/cemt/variants/A54763_3_lane_gembs
BACK
SAMPLE A54763_3_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1166201444 |
563385601 |
48.31 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1166201444 |
100% |
1139497365 |
97.71 % |
26704079 |
2.29 % |
| |
|
|
|
|
|
|
| Passed |
567845864 |
48.69 % |
561380186 |
49.27 % |
6465678 |
1.14 % |
| Filtered |
598355580 |
51.31 % |
578117179 |
50.73 % |
20238401 |
3.56 % |
| |
|
|
|
|
|
|
| q20 |
537326386 |
89.80 % |
531159176 |
91.88 % |
6167210 |
30.47 % |
| q20,qd2 |
32951683 |
5.51 % |
19695764 |
3.41 % |
13255919 |
65.50 % |
| q20,mq40 |
11790106 |
1.97 % |
11576693 |
2.00 % |
213413 |
1.05 % |
| qd2 |
11013480 |
1.84 % |
10814698 |
1.87 % |
198782 |
0.98 % |
| q20,qd2,mq40 |
3720325 |
0.62 % |
3499936 |
0.61 % |
220389 |
1.09 % |
| mq40 |
1468288 |
0.25 % |
1309019 |
0.23 % |
159269 |
0.79 % |
| qd2,mq40 |
72977 |
0.01 % |
61893 |
0.01 % |
11084 |
0.05 % |
| q20,qd2,fs60 |
3974 |
0.00 % |
0 |
0.00 % |
3974 |
0.02 % |
| qd2,fs60 |
3699 |
0.00 % |
0 |
0.00 % |
3699 |
0.02 % |
| fs60 |
2462 |
0.00 % |
0 |
0.00 % |
2462 |
0.01 % |
| qd2,fs60,mq40 |
1473 |
0.00 % |
0 |
0.00 % |
1473 |
0.01 % |
| fs60,mq40 |
443 |
0.00 % |
0 |
0.00 % |
443 |
0.00 % |
| q20,qd2,fs60,mq40 |
278 |
0.00 % |
0 |
0.00 % |
278 |
0.00 % |
| q20,fs60 |
6 |
0.00 % |
0 |
0.00 % |
6 |
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 |
9203663 |
30.77 % |
| Transition |
G>A |
All |
2576497 |
8.62 % |
| Transition |
T>C |
All |
6727893 |
22.50 % |
| Transition |
C>T |
All |
2661302 |
8.90 % |
| Transversion |
A>C |
All |
498788 |
1.67 % |
| Transversion |
C>A |
All |
1897259 |
6.34 % |
| Transversion |
T>G |
All |
655105 |
2.19 % |
| Transversion |
G>T |
All |
1784054 |
5.97 % |
| Transversion |
A>T |
All |
1389130 |
4.64 % |
| Transversion |
T>A |
All |
1508483 |
5.04 % |
| Transversion |
C>G |
All |
570977 |
1.91 % |
| Transversion |
G>C |
All |
433158 |
1.45 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
550176 |
20.42 % |
| Transition |
G>A |
Passed |
395219 |
14.67 % |
| Transition |
T>C |
Passed |
474724 |
17.62 % |
| Transition |
C>T |
Passed |
400172 |
14.85 % |
| Transversion |
A>C |
Passed |
106486 |
3.95 % |
| Transversion |
C>A |
Passed |
117865 |
4.37 % |
| Transversion |
T>G |
Passed |
110975 |
4.12 % |
| Transversion |
G>T |
Passed |
117436 |
4.36 % |
| Transversion |
A>T |
Passed |
104717 |
3.89 % |
| Transversion |
T>A |
Passed |
106389 |
3.95 % |
| Transversion |
C>G |
Passed |
106846 |
3.96 % |
| Transversion |
G>C |
Passed |
103875 |
3.85 % |
| |
|
|
|
|
| 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 |
2.42 |
21169355 |
8736954 |
| Passed |
2.08 |
1820291 |
874589 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |