/cemt/variants/A54768_3_lane_gembs
BACK
SAMPLE A54768_3_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1157326898 |
597252976 |
51.61 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1157326898 |
100% |
1134143162 |
98.00 % |
23183736 |
2.00 % |
| |
|
|
|
|
|
|
| Passed |
600901669 |
51.92 % |
595251367 |
52.48 % |
5650302 |
0.94 % |
| Filtered |
556425229 |
48.08 % |
538891795 |
47.52 % |
17533434 |
2.92 % |
| |
|
|
|
|
|
|
| q20 |
493211627 |
88.64 % |
488129670 |
90.58 % |
5081957 |
28.98 % |
| q20,qd2 |
31170810 |
5.60 % |
19548972 |
3.63 % |
11621838 |
66.28 % |
| qd2 |
15482388 |
2.78 % |
15252762 |
2.83 % |
229626 |
1.31 % |
| q20,mq40 |
11226207 |
2.02 % |
11024277 |
2.05 % |
201930 |
1.15 % |
| q20,qd2,mq40 |
3620817 |
0.65 % |
3407025 |
0.63 % |
213792 |
1.22 % |
| mq40 |
1619637 |
0.29 % |
1468223 |
0.27 % |
151414 |
0.86 % |
| qd2,mq40 |
71928 |
0.01 % |
60866 |
0.01 % |
11062 |
0.06 % |
| q20,qd2,fs60 |
8112 |
0.00 % |
0 |
0.00 % |
8112 |
0.05 % |
| qd2,fs60 |
5999 |
0.00 % |
0 |
0.00 % |
5999 |
0.03 % |
| fs60 |
5042 |
0.00 % |
0 |
0.00 % |
5042 |
0.03 % |
| qd2,fs60,mq40 |
1815 |
0.00 % |
0 |
0.00 % |
1815 |
0.01 % |
| fs60,mq40 |
498 |
0.00 % |
0 |
0.00 % |
498 |
0.00 % |
| q20,qd2,fs60,mq40 |
336 |
0.00 % |
0 |
0.00 % |
336 |
0.00 % |
| q20,fs60 |
13 |
0.00 % |
0 |
0.00 % |
13 |
0.00 % |
| q20,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 |
7467602 |
28.02 % |
| Transition |
G>A |
All |
2721882 |
10.21 % |
| Transition |
T>C |
All |
6076022 |
22.80 % |
| Transition |
C>T |
All |
2745392 |
10.30 % |
| Transversion |
A>C |
All |
446788 |
1.68 % |
| Transversion |
C>A |
All |
1593597 |
5.98 % |
| Transversion |
T>G |
All |
521614 |
1.96 % |
| Transversion |
G>T |
All |
1535981 |
5.76 % |
| Transversion |
A>T |
All |
1324113 |
4.97 % |
| Transversion |
T>A |
All |
1380201 |
5.18 % |
| Transversion |
C>G |
All |
449816 |
1.69 % |
| Transversion |
G>C |
All |
384375 |
1.44 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
517714 |
19.04 % |
| Transition |
G>A |
Passed |
412379 |
15.17 % |
| Transition |
T>C |
Passed |
481240 |
17.70 % |
| Transition |
C>T |
Passed |
414343 |
15.24 % |
| Transversion |
A>C |
Passed |
109415 |
4.02 % |
| Transversion |
C>A |
Passed |
122319 |
4.50 % |
| Transversion |
T>G |
Passed |
111898 |
4.12 % |
| Transversion |
G>T |
Passed |
120920 |
4.45 % |
| Transversion |
A>T |
Passed |
108500 |
3.99 % |
| Transversion |
T>A |
Passed |
111131 |
4.09 % |
| Transversion |
C>G |
Passed |
104732 |
3.85 % |
| Transversion |
G>C |
Passed |
104420 |
3.84 % |
| |
|
|
|
|
| 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 |
2.49 |
19010898 |
7636485 |
| Passed |
2.04 |
1825676 |
893335 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |