/Martin Hirst/variants/PX1413_AGCATC_4_lane_gembs
BACK
SAMPLE PX1413_AGCATC_4_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1318188973 |
593181913 |
45.00 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1318188973 |
100% |
1108811593 |
84.12 % |
209377380 |
15.88 % |
| |
|
|
|
|
|
|
| Passed |
638675496 |
48.45 % |
577748624 |
52.11 % |
60926872 |
9.54 % |
| Filtered |
679513477 |
51.55 % |
531062969 |
47.89 % |
148450508 |
23.24 % |
| |
|
|
|
|
|
|
| q20 |
504533477 |
74.25 % |
469598603 |
88.43 % |
34934874 |
23.53 % |
| q20,qd2 |
151235797 |
22.26 % |
40058478 |
7.54 % |
111177319 |
74.89 % |
| qd2 |
11034495 |
1.62 % |
9882008 |
1.86 % |
1152487 |
0.78 % |
| q20,mq40 |
8463499 |
1.25 % |
8135648 |
1.53 % |
327851 |
0.22 % |
| q20,qd2,mq40 |
3184841 |
0.47 % |
2837000 |
0.53 % |
347841 |
0.23 % |
| mq40 |
1022306 |
0.15 % |
522678 |
0.10 % |
499628 |
0.34 % |
| qd2,mq40 |
38896 |
0.01 % |
28554 |
0.01 % |
10342 |
0.01 % |
| qd2,fs60 |
88 |
0.00 % |
0 |
0.00 % |
88 |
0.00 % |
| qd2,fs60,mq40 |
36 |
0.00 % |
0 |
0.00 % |
36 |
0.00 % |
| fs60,mq40 |
22 |
0.00 % |
0 |
0.00 % |
22 |
0.00 % |
| fs60 |
15 |
0.00 % |
0 |
0.00 % |
15 |
0.00 % |
| q20,qd2,fs60 |
5 |
0.00 % |
0 |
0.00 % |
5 |
0.00 % |
| q20,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 |
53552282 |
25.37 % |
| Transition |
G>A |
All |
9560859 |
4.53 % |
| Transition |
T>C |
All |
45472533 |
21.55 % |
| Transition |
C>T |
All |
10195731 |
4.83 % |
| Transversion |
A>C |
All |
6260850 |
2.97 % |
| Transversion |
C>A |
All |
11721349 |
5.55 % |
| Transversion |
T>G |
All |
7294535 |
3.46 % |
| Transversion |
G>T |
All |
11621154 |
5.51 % |
| Transversion |
A>T |
All |
23040792 |
10.92 % |
| Transversion |
T>A |
All |
22678620 |
10.75 % |
| Transversion |
C>G |
All |
5206796 |
2.47 % |
| Transversion |
G>C |
All |
4445354 |
2.11 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
4272369 |
27.48 % |
| Transition |
G>A |
Passed |
798604 |
5.14 % |
| Transition |
T>C |
Passed |
3324985 |
21.39 % |
| Transition |
C>T |
Passed |
880057 |
5.66 % |
| Transversion |
A>C |
Passed |
1021178 |
6.57 % |
| Transversion |
C>A |
Passed |
492226 |
3.17 % |
| Transversion |
T>G |
Passed |
1163288 |
7.48 % |
| Transversion |
G>T |
Passed |
538203 |
3.46 % |
| Transversion |
A>T |
Passed |
773986 |
4.98 % |
| Transversion |
T>A |
Passed |
709569 |
4.56 % |
| Transversion |
C>G |
Passed |
833082 |
5.36 % |
| Transversion |
G>C |
Passed |
739766 |
4.76 % |
| |
|
|
|
|
| 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 |
1.29 |
118781405 |
92269450 |
| Passed |
1.48 |
9276015 |
6271298 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |