/EXTERNAL BLUEPRINT/variants/K010380_K011765_32libs_32_lane_gembs
BACK
SAMPLE K010380_K011765_32libs_32_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1089638420 |
95420353 |
8.76 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1089638420 |
100% |
1044232828 |
95.83 % |
45405592 |
4.17 % |
| |
|
|
|
|
|
|
| Passed |
113177588 |
10.39 % |
92553694 |
8.86 % |
20623894 |
18.22 % |
| Filtered |
976460832 |
89.61 % |
951679134 |
91.14 % |
24781698 |
21.90 % |
| |
|
|
|
|
|
|
| q20 |
851523362 |
87.21 % |
837311841 |
87.98 % |
14211521 |
57.35 % |
| q20,mq40 |
65244539 |
6.68 % |
64429141 |
6.77 % |
815398 |
3.29 % |
| q20,qd2 |
45446315 |
4.65 % |
37075653 |
3.90 % |
8370662 |
33.78 % |
| q20,qd2,mq40 |
11837167 |
1.21 % |
11563685 |
1.22 % |
273482 |
1.10 % |
| mq40 |
2345803 |
0.24 % |
1249869 |
0.13 % |
1095934 |
4.42 % |
| qd2 |
56116 |
0.01 % |
43270 |
0.00 % |
12846 |
0.05 % |
| qd2,mq40 |
7385 |
0.00 % |
5675 |
0.00 % |
1710 |
0.01 % |
| fs60,mq40 |
64 |
0.00 % |
0 |
0.00 % |
64 |
0.00 % |
| qd2,fs60,mq40 |
37 |
0.00 % |
0 |
0.00 % |
37 |
0.00 % |
| fs60 |
21 |
0.00 % |
0 |
0.00 % |
21 |
0.00 % |
| qd2,fs60 |
18 |
0.00 % |
0 |
0.00 % |
18 |
0.00 % |
| q20,qd2,fs60,mq40 |
5 |
0.00 % |
0 |
0.00 % |
5 |
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 |
11037231 |
22.76 % |
| Transition |
G>A |
All |
3765598 |
7.76 % |
| Transition |
T>C |
All |
13868965 |
28.59 % |
| Transition |
C>T |
All |
1710465 |
3.53 % |
| Transversion |
A>C |
All |
1817930 |
3.75 % |
| Transversion |
C>A |
All |
2912262 |
6.00 % |
| Transversion |
T>G |
All |
1992330 |
4.11 % |
| Transversion |
G>T |
All |
2638302 |
5.44 % |
| Transversion |
A>T |
All |
2154289 |
4.44 % |
| Transversion |
T>A |
All |
2972928 |
6.13 % |
| Transversion |
C>G |
All |
1684835 |
3.47 % |
| Transversion |
G>C |
All |
1949114 |
4.02 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
528969 |
18.34 % |
| Transition |
G>A |
Passed |
327206 |
11.34 % |
| Transition |
T>C |
Passed |
931297 |
32.28 % |
| Transition |
C>T |
Passed |
152669 |
5.29 % |
| Transversion |
A>C |
Passed |
121358 |
4.21 % |
| Transversion |
C>A |
Passed |
131754 |
4.57 % |
| Transversion |
T>G |
Passed |
121520 |
4.21 % |
| Transversion |
G>T |
Passed |
81693 |
2.83 % |
| Transversion |
A>T |
Passed |
67539 |
2.34 % |
| Transversion |
T>A |
Passed |
151915 |
5.27 % |
| Transversion |
C>G |
Passed |
118631 |
4.11 % |
| Transversion |
G>C |
Passed |
150182 |
5.21 % |
| |
|
|
|
|
| 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 |
1.68 |
30382259 |
18121990 |
| Passed |
2.05 |
1940141 |
944592 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |