/Martin Hirst/variants/PX0681_GCACTT_3_lane_gembs
BACK
SAMPLE PX0681_GCACTT_3_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1091108295 |
206624344 |
18.94 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1091108295 |
100% |
1027080085 |
94.13 % |
64028210 |
5.87 % |
| |
|
|
|
|
|
|
| Passed |
227983265 |
20.89 % |
203424167 |
19.81 % |
24559098 |
10.77 % |
| Filtered |
863125030 |
79.11 % |
823655918 |
80.19 % |
39469112 |
17.31 % |
| |
|
|
|
|
|
|
| q20 |
719547239 |
83.37 % |
704311472 |
85.51 % |
15235767 |
38.60 % |
| q20,qd2 |
111628777 |
12.93 % |
88089943 |
10.69 % |
23538834 |
59.64 % |
| q20,mq40 |
18537348 |
2.15 % |
18325721 |
2.22 % |
211627 |
0.54 % |
| q20,qd2,mq40 |
11411041 |
1.32 % |
11307095 |
1.37 % |
103946 |
0.26 % |
| qd2 |
1664817 |
0.19 % |
1512864 |
0.18 % |
151953 |
0.38 % |
| mq40 |
325958 |
0.04 % |
101542 |
0.01 % |
224416 |
0.57 % |
| qd2,mq40 |
9849 |
0.00 % |
7281 |
0.00 % |
2568 |
0.01 % |
| 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 % |
| 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 |
12223403 |
17.76 % |
| Transition |
G>A |
All |
3377451 |
4.91 % |
| Transition |
T>C |
All |
13153318 |
19.11 % |
| Transition |
C>T |
All |
3354077 |
4.87 % |
| Transversion |
A>C |
All |
3450569 |
5.01 % |
| Transversion |
C>A |
All |
4913069 |
7.14 % |
| Transversion |
T>G |
All |
3245469 |
4.71 % |
| Transversion |
G>T |
All |
5041471 |
7.32 % |
| Transversion |
A>T |
All |
7544491 |
10.96 % |
| Transversion |
T>A |
All |
7489296 |
10.88 % |
| Transversion |
C>G |
All |
2424584 |
3.52 % |
| Transversion |
G>C |
All |
2621296 |
3.81 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
629993 |
19.44 % |
| Transition |
G>A |
Passed |
275355 |
8.50 % |
| Transition |
T>C |
Passed |
710030 |
21.91 % |
| Transition |
C>T |
Passed |
294593 |
9.09 % |
| Transversion |
A>C |
Passed |
217762 |
6.72 % |
| Transversion |
C>A |
Passed |
121312 |
3.74 % |
| Transversion |
T>G |
Passed |
196341 |
6.06 % |
| Transversion |
G>T |
Passed |
133403 |
4.12 % |
| Transversion |
A>T |
Passed |
129180 |
3.99 % |
| Transversion |
T>A |
Passed |
115682 |
3.57 % |
| Transversion |
C>G |
Passed |
197902 |
6.11 % |
| Transversion |
G>C |
Passed |
218540 |
6.74 % |
| |
|
|
|
|
| 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 |
0.87 |
32108249 |
36730245 |
| Passed |
1.44 |
1909971 |
1330122 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |