/TFF-PPG/variants/PX0587_CTATAC_10_lane_gembs
BACK
SAMPLE PX0587_CTATAC_10_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1201785176 |
663545198 |
55.21 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1201785176 |
100% |
1123285905 |
93.47 % |
78499271 |
6.53 % |
| |
|
|
|
|
|
|
| Passed |
682391685 |
56.78 % |
658207221 |
58.60 % |
24184464 |
3.54 % |
| Filtered |
519393491 |
43.22 % |
465078684 |
41.40 % |
54314807 |
7.96 % |
| |
|
|
|
|
|
|
| q20 |
426417151 |
82.10 % |
410083699 |
88.18 % |
16333452 |
30.07 % |
| q20,qd2 |
68027774 |
13.10 % |
31646041 |
6.80 % |
36381733 |
66.98 % |
| qd2 |
12409978 |
2.39 % |
11428321 |
2.46 % |
981657 |
1.81 % |
| q20,mq40 |
8043721 |
1.55 % |
7838878 |
1.69 % |
204843 |
0.38 % |
| q20,qd2,mq40 |
3784228 |
0.73 % |
3620609 |
0.78 % |
163619 |
0.30 % |
| mq40 |
681780 |
0.13 % |
439769 |
0.09 % |
242011 |
0.45 % |
| qd2,mq40 |
28858 |
0.01 % |
21367 |
0.00 % |
7491 |
0.01 % |
| q20,qd2,fs60 |
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 % |
| 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 % |
| qd2,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 |
20046376 |
24.64 % |
| Transition |
G>A |
All |
4284571 |
5.27 % |
| Transition |
T>C |
All |
20310490 |
24.96 % |
| Transition |
C>T |
All |
4347830 |
5.34 % |
| Transversion |
A>C |
All |
3217478 |
3.95 % |
| Transversion |
C>A |
All |
3734481 |
4.59 % |
| Transversion |
T>G |
All |
3093693 |
3.80 % |
| Transversion |
G>T |
All |
3843295 |
4.72 % |
| Transversion |
A>T |
All |
7527318 |
9.25 % |
| Transversion |
T>A |
All |
7359310 |
9.04 % |
| Transversion |
C>G |
All |
1771067 |
2.18 % |
| Transversion |
G>C |
All |
1831855 |
2.25 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
1481753 |
25.33 % |
| Transition |
G>A |
Passed |
502567 |
8.59 % |
| Transition |
T>C |
Passed |
1580692 |
27.02 % |
| Transition |
C>T |
Passed |
522251 |
8.93 % |
| Transversion |
A>C |
Passed |
302273 |
5.17 % |
| Transversion |
C>A |
Passed |
162747 |
2.78 % |
| Transversion |
T>G |
Passed |
276752 |
4.73 % |
| Transversion |
G>T |
Passed |
170351 |
2.91 % |
| Transversion |
A>T |
Passed |
204831 |
3.50 % |
| Transversion |
T>A |
Passed |
187386 |
3.20 % |
| Transversion |
C>G |
Passed |
221474 |
3.79 % |
| Transversion |
G>C |
Passed |
235985 |
4.03 % |
| |
|
|
|
|
| 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 |
1.51 |
48989267 |
32378497 |
| Passed |
2.32 |
4087263 |
1761799 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |