/EXTERNAL BLUEPRINT/variants/K006274_11_lane_gembs
BACK
SAMPLE K006274_11_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1126642180 |
690442678 |
61.28 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1126642180 |
100% |
1113122486 |
98.80 % |
13519694 |
1.20 % |
| |
|
|
|
|
|
|
| Passed |
692520411 |
61.47 % |
688931795 |
61.89 % |
3588616 |
0.52 % |
| Filtered |
434121769 |
38.53 % |
424190691 |
38.11 % |
9931078 |
1.43 % |
| |
|
|
|
|
|
|
| q20 |
374522930 |
86.27 % |
372796342 |
87.88 % |
1726588 |
17.39 % |
| q20,qd2 |
33683761 |
7.76 % |
26030264 |
6.14 % |
7653497 |
77.07 % |
| q20,mq40 |
14286265 |
3.29 % |
14188845 |
3.34 % |
97420 |
0.98 % |
| mq40 |
5943059 |
1.37 % |
5772435 |
1.36 % |
170624 |
1.72 % |
| q20,qd2,mq40 |
3115229 |
0.72 % |
2945817 |
0.69 % |
169412 |
1.71 % |
| qd2 |
2492306 |
0.57 % |
2393512 |
0.56 % |
98794 |
0.99 % |
| qd2,mq40 |
73607 |
0.02 % |
63476 |
0.01 % |
10131 |
0.10 % |
| qd2,fs60,mq40 |
1232 |
0.00 % |
0 |
0.00 % |
1232 |
0.01 % |
| q20,qd2,fs60 |
959 |
0.00 % |
0 |
0.00 % |
959 |
0.01 % |
| fs60 |
880 |
0.00 % |
0 |
0.00 % |
880 |
0.01 % |
| qd2,fs60 |
596 |
0.00 % |
0 |
0.00 % |
596 |
0.01 % |
| fs60,mq40 |
507 |
0.00 % |
0 |
0.00 % |
507 |
0.01 % |
| q20,qd2,fs60,mq40 |
437 |
0.00 % |
0 |
0.00 % |
437 |
0.00 % |
| q20,fs60,mq40 |
1 |
0.00 % |
0 |
0.00 % |
1 |
0.00 % |
| q20,fs60 |
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 |
3708603 |
24.14 % |
| Transition |
G>A |
All |
2576857 |
16.77 % |
| Transition |
T>C |
All |
3606900 |
23.48 % |
| Transition |
C>T |
All |
2476777 |
16.12 % |
| Transversion |
A>C |
All |
219287 |
1.43 % |
| Transversion |
C>A |
All |
609756 |
3.97 % |
| Transversion |
T>G |
All |
228464 |
1.49 % |
| Transversion |
G>T |
All |
588477 |
3.83 % |
| Transversion |
A>T |
All |
476537 |
3.10 % |
| Transversion |
T>A |
All |
479415 |
3.12 % |
| Transversion |
C>G |
All |
198573 |
1.29 % |
| Transversion |
G>C |
All |
192596 |
1.25 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
418397 |
18.89 % |
| Transition |
G>A |
Passed |
371051 |
16.75 % |
| Transition |
T>C |
Passed |
417037 |
18.83 % |
| Transition |
C>T |
Passed |
368853 |
16.66 % |
| Transversion |
A>C |
Passed |
83876 |
3.79 % |
| Transversion |
C>A |
Passed |
80006 |
3.61 % |
| Transversion |
T>G |
Passed |
83528 |
3.77 % |
| Transversion |
G>T |
Passed |
79223 |
3.58 % |
| Transversion |
A>T |
Passed |
57828 |
2.61 % |
| Transversion |
T>A |
Passed |
57694 |
2.61 % |
| Transversion |
C>G |
Passed |
98248 |
4.44 % |
| Transversion |
G>C |
Passed |
98910 |
4.47 % |
| |
|
|
|
|
| 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 |
4.13 |
12369137 |
2993105 |
| Passed |
2.46 |
1575338 |
639313 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |