/EXTERNAL BLUEPRINT/variants/K012135_1_lane_gembs
BACK
SAMPLE K012135_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
708788384 |
516814 |
0.07 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
708788384 |
100% |
698771324 |
98.59 % |
10017060 |
1.41 % |
| |
|
|
|
|
|
|
| Passed |
5045859 |
0.71 % |
406658 |
0.06 % |
4639201 |
91.94 % |
| Filtered |
703742525 |
99.29 % |
698364666 |
99.94 % |
5377859 |
106.58 % |
| |
|
|
|
|
|
|
| q20 |
462276010 |
65.69 % |
457958343 |
65.58 % |
4317667 |
80.29 % |
| q20,qd2 |
172286617 |
24.48 % |
171858321 |
24.61 % |
428296 |
7.96 % |
| q20,mq40 |
44068855 |
6.26 % |
43761389 |
6.27 % |
307466 |
5.72 % |
| q20,qd2,mq40 |
24790100 |
3.52 % |
24755558 |
3.54 % |
34542 |
0.64 % |
| mq40 |
319781 |
0.05 % |
30059 |
0.00 % |
289722 |
5.39 % |
| qd2,mq40 |
671 |
0.00 % |
560 |
0.00 % |
111 |
0.00 % |
| qd2 |
486 |
0.00 % |
436 |
0.00 % |
50 |
0.00 % |
| fs60 |
2 |
0.00 % |
0 |
0.00 % |
2 |
0.00 % |
| fs60,mq40 |
2 |
0.00 % |
0 |
0.00 % |
2 |
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 % |
| qd2,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 |
3568024 |
23.45 % |
| Transition |
G>A |
All |
1082998 |
7.12 % |
| Transition |
T>C |
All |
4471073 |
29.39 % |
| Transition |
C>T |
All |
512400 |
3.37 % |
| Transversion |
A>C |
All |
755345 |
4.97 % |
| Transversion |
C>A |
All |
744225 |
4.89 % |
| Transversion |
T>G |
All |
913278 |
6.00 % |
| Transversion |
G>T |
All |
659781 |
4.34 % |
| Transversion |
A>T |
All |
549824 |
3.61 % |
| Transversion |
T>A |
All |
772196 |
5.08 % |
| Transversion |
C>G |
All |
565124 |
3.71 % |
| Transversion |
G>C |
All |
619001 |
4.07 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
16268 |
15.09 % |
| Transition |
G>A |
Passed |
15613 |
14.49 % |
| Transition |
T>C |
Passed |
28914 |
26.83 % |
| Transition |
C>T |
Passed |
6694 |
6.21 % |
| Transversion |
A>C |
Passed |
5009 |
4.65 % |
| Transversion |
C>A |
Passed |
6109 |
5.67 % |
| Transversion |
T>G |
Passed |
5150 |
4.78 % |
| Transversion |
G>T |
Passed |
3552 |
3.30 % |
| Transversion |
A>T |
Passed |
2308 |
2.14 % |
| Transversion |
T>A |
Passed |
5561 |
5.16 % |
| Transversion |
C>G |
Passed |
5162 |
4.79 % |
| Transversion |
G>C |
Passed |
7436 |
6.90 % |
| |
|
|
|
|
| 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 |
1.73 |
9634495 |
5578774 |
| Passed |
1.68 |
67489 |
40287 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |