/EXTERNAL BLUEPRINT/variants/K006342_12_lane_gembs
BACK
SAMPLE K006342_12_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1090611726 |
582865694 |
53.44 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1090611726 |
100% |
1073381859 |
98.42 % |
17229867 |
1.58 % |
| |
|
|
|
|
|
|
| Passed |
584441067 |
53.59 % |
581676065 |
54.19 % |
2765002 |
0.47 % |
| Filtered |
506170659 |
46.41 % |
491705794 |
45.81 % |
14464865 |
2.47 % |
| |
|
|
|
|
|
|
| q20 |
421812207 |
83.33 % |
420085575 |
85.43 % |
1726632 |
11.94 % |
| q20,qd2 |
56090169 |
11.08 % |
43925716 |
8.93 % |
12164453 |
84.10 % |
| q20,mq40 |
15633236 |
3.09 % |
15518677 |
3.16 % |
114559 |
0.79 % |
| mq40 |
6651365 |
1.31 % |
6495065 |
1.32 % |
156300 |
1.08 % |
| q20,qd2,mq40 |
3551289 |
0.70 % |
3347097 |
0.68 % |
204192 |
1.41 % |
| qd2 |
2339218 |
0.46 % |
2259705 |
0.46 % |
79513 |
0.55 % |
| qd2,mq40 |
84730 |
0.02 % |
73959 |
0.02 % |
10771 |
0.07 % |
| q20,qd2,fs60 |
2576 |
0.00 % |
0 |
0.00 % |
2576 |
0.02 % |
| fs60 |
1785 |
0.00 % |
0 |
0.00 % |
1785 |
0.01 % |
| qd2,fs60,mq40 |
1496 |
0.00 % |
0 |
0.00 % |
1496 |
0.01 % |
| qd2,fs60 |
1315 |
0.00 % |
0 |
0.00 % |
1315 |
0.01 % |
| q20,qd2,fs60,mq40 |
658 |
0.00 % |
0 |
0.00 % |
658 |
0.00 % |
| fs60,mq40 |
612 |
0.00 % |
0 |
0.00 % |
612 |
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 |
2966793 |
13.52 % |
| Transition |
G>A |
All |
6664281 |
30.38 % |
| Transition |
T>C |
All |
2784109 |
12.69 % |
| Transition |
C>T |
All |
6496263 |
29.61 % |
| Transversion |
A>C |
All |
225255 |
1.03 % |
| Transversion |
C>A |
All |
637269 |
2.90 % |
| Transversion |
T>G |
All |
242116 |
1.10 % |
| Transversion |
G>T |
All |
633268 |
2.89 % |
| Transversion |
A>T |
All |
454575 |
2.07 % |
| Transversion |
T>A |
All |
451033 |
2.06 % |
| Transversion |
C>G |
All |
196146 |
0.89 % |
| Transversion |
G>C |
All |
187316 |
0.85 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
334573 |
18.83 % |
| Transition |
G>A |
Passed |
307955 |
17.33 % |
| Transition |
T>C |
Passed |
333575 |
18.77 % |
| Transition |
C>T |
Passed |
308934 |
17.39 % |
| Transversion |
A>C |
Passed |
65776 |
3.70 % |
| Transversion |
C>A |
Passed |
59788 |
3.36 % |
| Transversion |
T>G |
Passed |
65543 |
3.69 % |
| Transversion |
G>T |
Passed |
60367 |
3.40 % |
| Transversion |
A>T |
Passed |
39347 |
2.21 % |
| Transversion |
T>A |
Passed |
39333 |
2.21 % |
| Transversion |
C>G |
Passed |
80404 |
4.52 % |
| Transversion |
G>C |
Passed |
81352 |
4.58 % |
| |
|
|
|
|
| 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 |
6.25 |
18911446 |
3026978 |
| Passed |
2.61 |
1285037 |
491910 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |