/EXTERNAL CREST/variants/K006471_1_lane_gembs
BACK
SAMPLE K006471_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1145698611 |
67731775 |
5.91 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1145698611 |
100% |
1083971860 |
94.61 % |
61726751 |
5.39 % |
| |
|
|
|
|
|
|
| Passed |
89672572 |
7.83 % |
66561951 |
6.14 % |
23110621 |
25.77 % |
| Filtered |
1056026039 |
92.17 % |
1017409909 |
93.86 % |
38616130 |
43.06 % |
| |
|
|
|
|
|
|
| q20 |
907228351 |
85.91 % |
891006977 |
87.58 % |
16221374 |
42.01 % |
| q20,qd2 |
68137099 |
6.45 % |
48775161 |
4.79 % |
19361938 |
50.14 % |
| q20,mq40 |
64475762 |
6.11 % |
63553914 |
6.25 % |
921848 |
2.39 % |
| q20,qd2,mq40 |
13169887 |
1.25 % |
12525820 |
1.23 % |
644067 |
1.67 % |
| mq40 |
3002926 |
0.28 % |
1538663 |
0.15 % |
1464263 |
3.79 % |
| qd2 |
7827 |
0.00 % |
6416 |
0.00 % |
1411 |
0.00 % |
| qd2,mq40 |
4153 |
0.00 % |
2958 |
0.00 % |
1195 |
0.00 % |
| fs60,mq40 |
25 |
0.00 % |
0 |
0.00 % |
25 |
0.00 % |
| fs60 |
4 |
0.00 % |
0 |
0.00 % |
4 |
0.00 % |
| qd2,fs60,mq40 |
3 |
0.00 % |
0 |
0.00 % |
3 |
0.00 % |
| q20,qd2,fs60 |
1 |
0.00 % |
0 |
0.00 % |
1 |
0.00 % |
| q20,qd2,fs60,mq40 |
1 |
0.00 % |
0 |
0.00 % |
1 |
0.00 % |
| q20,fs60 |
0 |
0.00 % |
0 |
0.00 % |
0 |
0.00 % |
| qd2,fs60 |
0 |
0.00 % |
0 |
0.00 % |
0 |
0.00 % |
| q20,fs60,mq40 |
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 |
10123330 |
15.48 % |
| Transition |
G>A |
All |
4237251 |
6.48 % |
| Transition |
T>C |
All |
9793586 |
14.97 % |
| Transition |
C>T |
All |
2662338 |
4.07 % |
| Transversion |
A>C |
All |
1959859 |
3.00 % |
| Transversion |
C>A |
All |
5767753 |
8.82 % |
| Transversion |
T>G |
All |
3974416 |
6.08 % |
| Transversion |
G>T |
All |
6022403 |
9.21 % |
| Transversion |
A>T |
All |
8397569 |
12.84 % |
| Transversion |
T>A |
All |
8121471 |
12.42 % |
| Transversion |
C>G |
All |
2782627 |
4.25 % |
| Transversion |
G>C |
All |
1565295 |
2.39 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
211362 |
17.55 % |
| Transition |
G>A |
Passed |
135419 |
11.24 % |
| Transition |
T>C |
Passed |
200747 |
16.67 % |
| Transition |
C>T |
Passed |
85452 |
7.09 % |
| Transversion |
A>C |
Passed |
57971 |
4.81 % |
| Transversion |
C>A |
Passed |
77652 |
6.45 % |
| Transversion |
T>G |
Passed |
101980 |
8.47 % |
| Transversion |
G>T |
Passed |
53460 |
4.44 % |
| Transversion |
A>T |
Passed |
49613 |
4.12 % |
| Transversion |
T>A |
Passed |
89920 |
7.47 % |
| Transversion |
C>G |
Passed |
83033 |
6.89 % |
| Transversion |
G>C |
Passed |
57849 |
4.80 % |
| |
|
|
|
|
| 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 |
0.69 |
26816505 |
38591393 |
| Passed |
1.11 |
632980 |
571478 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |