/EXTERNAL BLUEPRINT/variants/K011718_1_lane_gembs
BACK
SAMPLE K011718_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
539895718 |
56438 |
0.01 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
539895718 |
100% |
535357908 |
99.16 % |
4537810 |
0.84 % |
| |
|
|
|
|
|
|
| Passed |
2087458 |
0.39 % |
32823 |
0.01 % |
2054635 |
98.43 % |
| Filtered |
537808260 |
99.61 % |
535325085 |
99.99 % |
2483175 |
118.96 % |
| |
|
|
|
|
|
|
| q20 |
330383842 |
61.43 % |
328339785 |
61.33 % |
2044057 |
82.32 % |
| q20,qd2 |
153111146 |
28.47 % |
152960232 |
28.57 % |
150914 |
6.08 % |
| q20,mq40 |
33583788 |
6.24 % |
33436955 |
6.25 % |
146833 |
5.91 % |
| q20,qd2,mq40 |
20588064 |
3.83 % |
20574110 |
3.84 % |
13954 |
0.56 % |
| mq40 |
137082 |
0.03 % |
9787 |
0.00 % |
127295 |
5.13 % |
| qd2 |
4007 |
0.00 % |
3973 |
0.00 % |
34 |
0.00 % |
| qd2,mq40 |
302 |
0.00 % |
243 |
0.00 % |
59 |
0.00 % |
| qd2,fs60 |
16 |
0.00 % |
0 |
0.00 % |
16 |
0.00 % |
| fs60 |
8 |
0.00 % |
0 |
0.00 % |
8 |
0.00 % |
| fs60,mq40 |
4 |
0.00 % |
0 |
0.00 % |
4 |
0.00 % |
| qd2,fs60,mq40 |
1 |
0.00 % |
0 |
0.00 % |
1 |
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 % |
| q20,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 |
2127589 |
23.06 % |
| Transition |
G>A |
All |
653131 |
7.08 % |
| Transition |
T>C |
All |
2700723 |
29.27 % |
| Transition |
C>T |
All |
321943 |
3.49 % |
| Transversion |
A>C |
All |
452465 |
4.90 % |
| Transversion |
C>A |
All |
453071 |
4.91 % |
| Transversion |
T>G |
All |
548982 |
5.95 % |
| Transversion |
G>T |
All |
410715 |
4.45 % |
| Transversion |
A>T |
All |
342361 |
3.71 % |
| Transversion |
T>A |
All |
476770 |
5.17 % |
| Transversion |
C>G |
All |
352452 |
3.82 % |
| Transversion |
G>C |
All |
387411 |
4.20 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
3415 |
14.76 % |
| Transition |
G>A |
Passed |
3113 |
13.46 % |
| Transition |
T>C |
Passed |
5661 |
24.47 % |
| Transition |
C>T |
Passed |
1671 |
7.22 % |
| Transversion |
A>C |
Passed |
1090 |
4.71 % |
| Transversion |
C>A |
Passed |
1248 |
5.40 % |
| Transversion |
T>G |
Passed |
1195 |
5.17 % |
| Transversion |
G>T |
Passed |
1030 |
4.45 % |
| Transversion |
A>T |
Passed |
651 |
2.81 % |
| Transversion |
T>A |
Passed |
1095 |
4.73 % |
| Transversion |
C>G |
Passed |
1291 |
5.58 % |
| Transversion |
G>C |
Passed |
1670 |
7.22 % |
| |
|
|
|
|
| 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 |
1.69 |
5803386 |
3424227 |
| Passed |
1.50 |
13860 |
9270 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |