/cemt/variants/A77951_1_lane_gembs
BACK
SAMPLE A77951_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1177641137 |
976615452 |
82.93 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1177641137 |
100% |
1156498055 |
98.20 % |
21143082 |
1.80 % |
| |
|
|
|
|
|
|
| Passed |
979754843 |
83.20 % |
973218087 |
84.15 % |
6536756 |
0.67 % |
| Filtered |
197886294 |
16.80 % |
183279968 |
15.85 % |
14606326 |
1.49 % |
| |
|
|
|
|
|
|
| q20 |
161610533 |
81.67 % |
160413468 |
87.52 % |
1197065 |
8.20 % |
| q20,qd2 |
17354746 |
8.77 % |
5038507 |
2.75 % |
12316239 |
84.32 % |
| q20,mq40 |
11054338 |
5.59 % |
10927409 |
5.96 % |
126929 |
0.87 % |
| q20,qd2,mq40 |
2744035 |
1.39 % |
2578476 |
1.41 % |
165559 |
1.13 % |
| qd2 |
2690903 |
1.36 % |
2181410 |
1.19 % |
509493 |
3.49 % |
| mq40 |
2379381 |
1.20 % |
2099533 |
1.15 % |
279848 |
1.92 % |
| qd2,mq40 |
50699 |
0.03 % |
41165 |
0.02 % |
9534 |
0.07 % |
| qd2,fs60,mq40 |
735 |
0.00 % |
0 |
0.00 % |
735 |
0.01 % |
| qd2,fs60 |
326 |
0.00 % |
0 |
0.00 % |
326 |
0.00 % |
| fs60,mq40 |
300 |
0.00 % |
0 |
0.00 % |
300 |
0.00 % |
| fs60 |
190 |
0.00 % |
0 |
0.00 % |
190 |
0.00 % |
| q20,qd2,fs60,mq40 |
61 |
0.00 % |
0 |
0.00 % |
61 |
0.00 % |
| q20,qd2,fs60 |
41 |
0.00 % |
0 |
0.00 % |
41 |
0.00 % |
| q20,fs60,mq40 |
6 |
0.00 % |
0 |
0.00 % |
6 |
0.00 % |
| q20,fs60 |
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 |
8282542 |
36.18 % |
| Transition |
G>A |
All |
992498 |
4.34 % |
| Transition |
T>C |
All |
8270478 |
36.13 % |
| Transition |
C>T |
All |
998605 |
4.36 % |
| Transversion |
A>C |
All |
341457 |
1.49 % |
| Transversion |
C>A |
All |
1070510 |
4.68 % |
| Transversion |
T>G |
All |
343359 |
1.50 % |
| Transversion |
G>T |
All |
875531 |
3.82 % |
| Transversion |
A>T |
All |
533848 |
2.33 % |
| Transversion |
T>A |
All |
556010 |
2.43 % |
| Transversion |
C>G |
All |
317677 |
1.39 % |
| Transversion |
G>C |
All |
310821 |
1.36 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
899791 |
19.77 % |
| Transition |
G>A |
Passed |
578217 |
12.70 % |
| Transition |
T>C |
Passed |
863636 |
18.97 % |
| Transition |
C>T |
Passed |
578043 |
12.70 % |
| Transversion |
A>C |
Passed |
167066 |
3.67 % |
| Transversion |
C>A |
Passed |
364159 |
8.00 % |
| Transversion |
T>G |
Passed |
169694 |
3.73 % |
| Transversion |
G>T |
Passed |
286856 |
6.30 % |
| Transversion |
A>T |
Passed |
157475 |
3.46 % |
| Transversion |
T>A |
Passed |
165155 |
3.63 % |
| Transversion |
C>G |
Passed |
161421 |
3.55 % |
| Transversion |
G>C |
Passed |
159941 |
3.51 % |
| |
|
|
|
|
| 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 |
4.26 |
18544123 |
4349213 |
| Passed |
1.79 |
2919687 |
1631767 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |