/cemt/variants/A54774_3_lane_gembs
BACK
SAMPLE A54774_3_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1166824318 |
631842135 |
54.15 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1166824318 |
100% |
1143256037 |
97.98 % |
23568281 |
2.02 % |
| |
|
|
|
|
|
|
| Passed |
635385458 |
54.45 % |
629761548 |
55.08 % |
5623910 |
0.89 % |
| Filtered |
531438860 |
45.55 % |
513494489 |
44.92 % |
17944371 |
2.82 % |
| |
|
|
|
|
|
|
| q20 |
467803969 |
88.03 % |
462655299 |
90.10 % |
5148670 |
28.69 % |
| q20,qd2 |
28367772 |
5.34 % |
16491285 |
3.21 % |
11876487 |
66.19 % |
| qd2 |
18327567 |
3.45 % |
18073028 |
3.52 % |
254539 |
1.42 % |
| q20,mq40 |
11513989 |
2.17 % |
11298893 |
2.20 % |
215096 |
1.20 % |
| q20,qd2,mq40 |
3566593 |
0.67 % |
3329025 |
0.65 % |
237568 |
1.32 % |
| mq40 |
1742200 |
0.33 % |
1575905 |
0.31 % |
166295 |
0.93 % |
| qd2,mq40 |
83388 |
0.02 % |
71054 |
0.01 % |
12334 |
0.07 % |
| q20,qd2,fs60 |
11904 |
0.00 % |
0 |
0.00 % |
11904 |
0.07 % |
| fs60 |
9644 |
0.00 % |
0 |
0.00 % |
9644 |
0.05 % |
| qd2,fs60 |
9079 |
0.00 % |
0 |
0.00 % |
9079 |
0.05 % |
| qd2,fs60,mq40 |
1895 |
0.00 % |
0 |
0.00 % |
1895 |
0.01 % |
| fs60,mq40 |
555 |
0.00 % |
0 |
0.00 % |
555 |
0.00 % |
| q20,qd2,fs60,mq40 |
289 |
0.00 % |
0 |
0.00 % |
289 |
0.00 % |
| q20,fs60 |
14 |
0.00 % |
0 |
0.00 % |
14 |
0.00 % |
| q20,fs60,mq40 |
2 |
0.00 % |
0 |
0.00 % |
2 |
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 |
8005226 |
30.14 % |
| Transition |
G>A |
All |
2285557 |
8.60 % |
| Transition |
T>C |
All |
6101643 |
22.97 % |
| Transition |
C>T |
All |
2394054 |
9.01 % |
| Transversion |
A>C |
All |
458357 |
1.73 % |
| Transversion |
C>A |
All |
1480564 |
5.57 % |
| Transversion |
T>G |
All |
568225 |
2.14 % |
| Transversion |
G>T |
All |
1403664 |
5.28 % |
| Transversion |
A>T |
All |
1436847 |
5.41 % |
| Transversion |
T>A |
All |
1514549 |
5.70 % |
| Transversion |
C>G |
All |
512211 |
1.93 % |
| Transversion |
G>C |
All |
401600 |
1.51 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
568635 |
19.36 % |
| Transition |
G>A |
Passed |
434922 |
14.81 % |
| Transition |
T>C |
Passed |
506755 |
17.26 % |
| Transition |
C>T |
Passed |
438084 |
14.92 % |
| Transversion |
A>C |
Passed |
118395 |
4.03 % |
| Transversion |
C>A |
Passed |
139075 |
4.74 % |
| Transversion |
T>G |
Passed |
122344 |
4.17 % |
| Transversion |
G>T |
Passed |
135992 |
4.63 % |
| Transversion |
A>T |
Passed |
123341 |
4.20 % |
| Transversion |
T>A |
Passed |
126562 |
4.31 % |
| Transversion |
C>G |
Passed |
112582 |
3.83 % |
| Transversion |
G>C |
Passed |
109979 |
3.75 % |
| |
|
|
|
|
| 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 |
18786480 |
7776017 |
| Passed |
1.97 |
1948396 |
988270 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |