/TFF-PPG/variants/PX0587_AGGCCG_10_lane_gembs
BACK
SAMPLE PX0587_AGGCCG_10_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1199750753 |
628858110 |
52.42 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1199750753 |
100% |
1120434149 |
93.39 % |
79316604 |
6.61 % |
| |
|
|
|
|
|
|
| Passed |
648309861 |
54.04 % |
623763483 |
55.67 % |
24546378 |
3.79 % |
| Filtered |
551440892 |
45.96 % |
496670666 |
44.33 % |
54770226 |
8.45 % |
| |
|
|
|
|
|
|
| q20 |
457183804 |
82.91 % |
440611771 |
88.71 % |
16572033 |
30.26 % |
| q20,qd2 |
70516990 |
12.79 % |
33738151 |
6.79 % |
36778839 |
67.15 % |
| qd2 |
10833030 |
1.96 % |
9996451 |
2.01 % |
836579 |
1.53 % |
| q20,mq40 |
8296734 |
1.50 % |
8099554 |
1.63 % |
197180 |
0.36 % |
| q20,qd2,mq40 |
3983283 |
0.72 % |
3831236 |
0.77 % |
152047 |
0.28 % |
| mq40 |
604734 |
0.11 % |
376679 |
0.08 % |
228055 |
0.42 % |
| qd2,mq40 |
22315 |
0.00 % |
16824 |
0.00 % |
5491 |
0.01 % |
| fs60 |
1 |
0.00 % |
0 |
0.00 % |
1 |
0.00 % |
| qd2,fs60 |
1 |
0.00 % |
0 |
0.00 % |
1 |
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 % |
| 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 |
19750192 |
24.01 % |
| Transition |
G>A |
All |
4335799 |
5.27 % |
| Transition |
T>C |
All |
19877588 |
24.16 % |
| Transition |
C>T |
All |
4416737 |
5.37 % |
| Transversion |
A>C |
All |
3318003 |
4.03 % |
| Transversion |
C>A |
All |
3947283 |
4.80 % |
| Transversion |
T>G |
All |
3214218 |
3.91 % |
| Transversion |
G>T |
All |
4056508 |
4.93 % |
| Transversion |
A>T |
All |
7871521 |
9.57 % |
| Transversion |
T>A |
All |
7698733 |
9.36 % |
| Transversion |
C>G |
All |
1865129 |
2.27 % |
| Transversion |
G>C |
All |
1919875 |
2.33 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
1396153 |
25.02 % |
| Transition |
G>A |
Passed |
480114 |
8.60 % |
| Transition |
T>C |
Passed |
1470007 |
26.34 % |
| Transition |
C>T |
Passed |
502602 |
9.01 % |
| Transversion |
A>C |
Passed |
296980 |
5.32 % |
| Transversion |
C>A |
Passed |
158572 |
2.84 % |
| Transversion |
T>G |
Passed |
273862 |
4.91 % |
| Transversion |
G>T |
Passed |
166841 |
2.99 % |
| Transversion |
A>T |
Passed |
200049 |
3.58 % |
| Transversion |
T>A |
Passed |
182466 |
3.27 % |
| Transversion |
C>G |
Passed |
219184 |
3.93 % |
| Transversion |
G>C |
Passed |
233339 |
4.18 % |
| |
|
|
|
|
| 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 |
1.43 |
48380316 |
33891270 |
| Passed |
2.22 |
3848876 |
1731293 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |