/Martin Hirst/variants/PX0720_GGCTAC_10_lane_gembs
BACK
SAMPLE PX0720_GGCTAC_10_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1210271381 |
687577150 |
56.81 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1210271381 |
100% |
1131937173 |
93.53 % |
78334208 |
6.47 % |
| |
|
|
|
|
|
|
| Passed |
705112212 |
58.26 % |
682161990 |
60.27 % |
22950222 |
3.25 % |
| Filtered |
505159169 |
41.74 % |
449775183 |
39.73 % |
55383986 |
7.85 % |
| |
|
|
|
|
|
|
| q20 |
413969570 |
81.95 % |
397298518 |
88.33 % |
16671052 |
30.10 % |
| q20,qd2 |
65389888 |
12.94 % |
28253355 |
6.28 % |
37136533 |
67.05 % |
| qd2 |
13111419 |
2.60 % |
12191839 |
2.71 % |
919580 |
1.66 % |
| q20,mq40 |
8282203 |
1.64 % |
8064873 |
1.79 % |
217330 |
0.39 % |
| q20,qd2,mq40 |
3664497 |
0.73 % |
3488814 |
0.78 % |
175683 |
0.32 % |
| mq40 |
711032 |
0.14 % |
454188 |
0.10 % |
256844 |
0.46 % |
| qd2,mq40 |
30550 |
0.01 % |
23596 |
0.01 % |
6954 |
0.01 % |
| qd2,fs60 |
5 |
0.00 % |
0 |
0.00 % |
5 |
0.00 % |
| qd2,fs60,mq40 |
4 |
0.00 % |
0 |
0.00 % |
4 |
0.00 % |
| fs60,mq40 |
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 % |
| q20,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 |
19462504 |
24.04 % |
| Transition |
G>A |
All |
4604860 |
5.69 % |
| Transition |
T>C |
All |
19422725 |
23.99 % |
| Transition |
C>T |
All |
4668537 |
5.77 % |
| Transversion |
A>C |
All |
3271777 |
4.04 % |
| Transversion |
C>A |
All |
3812683 |
4.71 % |
| Transversion |
T>G |
All |
3179892 |
3.93 % |
| Transversion |
G>T |
All |
3900828 |
4.82 % |
| Transversion |
A>T |
All |
7611644 |
9.40 % |
| Transversion |
T>A |
All |
7435959 |
9.18 % |
| Transversion |
C>G |
All |
1782414 |
2.20 % |
| Transversion |
G>C |
All |
1818985 |
2.25 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
1471863 |
24.65 % |
| Transition |
G>A |
Passed |
537277 |
9.00 % |
| Transition |
T>C |
Passed |
1518765 |
25.43 % |
| Transition |
C>T |
Passed |
556403 |
9.32 % |
| Transversion |
A>C |
Passed |
322757 |
5.40 % |
| Transversion |
C>A |
Passed |
174904 |
2.93 % |
| Transversion |
T>G |
Passed |
300787 |
5.04 % |
| Transversion |
G>T |
Passed |
181365 |
3.04 % |
| Transversion |
A>T |
Passed |
219226 |
3.67 % |
| Transversion |
T>A |
Passed |
204294 |
3.42 % |
| Transversion |
C>G |
Passed |
235869 |
3.95 % |
| Transversion |
G>C |
Passed |
248457 |
4.16 % |
| |
|
|
|
|
| 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 |
1.47 |
48158626 |
32814182 |
| Passed |
2.16 |
4084308 |
1887659 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |