/EXTERNAL CREST/variants/K006437_1_lane_gembs
BACK
SAMPLE K006437_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1212720283 |
689033885 |
56.82 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1212720283 |
100% |
1115861514 |
92.01 % |
96858769 |
7.99 % |
| |
|
|
|
|
|
|
| Passed |
703633348 |
58.02 % |
682710225 |
61.18 % |
20923123 |
2.97 % |
| Filtered |
509086935 |
41.98 % |
433151289 |
38.82 % |
75935646 |
10.79 % |
| |
|
|
|
|
|
|
| q20 |
358175885 |
70.36 % |
338196904 |
78.08 % |
19978981 |
26.31 % |
| q20,qd2 |
74882204 |
14.71 % |
24872717 |
5.74 % |
50009487 |
65.86 % |
| q20,mq40 |
39405453 |
7.74 % |
37879661 |
8.75 % |
1525792 |
2.01 % |
| mq40 |
23430029 |
4.60 % |
21750057 |
5.02 % |
1679972 |
2.21 % |
| q20,qd2,mq40 |
6789042 |
1.33 % |
4674176 |
1.08 % |
2114866 |
2.79 % |
| qd2 |
6279311 |
1.23 % |
5678305 |
1.31 % |
601006 |
0.79 % |
| qd2,mq40 |
124406 |
0.02 % |
99469 |
0.02 % |
24937 |
0.03 % |
| fs60 |
358 |
0.00 % |
0 |
0.00 % |
358 |
0.00 % |
| fs60,mq40 |
190 |
0.00 % |
0 |
0.00 % |
190 |
0.00 % |
| q20,qd2,fs60 |
31 |
0.00 % |
0 |
0.00 % |
31 |
0.00 % |
| q20,fs60 |
10 |
0.00 % |
0 |
0.00 % |
10 |
0.00 % |
| qd2,fs60 |
6 |
0.00 % |
0 |
0.00 % |
6 |
0.00 % |
| q20,qd2,fs60,mq40 |
5 |
0.00 % |
0 |
0.00 % |
5 |
0.00 % |
| q20,fs60,mq40 |
3 |
0.00 % |
0 |
0.00 % |
3 |
0.00 % |
| qd2,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 |
25289538 |
25.57 % |
| Transition |
G>A |
All |
9005348 |
9.11 % |
| Transition |
T>C |
All |
27379345 |
27.69 % |
| Transition |
C>T |
All |
5980302 |
6.05 % |
| Transversion |
A>C |
All |
2255136 |
2.28 % |
| Transversion |
C>A |
All |
4155741 |
4.20 % |
| Transversion |
T>G |
All |
3865066 |
3.91 % |
| Transversion |
G>T |
All |
3674677 |
3.72 % |
| Transversion |
A>T |
All |
6253868 |
6.32 % |
| Transversion |
T>A |
All |
7078535 |
7.16 % |
| Transversion |
C>G |
All |
2338758 |
2.37 % |
| Transversion |
G>C |
All |
1611776 |
1.63 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
1559239 |
22.49 % |
| Transition |
G>A |
Passed |
686932 |
9.91 % |
| Transition |
T>C |
Passed |
2062796 |
29.75 % |
| Transition |
C>T |
Passed |
462657 |
6.67 % |
| Transversion |
A>C |
Passed |
231931 |
3.34 % |
| Transversion |
C>A |
Passed |
288327 |
4.16 % |
| Transversion |
T>G |
Passed |
394467 |
5.69 % |
| Transversion |
G>T |
Passed |
168621 |
2.43 % |
| Transversion |
A>T |
Passed |
189064 |
2.73 % |
| Transversion |
T>A |
Passed |
395304 |
5.70 % |
| Transversion |
C>G |
Passed |
288404 |
4.16 % |
| Transversion |
G>C |
Passed |
206592 |
2.98 % |
| |
|
|
|
|
| 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 |
2.17 |
67654533 |
31233557 |
| Passed |
2.21 |
4771624 |
2162710 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |