/EXTERNAL ENCODE/variants/K005724_K005706_2_lane_gembs
BACK
SAMPLE K005724_K005706_2_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1166886369 |
855023119 |
73.27 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1166886369 |
100% |
1151517673 |
98.68 % |
15368696 |
1.32 % |
| |
|
|
|
|
|
|
| Passed |
857122388 |
73.45 % |
852189441 |
74.01 % |
4932947 |
0.58 % |
| Filtered |
309763981 |
26.55 % |
299328232 |
25.99 % |
10435749 |
1.22 % |
| |
|
|
|
|
|
|
| q20 |
274424191 |
88.59 % |
272168937 |
90.93 % |
2255254 |
21.61 % |
| q20,mq40 |
12986545 |
4.19 % |
12745354 |
4.26 % |
241191 |
2.31 % |
| q20,qd2 |
12915215 |
4.17 % |
5841020 |
1.95 % |
7074195 |
67.79 % |
| mq40 |
3697029 |
1.19 % |
3388834 |
1.13 % |
308195 |
2.95 % |
| q20,qd2,mq40 |
3326157 |
1.07 % |
3054200 |
1.02 % |
271957 |
2.61 % |
| qd2 |
2343529 |
0.76 % |
2074808 |
0.69 % |
268721 |
2.58 % |
| qd2,mq40 |
68871 |
0.02 % |
55079 |
0.02 % |
13792 |
0.13 % |
| qd2,fs60,mq40 |
976 |
0.00 % |
0 |
0.00 % |
976 |
0.01 % |
| qd2,fs60 |
604 |
0.00 % |
0 |
0.00 % |
604 |
0.01 % |
| fs60 |
346 |
0.00 % |
0 |
0.00 % |
346 |
0.00 % |
| fs60,mq40 |
309 |
0.00 % |
0 |
0.00 % |
309 |
0.00 % |
| q20,qd2,fs60,mq40 |
115 |
0.00 % |
0 |
0.00 % |
115 |
0.00 % |
| q20,qd2,fs60 |
91 |
0.00 % |
0 |
0.00 % |
91 |
0.00 % |
| q20,fs60 |
2 |
0.00 % |
0 |
0.00 % |
2 |
0.00 % |
| q20,fs60,mq40 |
1 |
0.00 % |
0 |
0.00 % |
1 |
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 |
5350059 |
31.17 % |
| Transition |
G>A |
All |
1083939 |
6.32 % |
| Transition |
T>C |
All |
4989864 |
29.07 % |
| Transition |
C>T |
All |
1119010 |
6.52 % |
| Transversion |
A>C |
All |
592245 |
3.45 % |
| Transversion |
C>A |
All |
676001 |
3.94 % |
| Transversion |
T>G |
All |
673763 |
3.93 % |
| Transversion |
G>T |
All |
666707 |
3.88 % |
| Transversion |
A>T |
All |
419211 |
2.44 % |
| Transversion |
T>A |
All |
431116 |
2.51 % |
| Transversion |
C>G |
All |
584816 |
3.41 % |
| Transversion |
G>C |
All |
576481 |
3.36 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
703512 |
18.27 % |
| Transition |
G>A |
Passed |
579873 |
15.06 % |
| Transition |
T>C |
Passed |
700565 |
18.19 % |
| Transition |
C>T |
Passed |
583709 |
15.16 % |
| Transversion |
A>C |
Passed |
160510 |
4.17 % |
| Transversion |
C>A |
Passed |
175549 |
4.56 % |
| Transversion |
T>G |
Passed |
163939 |
4.26 % |
| Transversion |
G>T |
Passed |
167831 |
4.36 % |
| Transversion |
A>T |
Passed |
149439 |
3.88 % |
| Transversion |
T>A |
Passed |
152537 |
3.96 % |
| Transversion |
C>G |
Passed |
156838 |
4.07 % |
| Transversion |
G>C |
Passed |
156340 |
4.06 % |
| |
|
|
|
|
| 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 |
2.71 |
12542872 |
4620340 |
| Passed |
2.00 |
2567659 |
1282983 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |