/EXTERNAL ENCODE/variants/K005711_K005708_2_lane_gembs
BACK
SAMPLE K005711_K005708_2_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1168853291 |
1058361481 |
90.55 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1168853291 |
100% |
1154485009 |
98.77 % |
14368282 |
1.23 % |
| |
|
|
|
|
|
|
| Passed |
1059179170 |
90.62 % |
1055420109 |
91.42 % |
3759061 |
0.35 % |
| Filtered |
109674121 |
9.38 % |
99064900 |
8.58 % |
10609221 |
1.00 % |
| |
|
|
|
|
|
|
| q20 |
71864201 |
65.53 % |
70483818 |
71.15 % |
1380383 |
13.01 % |
| q20,qd2 |
13171433 |
12.01 % |
5233995 |
5.28 % |
7937438 |
74.82 % |
| q20,mq40 |
12316142 |
11.23 % |
12080074 |
12.19 % |
236068 |
2.23 % |
| qd2 |
5542011 |
5.05 % |
5074807 |
5.12 % |
467204 |
4.40 % |
| mq40 |
3629440 |
3.31 % |
3344168 |
3.38 % |
285272 |
2.69 % |
| q20,qd2,mq40 |
3081872 |
2.81 % |
2792620 |
2.82 % |
289252 |
2.73 % |
| qd2,mq40 |
66922 |
0.06 % |
55418 |
0.06 % |
11504 |
0.11 % |
| qd2,fs60,mq40 |
860 |
0.00 % |
0 |
0.00 % |
860 |
0.01 % |
| qd2,fs60 |
428 |
0.00 % |
0 |
0.00 % |
428 |
0.00 % |
| fs60 |
344 |
0.00 % |
0 |
0.00 % |
344 |
0.00 % |
| fs60,mq40 |
335 |
0.00 % |
0 |
0.00 % |
335 |
0.00 % |
| q20,qd2,fs60,mq40 |
70 |
0.00 % |
0 |
0.00 % |
70 |
0.00 % |
| q20,qd2,fs60 |
58 |
0.00 % |
0 |
0.00 % |
58 |
0.00 % |
| q20,fs60,mq40 |
5 |
0.00 % |
0 |
0.00 % |
5 |
0.00 % |
| q20,fs60 |
0 |
0.00 % |
0 |
0.00 % |
0 |
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 |
5026365 |
31.12 % |
| Transition |
G>A |
All |
1117733 |
6.92 % |
| Transition |
T>C |
All |
4461457 |
27.62 % |
| Transition |
C>T |
All |
1182495 |
7.32 % |
| Transversion |
A>C |
All |
309684 |
1.92 % |
| Transversion |
C>A |
All |
764046 |
4.73 % |
| Transversion |
T>G |
All |
326451 |
2.02 % |
| Transversion |
G>T |
All |
758859 |
4.70 % |
| Transversion |
A>T |
All |
818325 |
5.07 % |
| Transversion |
T>A |
All |
822217 |
5.09 % |
| Transversion |
C>G |
All |
291290 |
1.80 % |
| Transversion |
G>C |
All |
273418 |
1.69 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
850380 |
20.25 % |
| Transition |
G>A |
Passed |
619914 |
14.76 % |
| Transition |
T>C |
Passed |
789740 |
18.81 % |
| Transition |
C>T |
Passed |
623230 |
14.84 % |
| Transversion |
A>C |
Passed |
165519 |
3.94 % |
| Transversion |
C>A |
Passed |
170394 |
4.06 % |
| Transversion |
T>G |
Passed |
168947 |
4.02 % |
| Transversion |
G>T |
Passed |
169945 |
4.05 % |
| Transversion |
A>T |
Passed |
156340 |
3.72 % |
| Transversion |
T>A |
Passed |
157613 |
3.75 % |
| Transversion |
C>G |
Passed |
164379 |
3.91 % |
| Transversion |
G>C |
Passed |
162327 |
3.87 % |
| |
|
|
|
|
| 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 |
2.70 |
11788050 |
4364290 |
| Passed |
2.19 |
2883264 |
1315464 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |