/EXTERNAL ENCODE/variants/K005745_K005725_2_lane_gembs
BACK
SAMPLE K005745_K005725_2_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1172854483 |
1044774176 |
89.08 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1172854483 |
100% |
1151065603 |
98.14 % |
21788880 |
1.86 % |
| |
|
|
|
|
|
|
| Passed |
1045999733 |
89.18 % |
1040561904 |
90.40 % |
5437829 |
0.52 % |
| Filtered |
126854750 |
10.82 % |
110503699 |
9.60 % |
16351051 |
1.56 % |
| |
|
|
|
|
|
|
| q20 |
77028740 |
60.72 % |
75144121 |
68.00 % |
1884619 |
11.53 % |
| q20,qd2 |
19113504 |
15.07 % |
7196708 |
6.51 % |
11916796 |
72.88 % |
| q20,mq40 |
13369576 |
10.54 % |
12984804 |
11.75 % |
384772 |
2.35 % |
| qd2 |
8694035 |
6.85 % |
7411698 |
6.71 % |
1282337 |
7.84 % |
| mq40 |
5368636 |
4.23 % |
4903863 |
4.44 % |
464773 |
2.84 % |
| q20,qd2,mq40 |
3183979 |
2.51 % |
2786126 |
2.52 % |
397853 |
2.43 % |
| qd2,mq40 |
94334 |
0.07 % |
76379 |
0.07 % |
17955 |
0.11 % |
| qd2,fs60,mq40 |
1058 |
0.00 % |
0 |
0.00 % |
1058 |
0.01 % |
| fs60,mq40 |
366 |
0.00 % |
0 |
0.00 % |
366 |
0.00 % |
| qd2,fs60 |
239 |
0.00 % |
0 |
0.00 % |
239 |
0.00 % |
| fs60 |
169 |
0.00 % |
0 |
0.00 % |
169 |
0.00 % |
| q20,qd2,fs60,mq40 |
83 |
0.00 % |
0 |
0.00 % |
83 |
0.00 % |
| q20,qd2,fs60 |
26 |
0.00 % |
0 |
0.00 % |
26 |
0.00 % |
| q20,fs60 |
4 |
0.00 % |
0 |
0.00 % |
4 |
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 |
7956298 |
33.78 % |
| Transition |
G>A |
All |
1521765 |
6.46 % |
| Transition |
T>C |
All |
7560405 |
32.10 % |
| Transition |
C>T |
All |
1565588 |
6.65 % |
| Transversion |
A>C |
All |
575315 |
2.44 % |
| Transversion |
C>A |
All |
740854 |
3.15 % |
| Transversion |
T>G |
All |
585649 |
2.49 % |
| Transversion |
G>T |
All |
702059 |
2.98 % |
| Transversion |
A>T |
All |
686592 |
2.91 % |
| Transversion |
T>A |
All |
736859 |
3.13 % |
| Transversion |
C>G |
All |
475471 |
2.02 % |
| Transversion |
G>C |
All |
447671 |
1.90 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
1351467 |
24.99 % |
| Transition |
G>A |
Passed |
640736 |
11.85 % |
| Transition |
T>C |
Passed |
1254061 |
23.19 % |
| Transition |
C>T |
Passed |
639421 |
11.82 % |
| Transversion |
A>C |
Passed |
205569 |
3.80 % |
| Transversion |
C>A |
Passed |
199166 |
3.68 % |
| Transversion |
T>G |
Passed |
204866 |
3.79 % |
| Transversion |
G>T |
Passed |
191827 |
3.55 % |
| Transversion |
A>T |
Passed |
175702 |
3.25 % |
| Transversion |
T>A |
Passed |
179781 |
3.32 % |
| Transversion |
C>G |
Passed |
184298 |
3.41 % |
| Transversion |
G>C |
Passed |
181923 |
3.36 % |
| |
|
|
|
|
| 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 |
3.76 |
18604056 |
4950470 |
| Passed |
2.55 |
3885685 |
1523132 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |