/EXTERNAL ENCODE/variants/K005741_K005740_2_lane_gembs
BACK
SAMPLE K005741_K005740_2_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1159342039 |
1084607852 |
93.55 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1159342039 |
100% |
1149217178 |
99.13 % |
10124861 |
0.87 % |
| |
|
|
|
|
|
|
| Passed |
1085039558 |
93.59 % |
1081808617 |
94.13 % |
3230941 |
0.30 % |
| Filtered |
74302481 |
6.41 % |
67408561 |
5.87 % |
6893920 |
0.64 % |
| |
|
|
|
|
|
|
| q20 |
39239188 |
52.81 % |
38364574 |
56.91 % |
874614 |
12.69 % |
| q20,mq40 |
11959029 |
16.10 % |
11693092 |
17.35 % |
265937 |
3.86 % |
| q20,qd2 |
8237229 |
11.09 % |
3532286 |
5.24 % |
4704943 |
68.25 % |
| qd2 |
6580892 |
8.86 % |
6194345 |
9.19 % |
386547 |
5.61 % |
| mq40 |
5150067 |
6.93 % |
4848575 |
7.19 % |
301492 |
4.37 % |
| q20,qd2,mq40 |
3045059 |
4.10 % |
2701771 |
4.01 % |
343288 |
4.98 % |
| qd2,mq40 |
88624 |
0.12 % |
73918 |
0.11 % |
14706 |
0.21 % |
| qd2,fs60,mq40 |
944 |
0.00 % |
0 |
0.00 % |
944 |
0.01 % |
| qd2,fs60 |
472 |
0.00 % |
0 |
0.00 % |
472 |
0.01 % |
| fs60,mq40 |
409 |
0.00 % |
0 |
0.00 % |
409 |
0.01 % |
| fs60 |
379 |
0.00 % |
0 |
0.00 % |
379 |
0.01 % |
| q20,qd2,fs60,mq40 |
89 |
0.00 % |
0 |
0.00 % |
89 |
0.00 % |
| q20,qd2,fs60 |
88 |
0.00 % |
0 |
0.00 % |
88 |
0.00 % |
| q20,fs60 |
7 |
0.00 % |
0 |
0.00 % |
7 |
0.00 % |
| q20,fs60,mq40 |
5 |
0.00 % |
0 |
0.00 % |
5 |
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 |
3270474 |
27.57 % |
| Transition |
G>A |
All |
1003701 |
8.46 % |
| Transition |
T>C |
All |
3083519 |
25.99 % |
| Transition |
C>T |
All |
1023064 |
8.62 % |
| Transversion |
A>C |
All |
281827 |
2.38 % |
| Transversion |
C>A |
All |
584538 |
4.93 % |
| Transversion |
T>G |
All |
288183 |
2.43 % |
| Transversion |
G>T |
All |
584994 |
4.93 % |
| Transversion |
A>T |
All |
629759 |
5.31 % |
| Transversion |
T>A |
All |
611125 |
5.15 % |
| Transversion |
C>G |
All |
255325 |
2.15 % |
| Transversion |
G>C |
All |
248028 |
2.09 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
735027 |
18.14 % |
| Transition |
G>A |
Passed |
635536 |
15.69 % |
| Transition |
T>C |
Passed |
724032 |
17.87 % |
| Transition |
C>T |
Passed |
636418 |
15.71 % |
| Transversion |
A>C |
Passed |
166484 |
4.11 % |
| Transversion |
C>A |
Passed |
176330 |
4.35 % |
| Transversion |
T>G |
Passed |
167061 |
4.12 % |
| Transversion |
G>T |
Passed |
173062 |
4.27 % |
| Transversion |
A>T |
Passed |
154793 |
3.82 % |
| Transversion |
T>A |
Passed |
156599 |
3.86 % |
| Transversion |
C>G |
Passed |
163408 |
4.03 % |
| Transversion |
G>C |
Passed |
163079 |
4.02 % |
| |
|
|
|
|
| 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 |
2.41 |
8380758 |
3483779 |
| Passed |
2.07 |
2731013 |
1320816 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |