/EXTERNAL ENCODE/variants/K005746_K005730_2_lane_gembs
BACK
SAMPLE K005746_K005730_2_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1170088290 |
1117170495 |
95.48 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1170088290 |
100% |
1161794219 |
99.29 % |
8294071 |
0.71 % |
| |
|
|
|
|
|
|
| Passed |
1117449320 |
95.50 % |
1114154742 |
95.90 % |
3294578 |
0.29 % |
| Filtered |
52638970 |
4.50 % |
47639477 |
4.10 % |
4999493 |
0.45 % |
| |
|
|
|
|
|
|
| q20 |
19092262 |
36.27 % |
18588763 |
39.02 % |
503499 |
10.07 % |
| q20,mq40 |
10913632 |
20.73 % |
10610884 |
22.27 % |
302748 |
6.06 % |
| mq40 |
8084203 |
15.36 % |
7639318 |
16.04 % |
444885 |
8.90 % |
| qd2 |
7117777 |
13.52 % |
6562223 |
13.77 % |
555554 |
11.11 % |
| q20,qd2 |
4708638 |
8.95 % |
1922685 |
4.04 % |
2785953 |
55.72 % |
| q20,qd2,mq40 |
2551843 |
4.85 % |
2178510 |
4.57 % |
373333 |
7.47 % |
| qd2,mq40 |
164524 |
0.31 % |
137094 |
0.29 % |
27430 |
0.55 % |
| fs60 |
1707 |
0.00 % |
0 |
0.00 % |
1707 |
0.03 % |
| qd2,fs60,mq40 |
1579 |
0.00 % |
0 |
0.00 % |
1579 |
0.03 % |
| qd2,fs60 |
1229 |
0.00 % |
0 |
0.00 % |
1229 |
0.02 % |
| fs60,mq40 |
765 |
0.00 % |
0 |
0.00 % |
765 |
0.02 % |
| q20,qd2,fs60 |
558 |
0.00 % |
0 |
0.00 % |
558 |
0.01 % |
| q20,qd2,fs60,mq40 |
134 |
0.00 % |
0 |
0.00 % |
134 |
0.00 % |
| q20,fs60 |
113 |
0.00 % |
0 |
0.00 % |
113 |
0.00 % |
| q20,fs60,mq40 |
6 |
0.00 % |
0 |
0.00 % |
6 |
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 |
2466035 |
24.62 % |
| Transition |
G>A |
All |
944719 |
9.43 % |
| Transition |
T>C |
All |
2350441 |
23.47 % |
| Transition |
C>T |
All |
954157 |
9.53 % |
| Transversion |
A>C |
All |
370886 |
3.70 % |
| Transversion |
C>A |
All |
487320 |
4.87 % |
| Transversion |
T>G |
All |
379035 |
3.78 % |
| Transversion |
G>T |
All |
467320 |
4.67 % |
| Transversion |
A>T |
All |
490728 |
4.90 % |
| Transversion |
T>A |
All |
499939 |
4.99 % |
| Transversion |
C>G |
All |
308039 |
3.08 % |
| Transversion |
G>C |
All |
297338 |
2.97 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
758503 |
17.52 % |
| Transition |
G>A |
Passed |
661378 |
15.28 % |
| Transition |
T>C |
Passed |
744675 |
17.21 % |
| Transition |
C>T |
Passed |
662840 |
15.31 % |
| Transversion |
A>C |
Passed |
193844 |
4.48 % |
| Transversion |
C>A |
Passed |
201433 |
4.65 % |
| Transversion |
T>G |
Passed |
192871 |
4.46 % |
| Transversion |
G>T |
Passed |
193072 |
4.46 % |
| Transversion |
A>T |
Passed |
179094 |
4.14 % |
| Transversion |
T>A |
Passed |
179969 |
4.16 % |
| Transversion |
C>G |
Passed |
180536 |
4.17 % |
| Transversion |
G>C |
Passed |
179967 |
4.16 % |
| |
|
|
|
|
| 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 |
2.03 |
6715352 |
3300605 |
| Passed |
1.88 |
2827396 |
1500786 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |