/CEMT/variants/A77948_3_lane_gembs
BACK
SAMPLE A77948_3_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1175702744 |
1099006581 |
93.48 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1175702744 |
100% |
1160145049 |
98.68 % |
15557695 |
1.32 % |
| |
|
|
|
|
|
|
| Passed |
1100368493 |
93.59 % |
1095833056 |
94.46 % |
4535437 |
0.41 % |
| Filtered |
75334251 |
6.41 % |
64311993 |
5.54 % |
11022258 |
1.00 % |
| |
|
|
|
|
|
|
| q20 |
44198729 |
58.67 % |
43720751 |
67.98 % |
477978 |
4.34 % |
| q20,qd2 |
11532180 |
15.31 % |
2491296 |
3.87 % |
9040884 |
82.02 % |
| q20,mq40 |
10159648 |
13.49 % |
10027661 |
15.59 % |
131987 |
1.20 % |
| mq40 |
3932852 |
5.22 % |
3616171 |
5.62 % |
316681 |
2.87 % |
| qd2 |
2910109 |
3.86 % |
2086845 |
3.24 % |
823264 |
7.47 % |
| q20,qd2,mq40 |
2515561 |
3.34 % |
2302057 |
3.58 % |
213504 |
1.94 % |
| qd2,mq40 |
82915 |
0.11 % |
67212 |
0.10 % |
15703 |
0.14 % |
| qd2,fs60,mq40 |
706 |
0.00 % |
0 |
0.00 % |
706 |
0.01 % |
| fs60 |
522 |
0.00 % |
0 |
0.00 % |
522 |
0.00 % |
| qd2,fs60 |
457 |
0.00 % |
0 |
0.00 % |
457 |
0.00 % |
| fs60,mq40 |
373 |
0.00 % |
0 |
0.00 % |
373 |
0.00 % |
| q20,qd2,fs60 |
122 |
0.00 % |
0 |
0.00 % |
122 |
0.00 % |
| q20,qd2,fs60,mq40 |
68 |
0.00 % |
0 |
0.00 % |
68 |
0.00 % |
| q20,fs60,mq40 |
5 |
0.00 % |
0 |
0.00 % |
5 |
0.00 % |
| q20,fs60 |
4 |
0.00 % |
0 |
0.00 % |
4 |
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 |
6322012 |
36.22 % |
| Transition |
G>A |
All |
953165 |
5.46 % |
| Transition |
T>C |
All |
6243866 |
35.77 % |
| Transition |
C>T |
All |
949297 |
5.44 % |
| Transversion |
A>C |
All |
271141 |
1.55 % |
| Transversion |
C>A |
All |
496717 |
2.85 % |
| Transversion |
T>G |
All |
281895 |
1.61 % |
| Transversion |
G>T |
All |
459996 |
2.64 % |
| Transversion |
A>T |
All |
464195 |
2.66 % |
| Transversion |
T>A |
All |
502411 |
2.88 % |
| Transversion |
C>G |
All |
259850 |
1.49 % |
| Transversion |
G>C |
All |
251097 |
1.44 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
983034 |
21.34 % |
| Transition |
G>A |
Passed |
636388 |
13.82 % |
| Transition |
T>C |
Passed |
962187 |
20.89 % |
| Transition |
C>T |
Passed |
632373 |
13.73 % |
| Transversion |
A>C |
Passed |
169505 |
3.68 % |
| Transversion |
C>A |
Passed |
193053 |
4.19 % |
| Transversion |
T>G |
Passed |
171943 |
3.73 % |
| Transversion |
G>T |
Passed |
178973 |
3.89 % |
| Transversion |
A>T |
Passed |
160469 |
3.48 % |
| Transversion |
T>A |
Passed |
173083 |
3.76 % |
| Transversion |
C>G |
Passed |
172962 |
3.76 % |
| Transversion |
G>C |
Passed |
171644 |
3.73 % |
| |
|
|
|
|
| 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 |
4.84 |
14468340 |
2987302 |
| Passed |
2.31 |
3213982 |
1391632 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |