/EXTERNAL ENCODE/variants/K005734_K005709_2_lane_gembs
BACK
SAMPLE K005734_K005709_2_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1166607544 |
1039418911 |
89.10 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1166607544 |
100% |
1155106588 |
99.01 % |
11500956 |
0.99 % |
| |
|
|
|
|
|
|
| Passed |
1040722160 |
89.21 % |
1036328851 |
89.72 % |
4393309 |
0.42 % |
| Filtered |
125885384 |
10.79 % |
118777737 |
10.28 % |
7107647 |
0.68 % |
| |
|
|
|
|
|
|
| q20 |
97580258 |
77.52 % |
96597300 |
81.33 % |
982958 |
13.83 % |
| q20,mq40 |
10095447 |
8.02 % |
9923246 |
8.35 % |
172201 |
2.42 % |
| q20,qd2 |
7126852 |
5.66 % |
2249753 |
1.89 % |
4877099 |
68.62 % |
| mq40 |
5223269 |
4.15 % |
4833795 |
4.07 % |
389474 |
5.48 % |
| qd2 |
3112149 |
2.47 % |
2722143 |
2.29 % |
390006 |
5.49 % |
| q20,qd2,mq40 |
2588263 |
2.06 % |
2327377 |
1.96 % |
260886 |
3.67 % |
| qd2,mq40 |
150898 |
0.12 % |
124123 |
0.10 % |
26775 |
0.38 % |
| fs60 |
2443 |
0.00 % |
0 |
0.00 % |
2443 |
0.03 % |
| qd2,fs60 |
2228 |
0.00 % |
0 |
0.00 % |
2228 |
0.03 % |
| qd2,fs60,mq40 |
1996 |
0.00 % |
0 |
0.00 % |
1996 |
0.03 % |
| q20,qd2,fs60 |
805 |
0.00 % |
0 |
0.00 % |
805 |
0.01 % |
| fs60,mq40 |
613 |
0.00 % |
0 |
0.00 % |
613 |
0.01 % |
| q20,qd2,fs60,mq40 |
141 |
0.00 % |
0 |
0.00 % |
141 |
0.00 % |
| q20,fs60 |
16 |
0.00 % |
0 |
0.00 % |
16 |
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 |
4306295 |
32.40 % |
| Transition |
G>A |
All |
1029089 |
7.74 % |
| Transition |
T>C |
All |
3999713 |
30.09 % |
| Transition |
C>T |
All |
1068196 |
8.04 % |
| Transversion |
A>C |
All |
304183 |
2.29 % |
| Transversion |
C>A |
All |
453174 |
3.41 % |
| Transversion |
T>G |
All |
321359 |
2.42 % |
| Transversion |
G>T |
All |
447109 |
3.36 % |
| Transversion |
A>T |
All |
356319 |
2.68 % |
| Transversion |
T>A |
All |
365408 |
2.75 % |
| Transversion |
C>G |
All |
326032 |
2.45 % |
| Transversion |
G>C |
All |
315017 |
2.37 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
806402 |
18.65 % |
| Transition |
G>A |
Passed |
645209 |
14.92 % |
| Transition |
T>C |
Passed |
820554 |
18.98 % |
| Transition |
C>T |
Passed |
651119 |
15.06 % |
| Transversion |
A>C |
Passed |
178742 |
4.13 % |
| Transversion |
C>A |
Passed |
186314 |
4.31 % |
| Transversion |
T>G |
Passed |
180617 |
4.18 % |
| Transversion |
G>T |
Passed |
178579 |
4.13 % |
| Transversion |
A>T |
Passed |
163310 |
3.78 % |
| Transversion |
T>A |
Passed |
165155 |
3.82 % |
| Transversion |
C>G |
Passed |
173703 |
4.02 % |
| Transversion |
G>C |
Passed |
173883 |
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 |
3.60 |
10403293 |
2888601 |
| Passed |
2.09 |
2923284 |
1400303 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |