/TFF-PPG/variants/PX0587_CAACTA_10_lane_gembs
BACK
SAMPLE PX0587_CAACTA_10_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1212652917 |
746344717 |
61.55 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1212652917 |
100% |
1138526703 |
93.89 % |
74126214 |
6.11 % |
| |
|
|
|
|
|
|
| Passed |
762897848 |
62.91 % |
740670184 |
65.06 % |
22227664 |
2.91 % |
| Filtered |
449755069 |
37.09 % |
397856519 |
34.94 % |
51898550 |
6.80 % |
| |
|
|
|
|
|
|
| q20 |
362247075 |
80.54 % |
347659512 |
87.38 % |
14587563 |
28.11 % |
| q20,qd2 |
59735124 |
13.28 % |
24311353 |
6.11 % |
35423771 |
68.26 % |
| qd2 |
16320561 |
3.63 % |
15101511 |
3.80 % |
1219050 |
2.35 % |
| q20,mq40 |
7375042 |
1.64 % |
7161907 |
1.80 % |
213135 |
0.41 % |
| q20,qd2,mq40 |
3237825 |
0.72 % |
3052523 |
0.77 % |
185302 |
0.36 % |
| mq40 |
809353 |
0.18 % |
546562 |
0.14 % |
262791 |
0.51 % |
| qd2,mq40 |
30074 |
0.01 % |
23151 |
0.01 % |
6923 |
0.01 % |
| qd2,fs60 |
7 |
0.00 % |
0 |
0.00 % |
7 |
0.00 % |
| fs60 |
6 |
0.00 % |
0 |
0.00 % |
6 |
0.00 % |
| q20,qd2,fs60 |
2 |
0.00 % |
0 |
0.00 % |
2 |
0.00 % |
| q20,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 |
19902844 |
25.92 % |
| Transition |
G>A |
All |
4076252 |
5.31 % |
| Transition |
T>C |
All |
20041247 |
26.10 % |
| Transition |
C>T |
All |
4126503 |
5.37 % |
| Transversion |
A>C |
All |
2810336 |
3.66 % |
| Transversion |
C>A |
All |
3243481 |
4.22 % |
| Transversion |
T>G |
All |
2710362 |
3.53 % |
| Transversion |
G>T |
All |
3330380 |
4.34 % |
| Transversion |
A>T |
All |
6820391 |
8.88 % |
| Transversion |
T>A |
All |
6660590 |
8.67 % |
| Transversion |
C>G |
All |
1515526 |
1.97 % |
| Transversion |
G>C |
All |
1555589 |
2.03 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
1658673 |
26.13 % |
| Transition |
G>A |
Passed |
540724 |
8.52 % |
| Transition |
T>C |
Passed |
1745054 |
27.49 % |
| Transition |
C>T |
Passed |
559964 |
8.82 % |
| Transversion |
A>C |
Passed |
313258 |
4.94 % |
| Transversion |
C>A |
Passed |
173141 |
2.73 % |
| Transversion |
T>G |
Passed |
287405 |
4.53 % |
| Transversion |
G>T |
Passed |
179746 |
2.83 % |
| Transversion |
A>T |
Passed |
222702 |
3.51 % |
| Transversion |
T>A |
Passed |
204546 |
3.22 % |
| Transversion |
C>G |
Passed |
224880 |
3.54 % |
| Transversion |
G>C |
Passed |
237355 |
3.74 % |
| |
|
|
|
|
| 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 |
1.68 |
48146846 |
28646655 |
| Passed |
2.44 |
4504415 |
1843033 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |