/EXTERNAL BLUEPRINT/variants/K011723_1_lane_gembs
BACK
SAMPLE K011723_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
714471563 |
794641 |
0.11 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
714471563 |
100% |
705900227 |
98.80 % |
8571336 |
1.20 % |
| |
|
|
|
|
|
|
| Passed |
5259236 |
0.74 % |
645202 |
0.09 % |
4614034 |
87.73 % |
| Filtered |
709212327 |
99.26 % |
705255025 |
99.91 % |
3957302 |
75.24 % |
| |
|
|
|
|
|
|
| q20 |
480686560 |
67.78 % |
477645543 |
67.73 % |
3041017 |
76.85 % |
| q20,qd2 |
169272683 |
23.87 % |
168829661 |
23.94 % |
443022 |
11.20 % |
| q20,mq40 |
38145542 |
5.38 % |
37955438 |
5.38 % |
190104 |
4.80 % |
| q20,qd2,mq40 |
20817079 |
2.94 % |
20784264 |
2.95 % |
32815 |
0.83 % |
| mq40 |
286099 |
0.04 % |
35964 |
0.01 % |
250135 |
6.32 % |
| qd2 |
3744 |
0.00 % |
3687 |
0.00 % |
57 |
0.00 % |
| qd2,mq40 |
588 |
0.00 % |
468 |
0.00 % |
120 |
0.00 % |
| qd2,fs60 |
13 |
0.00 % |
0 |
0.00 % |
13 |
0.00 % |
| fs60 |
7 |
0.00 % |
0 |
0.00 % |
7 |
0.00 % |
| fs60,mq40 |
7 |
0.00 % |
0 |
0.00 % |
7 |
0.00 % |
| q20,qd2,fs60,mq40 |
3 |
0.00 % |
0 |
0.00 % |
3 |
0.00 % |
| q20,qd2,fs60 |
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 % |
| 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 |
2947959 |
22.77 % |
| Transition |
G>A |
All |
1053427 |
8.14 % |
| Transition |
T>C |
All |
3884302 |
30.01 % |
| Transition |
C>T |
All |
521895 |
4.03 % |
| Transversion |
A>C |
All |
442854 |
3.42 % |
| Transversion |
C>A |
All |
727980 |
5.62 % |
| Transversion |
T>G |
All |
547173 |
4.23 % |
| Transversion |
G>T |
All |
656596 |
5.07 % |
| Transversion |
A>T |
All |
540017 |
4.17 % |
| Transversion |
T>A |
All |
739938 |
5.72 % |
| Transversion |
C>G |
All |
405680 |
3.13 % |
| Transversion |
G>C |
All |
477378 |
3.69 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
23163 |
15.78 % |
| Transition |
G>A |
Passed |
21639 |
14.74 % |
| Transition |
T>C |
Passed |
39595 |
26.97 % |
| Transition |
C>T |
Passed |
8673 |
5.91 % |
| Transversion |
A>C |
Passed |
6105 |
4.16 % |
| Transversion |
C>A |
Passed |
8924 |
6.08 % |
| Transversion |
T>G |
Passed |
6594 |
4.49 % |
| Transversion |
G>T |
Passed |
4856 |
3.31 % |
| Transversion |
A>T |
Passed |
2993 |
2.04 % |
| Transversion |
T>A |
Passed |
7864 |
5.36 % |
| Transversion |
C>G |
Passed |
6637 |
4.52 % |
| Transversion |
G>C |
Passed |
9763 |
6.65 % |
| |
|
|
|
|
| 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 |
1.85 |
8407583 |
4537616 |
| Passed |
1.73 |
93070 |
53736 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |