/cemt/variants/A36014_3_lane_gembs
BACK
SAMPLE A36014_3_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1160524376 |
916876658 |
79.01 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1160524376 |
100% |
1144593898 |
98.63 % |
15930478 |
1.37 % |
| |
|
|
|
|
|
|
| Passed |
918368522 |
79.13 % |
914212927 |
79.87 % |
4155595 |
0.45 % |
| Filtered |
242155854 |
20.87 % |
230380971 |
20.13 % |
11774883 |
1.28 % |
| |
|
|
|
|
|
|
| q20 |
200693063 |
82.88 % |
198317400 |
86.08 % |
2375663 |
20.18 % |
| q20,qd2 |
17362129 |
7.17 % |
8972992 |
3.89 % |
8389137 |
71.25 % |
| q20,mq40 |
12079478 |
4.99 % |
11800225 |
5.12 % |
279253 |
2.37 % |
| qd2 |
5940511 |
2.45 % |
5717152 |
2.48 % |
223359 |
1.90 % |
| q20,qd2,mq40 |
3207744 |
1.32 % |
2915282 |
1.27 % |
292462 |
2.48 % |
| mq40 |
2804492 |
1.16 % |
2603013 |
1.13 % |
201479 |
1.71 % |
| qd2,mq40 |
65192 |
0.03 % |
54907 |
0.02 % |
10285 |
0.09 % |
| qd2,fs60,mq40 |
1042 |
0.00 % |
0 |
0.00 % |
1042 |
0.01 % |
| qd2,fs60 |
687 |
0.00 % |
0 |
0.00 % |
687 |
0.01 % |
| fs60 |
601 |
0.00 % |
0 |
0.00 % |
601 |
0.01 % |
| q20,qd2,fs60 |
488 |
0.00 % |
0 |
0.00 % |
488 |
0.00 % |
| fs60,mq40 |
313 |
0.00 % |
0 |
0.00 % |
313 |
0.00 % |
| q20,qd2,fs60,mq40 |
111 |
0.00 % |
0 |
0.00 % |
111 |
0.00 % |
| q20,fs60,mq40 |
3 |
0.00 % |
0 |
0.00 % |
3 |
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 |
5058244 |
28.45 % |
| Transition |
G>A |
All |
1460325 |
8.21 % |
| Transition |
T>C |
All |
4912342 |
27.62 % |
| Transition |
C>T |
All |
1478470 |
8.31 % |
| Transversion |
A>C |
All |
413536 |
2.33 % |
| Transversion |
C>A |
All |
869573 |
4.89 % |
| Transversion |
T>G |
All |
421103 |
2.37 % |
| Transversion |
G>T |
All |
868285 |
4.88 % |
| Transversion |
A>T |
All |
805551 |
4.53 % |
| Transversion |
T>A |
All |
812432 |
4.57 % |
| Transversion |
C>G |
All |
344089 |
1.94 % |
| Transversion |
G>C |
All |
338382 |
1.90 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
656742 |
17.56 % |
| Transition |
G>A |
Passed |
580192 |
15.51 % |
| Transition |
T>C |
Passed |
654527 |
17.50 % |
| Transition |
C>T |
Passed |
583536 |
15.60 % |
| Transversion |
A>C |
Passed |
156653 |
4.19 % |
| Transversion |
C>A |
Passed |
175058 |
4.68 % |
| Transversion |
T>G |
Passed |
157356 |
4.21 % |
| Transversion |
G>T |
Passed |
173404 |
4.64 % |
| Transversion |
A>T |
Passed |
155718 |
4.16 % |
| Transversion |
T>A |
Passed |
157348 |
4.21 % |
| Transversion |
C>G |
Passed |
144911 |
3.87 % |
| Transversion |
G>C |
Passed |
145373 |
3.89 % |
| |
|
|
|
|
| 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 |
2.65 |
12909381 |
4872951 |
| Passed |
1.96 |
2474997 |
1265821 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |