/EXTERNAL ENCODE/variants/K005729_K005715_2_lane_gembs
BACK
SAMPLE K005729_K005715_2_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1166339089 |
1068745411 |
91.63 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1166339089 |
100% |
1153410381 |
98.89 % |
12928708 |
1.11 % |
| |
|
|
|
|
|
|
| Passed |
1069259437 |
91.68 % |
1065808647 |
92.40 % |
3450790 |
0.32 % |
| Filtered |
97079652 |
8.32 % |
87601734 |
7.60 % |
9477918 |
0.89 % |
| |
|
|
|
|
|
|
| q20 |
59255293 |
61.04 % |
58105001 |
66.33 % |
1150292 |
12.14 % |
| q20,mq40 |
12747098 |
13.13 % |
12456220 |
14.22 % |
290878 |
3.07 % |
| q20,qd2 |
11696657 |
12.05 % |
4876242 |
5.57 % |
6820415 |
71.96 % |
| qd2 |
5881215 |
6.06 % |
5342635 |
6.10 % |
538580 |
5.68 % |
| mq40 |
3990304 |
4.11 % |
3710270 |
4.24 % |
280034 |
2.95 % |
| q20,qd2,mq40 |
3425143 |
3.53 % |
3044514 |
3.48 % |
380629 |
4.02 % |
| qd2,mq40 |
80540 |
0.08 % |
66852 |
0.08 % |
13688 |
0.14 % |
| qd2,fs60,mq40 |
1052 |
0.00 % |
0 |
0.00 % |
1052 |
0.01 % |
| fs60 |
759 |
0.00 % |
0 |
0.00 % |
759 |
0.01 % |
| qd2,fs60 |
609 |
0.00 % |
0 |
0.00 % |
609 |
0.01 % |
| q20,qd2,fs60 |
546 |
0.00 % |
0 |
0.00 % |
546 |
0.01 % |
| fs60,mq40 |
355 |
0.00 % |
0 |
0.00 % |
355 |
0.00 % |
| q20,qd2,fs60,mq40 |
75 |
0.00 % |
0 |
0.00 % |
75 |
0.00 % |
| q20,fs60,mq40 |
5 |
0.00 % |
0 |
0.00 % |
5 |
0.00 % |
| q20,fs60 |
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 |
4198321 |
28.42 % |
| Transition |
G>A |
All |
1080773 |
7.32 % |
| Transition |
T>C |
All |
4041718 |
27.36 % |
| Transition |
C>T |
All |
1097627 |
7.43 % |
| Transversion |
A>C |
All |
309665 |
2.10 % |
| Transversion |
C>A |
All |
734485 |
4.97 % |
| Transversion |
T>G |
All |
318299 |
2.15 % |
| Transversion |
G>T |
All |
715138 |
4.84 % |
| Transversion |
A>T |
All |
861396 |
5.83 % |
| Transversion |
T>A |
All |
886315 |
6.00 % |
| Transversion |
C>G |
All |
267254 |
1.81 % |
| Transversion |
G>C |
All |
260986 |
1.77 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
823054 |
19.60 % |
| Transition |
G>A |
Passed |
620196 |
14.77 % |
| Transition |
T>C |
Passed |
818315 |
19.48 % |
| Transition |
C>T |
Passed |
621111 |
14.79 % |
| Transversion |
A>C |
Passed |
166625 |
3.97 % |
| Transversion |
C>A |
Passed |
172302 |
4.10 % |
| Transversion |
T>G |
Passed |
168256 |
4.01 % |
| Transversion |
G>T |
Passed |
169924 |
4.05 % |
| Transversion |
A>T |
Passed |
156777 |
3.73 % |
| Transversion |
T>A |
Passed |
159892 |
3.81 % |
| Transversion |
C>G |
Passed |
161793 |
3.85 % |
| Transversion |
G>C |
Passed |
161490 |
3.85 % |
| |
|
|
|
|
| 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 |
2.39 |
10418439 |
4353538 |
| Passed |
2.19 |
2882676 |
1317059 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |