/Martin Hirst/variants/PX0681_TATAAT_3_lane_gembs
BACK
SAMPLE PX0681_TATAAT_3_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1075814732 |
181548596 |
16.88 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1075814732 |
100% |
1013777191 |
94.23 % |
62037541 |
5.77 % |
| |
|
|
|
|
|
|
| Passed |
202488140 |
18.82 % |
178610335 |
17.62 % |
23877805 |
11.79 % |
| Filtered |
873326592 |
81.18 % |
835166856 |
82.38 % |
38159736 |
18.85 % |
| |
|
|
|
|
|
|
| q20 |
724710147 |
82.98 % |
709816689 |
84.99 % |
14893458 |
39.03 % |
| q20,qd2 |
115747516 |
13.25 % |
93164872 |
11.16 % |
22582644 |
59.18 % |
| q20,mq40 |
19157419 |
2.19 % |
18940675 |
2.27 % |
216744 |
0.57 % |
| q20,qd2,mq40 |
11976309 |
1.37 % |
11867401 |
1.42 % |
108908 |
0.29 % |
| qd2 |
1398129 |
0.16 % |
1271639 |
0.15 % |
126490 |
0.33 % |
| mq40 |
327462 |
0.04 % |
98417 |
0.01 % |
229045 |
0.60 % |
| qd2,mq40 |
9610 |
0.00 % |
7163 |
0.00 % |
2447 |
0.01 % |
| 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 % |
| 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 |
11498138 |
17.15 % |
| Transition |
G>A |
All |
3331833 |
4.97 % |
| Transition |
T>C |
All |
12334702 |
18.40 % |
| Transition |
C>T |
All |
3311081 |
4.94 % |
| Transversion |
A>C |
All |
3344917 |
4.99 % |
| Transversion |
C>A |
All |
5014775 |
7.48 % |
| Transversion |
T>G |
All |
3172678 |
4.73 % |
| Transversion |
G>T |
All |
5150037 |
7.68 % |
| Transversion |
A>T |
All |
7433303 |
11.09 % |
| Transversion |
T>A |
All |
7371101 |
10.99 % |
| Transversion |
C>G |
All |
2456520 |
3.66 % |
| Transversion |
G>C |
All |
2629570 |
3.92 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
555612 |
18.71 % |
| Transition |
G>A |
Passed |
255017 |
8.59 % |
| Transition |
T>C |
Passed |
625690 |
21.07 % |
| Transition |
C>T |
Passed |
274218 |
9.23 % |
| Transversion |
A>C |
Passed |
201225 |
6.78 % |
| Transversion |
C>A |
Passed |
115136 |
3.88 % |
| Transversion |
T>G |
Passed |
182949 |
6.16 % |
| Transversion |
G>T |
Passed |
127642 |
4.30 % |
| Transversion |
A>T |
Passed |
121583 |
4.09 % |
| Transversion |
T>A |
Passed |
108644 |
3.66 % |
| Transversion |
C>G |
Passed |
191951 |
6.46 % |
| Transversion |
G>C |
Passed |
209959 |
7.07 % |
| |
|
|
|
|
| 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 |
0.83 |
30475754 |
36572901 |
| Passed |
1.36 |
1710537 |
1259089 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |