/EXTERNAL BLUEPRINT/variants/K010493_1_lane_gembs
BACK
SAMPLE K010493_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1108283405 |
646269577 |
58.31 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1108283405 |
100% |
1088939609 |
98.25 % |
19343796 |
1.75 % |
| |
|
|
|
|
|
|
| Passed |
648148987 |
58.48 % |
644928322 |
59.23 % |
3220665 |
0.50 % |
| Filtered |
460134418 |
41.52 % |
444011287 |
40.77 % |
16123131 |
2.49 % |
| |
|
|
|
|
|
|
| q20 |
382299381 |
83.08 % |
379740678 |
85.53 % |
2558703 |
15.87 % |
| q20,qd2 |
49501832 |
10.76 % |
36538114 |
8.23 % |
12963718 |
80.40 % |
| q20,mq40 |
15287844 |
3.32 % |
15167526 |
3.42 % |
120318 |
0.75 % |
| mq40 |
6868633 |
1.49 % |
6686586 |
1.51 % |
182047 |
1.13 % |
| q20,qd2,mq40 |
3468094 |
0.75 % |
3276465 |
0.74 % |
191629 |
1.19 % |
| qd2 |
2613985 |
0.57 % |
2526451 |
0.57 % |
87534 |
0.54 % |
| qd2,mq40 |
87478 |
0.02 % |
75467 |
0.02 % |
12011 |
0.07 % |
| q20,qd2,fs60 |
2394 |
0.00 % |
0 |
0.00 % |
2394 |
0.01 % |
| fs60 |
1419 |
0.00 % |
0 |
0.00 % |
1419 |
0.01 % |
| qd2,fs60,mq40 |
1231 |
0.00 % |
0 |
0.00 % |
1231 |
0.01 % |
| qd2,fs60 |
975 |
0.00 % |
0 |
0.00 % |
975 |
0.01 % |
| q20,qd2,fs60,mq40 |
623 |
0.00 % |
0 |
0.00 % |
623 |
0.00 % |
| fs60,mq40 |
526 |
0.00 % |
0 |
0.00 % |
526 |
0.00 % |
| q20,fs60 |
2 |
0.00 % |
0 |
0.00 % |
2 |
0.00 % |
| q20,fs60,mq40 |
1 |
0.00 % |
0 |
0.00 % |
1 |
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 |
3604569 |
14.54 % |
| Transition |
G>A |
All |
7333096 |
29.57 % |
| Transition |
T>C |
All |
3548425 |
14.31 % |
| Transition |
C>T |
All |
7208162 |
29.07 % |
| Transversion |
A>C |
All |
225615 |
0.91 % |
| Transversion |
C>A |
All |
592511 |
2.39 % |
| Transversion |
T>G |
All |
226950 |
0.92 % |
| Transversion |
G>T |
All |
592028 |
2.39 % |
| Transversion |
A>T |
All |
529348 |
2.13 % |
| Transversion |
T>A |
All |
519289 |
2.09 % |
| Transversion |
C>G |
All |
211466 |
0.85 % |
| Transversion |
G>C |
All |
206819 |
0.83 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
374897 |
18.72 % |
| Transition |
G>A |
Passed |
348002 |
17.38 % |
| Transition |
T>C |
Passed |
375886 |
18.77 % |
| Transition |
C>T |
Passed |
347791 |
17.37 % |
| Transversion |
A>C |
Passed |
72781 |
3.64 % |
| Transversion |
C>A |
Passed |
68315 |
3.41 % |
| Transversion |
T>G |
Passed |
72563 |
3.62 % |
| Transversion |
G>T |
Passed |
68224 |
3.41 % |
| Transversion |
A>T |
Passed |
47482 |
2.37 % |
| Transversion |
T>A |
Passed |
46941 |
2.34 % |
| Transversion |
C>G |
Passed |
89323 |
4.46 % |
| Transversion |
G>C |
Passed |
89960 |
4.49 % |
| |
|
|
|
|
| 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 |
6.99 |
21694252 |
3104026 |
| Passed |
2.60 |
1446576 |
555589 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |