/cemt/variants/K005723_0_lane_gembs
BACK
SAMPLE K005723_0_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1154961372 |
189740915 |
16.43 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1154961372 |
100% |
1122484333 |
97.19 % |
32477039 |
2.81 % |
| |
|
|
|
|
|
|
| Passed |
199092389 |
17.24 % |
187861216 |
16.74 % |
11231173 |
5.64 % |
| Filtered |
955868983 |
82.76 % |
934623117 |
83.26 % |
21245866 |
10.67 % |
| |
|
|
|
|
|
|
| q20 |
888864024 |
92.99 % |
880275994 |
94.19 % |
8588030 |
40.42 % |
| q20,qd2 |
48879412 |
5.11 % |
36684731 |
3.93 % |
12194681 |
57.40 % |
| q20,mq40 |
12848433 |
1.34 % |
12695396 |
1.36 % |
153037 |
0.72 % |
| q20,qd2,mq40 |
4574964 |
0.48 % |
4467972 |
0.48 % |
106992 |
0.50 % |
| mq40 |
598582 |
0.06 % |
414231 |
0.04 % |
184351 |
0.87 % |
| qd2 |
81656 |
0.01 % |
67709 |
0.01 % |
13947 |
0.07 % |
| qd2,mq40 |
21461 |
0.00 % |
17084 |
0.00 % |
4377 |
0.02 % |
| qd2,fs60,mq40 |
198 |
0.00 % |
0 |
0.00 % |
198 |
0.00 % |
| qd2,fs60 |
110 |
0.00 % |
0 |
0.00 % |
110 |
0.00 % |
| fs60,mq40 |
78 |
0.00 % |
0 |
0.00 % |
78 |
0.00 % |
| fs60 |
28 |
0.00 % |
0 |
0.00 % |
28 |
0.00 % |
| q20,qd2,fs60,mq40 |
24 |
0.00 % |
0 |
0.00 % |
24 |
0.00 % |
| q20,qd2,fs60 |
13 |
0.00 % |
0 |
0.00 % |
13 |
0.00 % |
| q20,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 |
10188193 |
29.33 % |
| Transition |
G>A |
All |
853561 |
2.46 % |
| Transition |
T>C |
All |
7431732 |
21.39 % |
| Transition |
C>T |
All |
1004372 |
2.89 % |
| Transversion |
A>C |
All |
2354236 |
6.78 % |
| Transversion |
C>A |
All |
2203931 |
6.34 % |
| Transversion |
T>G |
All |
3055201 |
8.79 % |
| Transversion |
G>T |
All |
1944465 |
5.60 % |
| Transversion |
A>T |
All |
1345545 |
3.87 % |
| Transversion |
T>A |
All |
1744259 |
5.02 % |
| Transversion |
C>G |
All |
1441697 |
4.15 % |
| Transversion |
G>C |
All |
1171557 |
3.37 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
515512 |
24.70 % |
| Transition |
G>A |
Passed |
202741 |
9.71 % |
| Transition |
T>C |
Passed |
448330 |
21.48 % |
| Transition |
C>T |
Passed |
220759 |
10.58 % |
| Transversion |
A>C |
Passed |
89541 |
4.29 % |
| Transversion |
C>A |
Passed |
85258 |
4.09 % |
| Transversion |
T>G |
Passed |
117100 |
5.61 % |
| Transversion |
G>T |
Passed |
91172 |
4.37 % |
| Transversion |
A>T |
Passed |
78141 |
3.74 % |
| Transversion |
T>A |
Passed |
73718 |
3.53 % |
| Transversion |
C>G |
Passed |
88868 |
4.26 % |
| Transversion |
G>C |
Passed |
75782 |
3.63 % |
| |
|
|
|
|
| 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 |
1.28 |
19477858 |
15260891 |
| Passed |
1.98 |
1387342 |
699580 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |