/EXTERNAL BLUEPRINT/variants/K006279_K006281_11_lane_gembs
BACK
SAMPLE K006279_K006281_11_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1117648885 |
650919307 |
58.24 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1117648885 |
100% |
1097880456 |
98.23 % |
19768429 |
1.77 % |
| |
|
|
|
|
|
|
| Passed |
652648938 |
58.39 % |
649710128 |
59.18 % |
2938810 |
0.45 % |
| Filtered |
464999947 |
41.61 % |
448170328 |
40.82 % |
16829619 |
2.58 % |
| |
|
|
|
|
|
|
| q20 |
362652418 |
77.99 % |
360857910 |
80.52 % |
1794508 |
10.66 % |
| q20,qd2 |
51033014 |
10.97 % |
36640769 |
8.18 % |
14392245 |
85.52 % |
| qd2 |
26673669 |
5.74 % |
26520326 |
5.92 % |
153343 |
0.91 % |
| q20,mq40 |
13616758 |
2.93 % |
13529084 |
3.02 % |
87674 |
0.52 % |
| mq40 |
7621946 |
1.64 % |
7451272 |
1.66 % |
170674 |
1.01 % |
| q20,qd2,mq40 |
3250520 |
0.70 % |
3055418 |
0.68 % |
195102 |
1.16 % |
| qd2,mq40 |
132504 |
0.03 % |
115549 |
0.03 % |
16955 |
0.10 % |
| q20,qd2,fs60 |
7458 |
0.00 % |
0 |
0.00 % |
7458 |
0.04 % |
| qd2,fs60 |
3921 |
0.00 % |
0 |
0.00 % |
3921 |
0.02 % |
| qd2,fs60,mq40 |
2778 |
0.00 % |
0 |
0.00 % |
2778 |
0.02 % |
| fs60 |
2775 |
0.00 % |
0 |
0.00 % |
2775 |
0.02 % |
| q20,qd2,fs60,mq40 |
1265 |
0.00 % |
0 |
0.00 % |
1265 |
0.01 % |
| fs60,mq40 |
908 |
0.00 % |
0 |
0.00 % |
908 |
0.01 % |
| q20,fs60 |
12 |
0.00 % |
0 |
0.00 % |
12 |
0.00 % |
| q20,fs60,mq40 |
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 |
3219572 |
8.29 % |
| Transition |
G>A |
All |
15071866 |
38.79 % |
| Transition |
T>C |
All |
3133846 |
8.07 % |
| Transition |
C>T |
All |
15066102 |
38.77 % |
| Transversion |
A>C |
All |
183031 |
0.47 % |
| Transversion |
C>A |
All |
471398 |
1.21 % |
| Transversion |
T>G |
All |
191720 |
0.49 % |
| Transversion |
G>T |
All |
462268 |
1.19 % |
| Transversion |
A>T |
All |
358700 |
0.92 % |
| Transversion |
T>A |
All |
346908 |
0.89 % |
| Transversion |
C>G |
All |
180732 |
0.47 % |
| Transversion |
G>C |
All |
169483 |
0.44 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
349315 |
18.67 % |
| Transition |
G>A |
Passed |
327352 |
17.49 % |
| Transition |
T>C |
Passed |
344765 |
18.42 % |
| Transition |
C>T |
Passed |
326571 |
17.45 % |
| Transversion |
A>C |
Passed |
68976 |
3.69 % |
| Transversion |
C>A |
Passed |
64861 |
3.47 % |
| Transversion |
T>G |
Passed |
68879 |
3.68 % |
| Transversion |
G>T |
Passed |
64095 |
3.43 % |
| Transversion |
A>T |
Passed |
46575 |
2.49 % |
| Transversion |
T>A |
Passed |
46540 |
2.49 % |
| Transversion |
C>G |
Passed |
81585 |
4.36 % |
| Transversion |
G>C |
Passed |
81801 |
4.37 % |
| |
|
|
|
|
| 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 |
15.43 |
36491386 |
2364240 |
| Passed |
2.58 |
1348003 |
523312 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |