/EXTERNAL Roadmap/variants/K006530_K006531_2_lane_gembs
BACK
SAMPLE K006530_K006531_2_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1157779594 |
1084964226 |
93.71 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1157779594 |
100% |
1149539235 |
99.29 % |
8240359 |
0.71 % |
| |
|
|
|
|
|
|
| Passed |
1085028297 |
93.72 % |
1080221936 |
93.97 % |
4806361 |
0.44 % |
| Filtered |
72751297 |
6.28 % |
69317299 |
6.03 % |
3433998 |
0.32 % |
| |
|
|
|
|
|
|
| mq40 |
49117039 |
67.51 % |
48536807 |
70.02 % |
580232 |
16.90 % |
| q20,mq40 |
13123041 |
18.04 % |
12916646 |
18.63 % |
206395 |
6.01 % |
| q20 |
4507044 |
6.20 % |
4386478 |
6.33 % |
120566 |
3.51 % |
| q20,qd2,mq40 |
2206967 |
3.03 % |
1568195 |
2.26 % |
638772 |
18.60 % |
| q20,qd2 |
1507087 |
2.07 % |
519129 |
0.75 % |
987958 |
28.77 % |
| qd2 |
1444763 |
1.99 % |
1032327 |
1.49 % |
412436 |
12.01 % |
| qd2,mq40 |
462348 |
0.64 % |
357717 |
0.52 % |
104631 |
3.05 % |
| fs60 |
193913 |
0.27 % |
0 |
0.00 % |
193913 |
5.65 % |
| q20,qd2,fs60 |
107143 |
0.15 % |
0 |
0.00 % |
107143 |
3.12 % |
| fs60,mq40 |
36409 |
0.05 % |
0 |
0.00 % |
36409 |
1.06 % |
| qd2,fs60 |
18727 |
0.03 % |
0 |
0.00 % |
18727 |
0.55 % |
| q20,fs60 |
15497 |
0.02 % |
0 |
0.00 % |
15497 |
0.45 % |
| qd2,fs60,mq40 |
7279 |
0.01 % |
0 |
0.00 % |
7279 |
0.21 % |
| q20,qd2,fs60,mq40 |
3739 |
0.01 % |
0 |
0.00 % |
3739 |
0.11 % |
| q20,fs60,mq40 |
301 |
0.00 % |
0 |
0.00 % |
301 |
0.01 % |
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 |
1837916 |
20.22 % |
| Transition |
G>A |
All |
1293370 |
14.23 % |
| Transition |
T>C |
All |
1841848 |
20.26 % |
| Transition |
C>T |
All |
1305413 |
14.36 % |
| Transversion |
A>C |
All |
292505 |
3.22 % |
| Transversion |
C>A |
All |
423897 |
4.66 % |
| Transversion |
T>G |
All |
294478 |
3.24 % |
| Transversion |
G>T |
All |
431452 |
4.75 % |
| Transversion |
A>T |
All |
401400 |
4.42 % |
| Transversion |
T>A |
All |
387736 |
4.27 % |
| Transversion |
C>G |
All |
288342 |
3.17 % |
| Transversion |
G>C |
All |
290530 |
3.20 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
919436 |
17.04 % |
| Transition |
G>A |
Passed |
873860 |
16.20 % |
| Transition |
T>C |
Passed |
934393 |
17.32 % |
| Transition |
C>T |
Passed |
893973 |
16.57 % |
| Transversion |
A>C |
Passed |
226251 |
4.19 % |
| Transversion |
C>A |
Passed |
229824 |
4.26 % |
| Transversion |
T>G |
Passed |
223812 |
4.15 % |
| Transversion |
G>T |
Passed |
227570 |
4.22 % |
| Transversion |
A>T |
Passed |
204612 |
3.79 % |
| Transversion |
T>A |
Passed |
203299 |
3.77 % |
| Transversion |
C>G |
Passed |
227832 |
4.22 % |
| Transversion |
G>C |
Passed |
229800 |
4.26 % |
| |
|
|
|
|
| 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 |
2.23 |
6278547 |
2810340 |
| Passed |
2.04 |
3621662 |
1773000 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |