/EXTERNAL BLUEPRINT/variants/K006324_15_lane_gembs
BACK
SAMPLE K006324_15_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1059840839 |
519228253 |
48.99 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1059840839 |
100% |
1040808041 |
98.20 % |
19032798 |
1.80 % |
| |
|
|
|
|
|
|
| Passed |
521015277 |
49.16 % |
518200688 |
49.79 % |
2814589 |
0.54 % |
| Filtered |
538825562 |
50.84 % |
522607353 |
50.21 % |
16218209 |
3.11 % |
| |
|
|
|
|
|
|
| q20 |
432169528 |
80.21 % |
430058857 |
82.29 % |
2110671 |
13.01 % |
| q20,qd2 |
67887278 |
12.60 % |
54439198 |
10.42 % |
13448080 |
82.92 % |
| q20,mq40 |
16485754 |
3.06 % |
16362221 |
3.13 % |
123533 |
0.76 % |
| qd2 |
10638248 |
1.97 % |
10533546 |
2.02 % |
104702 |
0.65 % |
| mq40 |
7697467 |
1.43 % |
7520919 |
1.44 % |
176548 |
1.09 % |
| q20,qd2,mq40 |
3825932 |
0.71 % |
3599044 |
0.69 % |
226888 |
1.40 % |
| qd2,mq40 |
106133 |
0.02 % |
93568 |
0.02 % |
12565 |
0.08 % |
| q20,qd2,fs60 |
5721 |
0.00 % |
0 |
0.00 % |
5721 |
0.04 % |
| qd2,fs60 |
3472 |
0.00 % |
0 |
0.00 % |
3472 |
0.02 % |
| fs60 |
2895 |
0.00 % |
0 |
0.00 % |
2895 |
0.02 % |
| qd2,fs60,mq40 |
1673 |
0.00 % |
0 |
0.00 % |
1673 |
0.01 % |
| q20,qd2,fs60,mq40 |
848 |
0.00 % |
0 |
0.00 % |
848 |
0.01 % |
| fs60,mq40 |
605 |
0.00 % |
0 |
0.00 % |
605 |
0.00 % |
| q20,fs60 |
6 |
0.00 % |
0 |
0.00 % |
6 |
0.00 % |
| q20,fs60,mq40 |
2 |
0.00 % |
0 |
0.00 % |
2 |
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 |
3399829 |
10.58 % |
| Transition |
G>A |
All |
11575484 |
36.02 % |
| Transition |
T>C |
All |
2844941 |
8.85 % |
| Transition |
C>T |
All |
11342286 |
35.30 % |
| Transversion |
A>C |
All |
216453 |
0.67 % |
| Transversion |
C>A |
All |
580088 |
1.81 % |
| Transversion |
T>G |
All |
266061 |
0.83 % |
| Transversion |
G>T |
All |
551096 |
1.72 % |
| Transversion |
A>T |
All |
459565 |
1.43 % |
| Transversion |
T>A |
All |
491605 |
1.53 % |
| Transversion |
C>G |
All |
212624 |
0.66 % |
| Transversion |
G>C |
All |
192197 |
0.60 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
306714 |
20.04 % |
| Transition |
G>A |
Passed |
260044 |
16.99 % |
| Transition |
T>C |
Passed |
304930 |
19.92 % |
| Transition |
C>T |
Passed |
259694 |
16.97 % |
| Transversion |
A>C |
Passed |
53751 |
3.51 % |
| Transversion |
C>A |
Passed |
46689 |
3.05 % |
| Transversion |
T>G |
Passed |
53328 |
3.48 % |
| Transversion |
G>T |
Passed |
46707 |
3.05 % |
| Transversion |
A>T |
Passed |
29815 |
1.95 % |
| Transversion |
T>A |
Passed |
29502 |
1.93 % |
| Transversion |
C>G |
Passed |
69899 |
4.57 % |
| Transversion |
G>C |
Passed |
69477 |
4.54 % |
| |
|
|
|
|
| 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 |
9.82 |
29162540 |
2969689 |
| Passed |
2.83 |
1131382 |
399168 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |