/EXTERNAL BLUEPRINT/variants/K010391_K011797_30libs_30_lane_gembs
BACK
SAMPLE K010391_K011797_30libs_30_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1101662615 |
125314146 |
11.38 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1101662615 |
100% |
1055471573 |
95.81 % |
46191042 |
4.19 % |
| |
|
|
|
|
|
|
| Passed |
143275096 |
13.01 % |
121961690 |
11.56 % |
21313406 |
14.88 % |
| Filtered |
958387519 |
86.99 % |
933509883 |
88.44 % |
24877636 |
17.36 % |
| |
|
|
|
|
|
|
| q20 |
848348550 |
88.52 % |
834436362 |
89.39 % |
13912188 |
55.92 % |
| q20,mq40 |
60834280 |
6.35 % |
60097371 |
6.44 % |
736909 |
2.96 % |
| q20,qd2 |
36857566 |
3.85 % |
27931967 |
2.99 % |
8925599 |
35.88 % |
| q20,qd2,mq40 |
9858800 |
1.03 % |
9608465 |
1.03 % |
250335 |
1.01 % |
| mq40 |
2405312 |
0.25 % |
1374181 |
0.15 % |
1031131 |
4.14 % |
| qd2 |
75365 |
0.01 % |
55895 |
0.01 % |
19470 |
0.08 % |
| qd2,mq40 |
7471 |
0.00 % |
5642 |
0.00 % |
1829 |
0.01 % |
| fs60,mq40 |
74 |
0.00 % |
0 |
0.00 % |
74 |
0.00 % |
| qd2,fs60,mq40 |
44 |
0.00 % |
0 |
0.00 % |
44 |
0.00 % |
| fs60 |
27 |
0.00 % |
0 |
0.00 % |
27 |
0.00 % |
| qd2,fs60 |
26 |
0.00 % |
0 |
0.00 % |
26 |
0.00 % |
| q20,qd2,fs60 |
3 |
0.00 % |
0 |
0.00 % |
3 |
0.00 % |
| q20,qd2,fs60,mq40 |
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 % |
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 |
11614653 |
23.67 % |
| Transition |
G>A |
All |
3873764 |
7.89 % |
| Transition |
T>C |
All |
14622108 |
29.80 % |
| Transition |
C>T |
All |
1790520 |
3.65 % |
| Transversion |
A>C |
All |
1809037 |
3.69 % |
| Transversion |
C>A |
All |
2635350 |
5.37 % |
| Transversion |
T>G |
All |
1920313 |
3.91 % |
| Transversion |
G>T |
All |
2381721 |
4.85 % |
| Transversion |
A>T |
All |
2110898 |
4.30 % |
| Transversion |
T>A |
All |
2910779 |
5.93 % |
| Transversion |
C>G |
All |
1561546 |
3.18 % |
| Transversion |
G>C |
All |
1841612 |
3.75 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
624376 |
18.46 % |
| Transition |
G>A |
Passed |
381280 |
11.27 % |
| Transition |
T>C |
Passed |
1145047 |
33.85 % |
| Transition |
C>T |
Passed |
175865 |
5.20 % |
| Transversion |
A>C |
Passed |
144434 |
4.27 % |
| Transversion |
C>A |
Passed |
138264 |
4.09 % |
| Transversion |
T>G |
Passed |
136237 |
4.03 % |
| Transversion |
G>T |
Passed |
86392 |
2.55 % |
| Transversion |
A>T |
Passed |
79335 |
2.35 % |
| Transversion |
T>A |
Passed |
179322 |
5.30 % |
| Transversion |
C>G |
Passed |
123016 |
3.64 % |
| Transversion |
G>C |
Passed |
169012 |
5.00 % |
| |
|
|
|
|
| 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 |
1.86 |
31901045 |
17171256 |
| Passed |
2.20 |
2326568 |
1056012 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |