/cemt/variants/K005717_0_lane_gembs
BACK
SAMPLE K005717_0_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1173393623 |
825411304 |
70.34 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1173393623 |
100% |
1155936655 |
98.51 % |
17456968 |
1.49 % |
| |
|
|
|
|
|
|
| Passed |
829210754 |
70.67 % |
822642046 |
71.17 % |
6568708 |
0.79 % |
| Filtered |
344182869 |
29.33 % |
333294609 |
28.83 % |
10888260 |
1.31 % |
| |
|
|
|
|
|
|
| q20 |
313870530 |
91.19 % |
312102729 |
93.64 % |
1767801 |
16.24 % |
| q20,qd2 |
13791923 |
4.01 % |
5519018 |
1.66 % |
8272905 |
75.98 % |
| q20,mq40 |
9097698 |
2.64 % |
8996084 |
2.70 % |
101614 |
0.93 % |
| qd2 |
2721881 |
0.79 % |
2364025 |
0.71 % |
357856 |
3.29 % |
| q20,qd2,mq40 |
2373946 |
0.69 % |
2231605 |
0.67 % |
142341 |
1.31 % |
| mq40 |
2267743 |
0.66 % |
2035441 |
0.61 % |
232302 |
2.13 % |
| qd2,mq40 |
56622 |
0.02 % |
45707 |
0.01 % |
10915 |
0.10 % |
| qd2,fs60,mq40 |
1058 |
0.00 % |
0 |
0.00 % |
1058 |
0.01 % |
| qd2,fs60 |
655 |
0.00 % |
0 |
0.00 % |
655 |
0.01 % |
| fs60 |
347 |
0.00 % |
0 |
0.00 % |
347 |
0.00 % |
| fs60,mq40 |
261 |
0.00 % |
0 |
0.00 % |
261 |
0.00 % |
| q20,qd2,fs60 |
115 |
0.00 % |
0 |
0.00 % |
115 |
0.00 % |
| q20,qd2,fs60,mq40 |
88 |
0.00 % |
0 |
0.00 % |
88 |
0.00 % |
| q20,fs60 |
2 |
0.00 % |
0 |
0.00 % |
2 |
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 |
7080992 |
36.77 % |
| Transition |
G>A |
All |
938993 |
4.88 % |
| Transition |
T>C |
All |
6519973 |
33.86 % |
| Transition |
C>T |
All |
972743 |
5.05 % |
| Transversion |
A>C |
All |
322238 |
1.67 % |
| Transversion |
C>A |
All |
765596 |
3.98 % |
| Transversion |
T>G |
All |
350968 |
1.82 % |
| Transversion |
G>T |
All |
738580 |
3.84 % |
| Transversion |
A>T |
All |
380159 |
1.97 % |
| Transversion |
T>A |
All |
405701 |
2.11 % |
| Transversion |
C>G |
All |
403387 |
2.09 % |
| Transversion |
G>C |
All |
378137 |
1.96 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
771178 |
20.61 % |
| Transition |
G>A |
Passed |
515839 |
13.79 % |
| Transition |
T>C |
Passed |
752138 |
20.10 % |
| Transition |
C>T |
Passed |
520632 |
13.91 % |
| Transversion |
A>C |
Passed |
146110 |
3.90 % |
| Transversion |
C>A |
Passed |
159172 |
4.25 % |
| Transversion |
T>G |
Passed |
149116 |
3.99 % |
| Transversion |
G>T |
Passed |
154573 |
4.13 % |
| Transversion |
A>T |
Passed |
138772 |
3.71 % |
| Transversion |
T>A |
Passed |
140064 |
3.74 % |
| Transversion |
C>G |
Passed |
147259 |
3.94 % |
| Transversion |
G>C |
Passed |
146768 |
3.92 % |
| |
|
|
|
|
| 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 |
4.14 |
15512701 |
3744766 |
| Passed |
2.17 |
2559787 |
1181834 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |