passed |
29859 |
4.05 % |
| Transversion |
G>C |
Passed |
42052 |
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 |
1.63 |
16977095 |
10388225 |
| Passed |
1.95 |
486445 |
250001 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |