/Martin Hirst/variants/PX0720_TGCTGG_10_lane_gembs
BACK
SAMPLE PX0720_TGCTGG_10_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1189275927 |
569268962 |
47.87 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1189275927 |
100% |
1110250245 |
93.36 % |
79025682 |
6.64 % |
| |
|
|
|
|
|
|
| Passed |
589245379 |
49.55 % |
564584566 |
50.85 % |
24660813 |
4.19 % |
| Filtered |
600030548 |
50.45 % |
545665679 |
49.15 % |
54364869 |
9.23 % |
| |
|
|
|
|
|
|
| q20 |
492610719 |
82.10 % |
474231072 |
86.91 % |
18379647 |
33.81 % |
| q20,qd2 |
78315263 |
13.05 % |
43788062 |
8.02 % |
34527201 |
63.51 % |
| qd2 |
11756743 |
1.96 % |
10976002 |
2.01 % |
780741 |
1.44 % |
| q20,mq40 |
10993015 |
1.83 % |
10748430 |
1.97 % |
244585 |
0.45 % |
| q20,qd2,mq40 |
5678525 |
0.95 % |
5512520 |
1.01 % |
166005 |
0.31 % |
| mq40 |
646998 |
0.11 % |
387003 |
0.07 % |
259995 |
0.48 % |
| qd2,mq40 |
29279 |
0.00 % |
22590 |
0.00 % |
6689 |
0.01 % |
| fs60 |
4 |
0.00 % |
0 |
0.00 % |
4 |
0.00 % |
| qd2,fs60 |
2 |
0.00 % |
0 |
0.00 % |
2 |
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 |
19012107 |
23.02 % |
| Transition |
G>A |
All |
4229312 |
5.12 % |
| Transition |
T>C |
All |
19046809 |
23.06 % |
| Transition |
C>T |
All |
4311819 |
5.22 % |
| Transversion |
A>C |
All |
3635203 |
4.40 % |
| Transversion |
C>A |
All |
4270592 |
5.17 % |
| Transversion |
T>G |
All |
3492008 |
4.23 % |
| Transversion |
G>T |
All |
4356297 |
5.27 % |
| Transversion |
A>T |
All |
8087751 |
9.79 % |
| Transversion |
T>A |
All |
7994086 |
9.68 % |
| Transversion |
C>G |
All |
2036362 |
2.47 % |
| Transversion |
G>C |
All |
2118518 |
2.57 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
1275420 |
24.92 % |
| Transition |
G>A |
Passed |
443284 |
8.66 % |
| Transition |
T>C |
Passed |
1335944 |
26.10 % |
| Transition |
C>T |
Passed |
455795 |
8.91 % |
| Transversion |
A>C |
Passed |
276177 |
5.40 % |
| Transversion |
C>A |
Passed |
146360 |
2.86 % |
| Transversion |
T>G |
Passed |
258521 |
5.05 % |
| Transversion |
G>T |
Passed |
152058 |
2.97 % |
| Transversion |
A>T |
Passed |
175030 |
3.42 % |
| Transversion |
T>A |
Passed |
164120 |
3.21 % |
| Transversion |
C>G |
Passed |
211251 |
4.13 % |
| Transversion |
G>C |
Passed |
224138 |
4.38 % |
| |
|
|
|
|
| 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 |
1.29 |
46600047 |
35990817 |
| Passed |
2.18 |
3510443 |
1607655 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |