/TFF-PPG/variants/PX0587_ACCGGC_10_lane_gembs
BACK
SAMPLE PX0587_ACCGGC_10_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1198859087 |
600625876 |
50.10 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1198859087 |
100% |
1120776353 |
93.49 % |
78082734 |
6.51 % |
| |
|
|
|
|
|
|
| Passed |
619871970 |
51.71 % |
595370232 |
53.12 % |
24501738 |
3.95 % |
| Filtered |
578987117 |
48.29 % |
525406121 |
46.88 % |
53580996 |
8.64 % |
| |
|
|
|
|
|
|
| q20 |
482329018 |
83.31 % |
465488973 |
88.60 % |
16840045 |
31.43 % |
| q20,qd2 |
72645140 |
12.55 % |
37273060 |
7.09 % |
35372080 |
66.02 % |
| qd2 |
9853767 |
1.70 % |
9105480 |
1.73 % |
748287 |
1.40 % |
| q20,mq40 |
9101255 |
1.57 % |
8886543 |
1.69 % |
214712 |
0.40 % |
| q20,qd2,mq40 |
4398273 |
0.76 % |
4238414 |
0.81 % |
159859 |
0.30 % |
| mq40 |
637808 |
0.11 % |
396903 |
0.08 % |
240905 |
0.45 % |
| qd2,mq40 |
21854 |
0.00 % |
16748 |
0.00 % |
5106 |
0.01 % |
| qd2,fs60 |
1 |
0.00 % |
0 |
0.00 % |
1 |
0.00 % |
| qd2,fs60,mq40 |
1 |
0.00 % |
0 |
0.00 % |
1 |
0.00 % |
| fs60 |
0 |
0.00 % |
0 |
0.00 % |
0 |
0.00 % |
| q20,fs60 |
0 |
0.00 % |
0 |
0.00 % |
0 |
0.00 % |
| q20,qd2,fs60 |
0 |
0.00 % |
0 |
0.00 % |
0 |
0.00 % |
| fs60,mq40 |
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 |
19141839 |
23.53 % |
| Transition |
G>A |
All |
4268419 |
5.25 % |
| Transition |
T>C |
All |
19505852 |
23.98 % |
| Transition |
C>T |
All |
4306478 |
5.29 % |
| Transversion |
A>C |
All |
3425394 |
4.21 % |
| Transversion |
C>A |
All |
3979261 |
4.89 % |
| Transversion |
T>G |
All |
3295587 |
4.05 % |
| Transversion |
G>T |
All |
4091071 |
5.03 % |
| Transversion |
A>T |
All |
7774988 |
9.56 % |
| Transversion |
T>A |
All |
7609797 |
9.36 % |
| Transversion |
C>G |
All |
1931703 |
2.37 % |
| Transversion |
G>C |
All |
2008592 |
2.47 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
1371880 |
23.79 % |
| Transition |
G>A |
Passed |
541315 |
9.39 % |
| Transition |
T>C |
Passed |
1470419 |
25.49 % |
| Transition |
C>T |
Passed |
561103 |
9.73 % |
| Transversion |
A>C |
Passed |
308179 |
5.34 % |
| Transversion |
C>A |
Passed |
173229 |
3.00 % |
| Transversion |
T>G |
Passed |
282888 |
4.90 % |
| Transversion |
G>T |
Passed |
180718 |
3.13 % |
| Transversion |
A>T |
Passed |
201121 |
3.49 % |
| Transversion |
T>A |
Passed |
185199 |
3.21 % |
| Transversion |
C>G |
Passed |
238768 |
4.14 % |
| Transversion |
G>C |
Passed |
253014 |
4.39 % |
| |
|
|
|
|
| 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 |
1.38 |
47222588 |
34116393 |
| Passed |
2.16 |
3944717 |
1823116 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |