/EXTERNAL BLUEPRINT/variants/K012013_K012014_K012015_K012016_K012017_K012018_K012019_K012020_K012021_9_lane_gembs
BACK
SAMPLE K012013_K012014_K012015_K012016_K012017_K012018_K012019_K012020_K012021_9_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
956015491 |
12856741 |
1.34 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
956015491 |
100% |
932458694 |
97.54 % |
23556797 |
2.46 % |
| |
|
|
|
|
|
|
| Passed |
25122060 |
2.63 % |
12193493 |
1.31 % |
12928567 |
51.46 % |
| Filtered |
930893431 |
97.37 % |
920265201 |
98.69 % |
10628230 |
42.31 % |
| |
|
|
|
|
|
|
| q20 |
759005431 |
81.54 % |
751899578 |
81.70 % |
7105853 |
66.86 % |
| q20,qd2 |
95976200 |
10.31 % |
93640025 |
10.18 % |
2336175 |
21.98 % |
| q20,mq40 |
57176384 |
6.14 % |
56760332 |
6.17 % |
416052 |
3.91 % |
| q20,qd2,mq40 |
17890297 |
1.92 % |
17777337 |
1.93 % |
112960 |
1.06 % |
| mq40 |
836064 |
0.09 % |
179770 |
0.02 % |
656294 |
6.18 % |
| qd2 |
6902 |
0.00 % |
6455 |
0.00 % |
447 |
0.00 % |
| qd2,mq40 |
2102 |
0.00 % |
1704 |
0.00 % |
398 |
0.00 % |
| fs60,mq40 |
21 |
0.00 % |
0 |
0.00 % |
21 |
0.00 % |
| qd2,fs60 |
11 |
0.00 % |
0 |
0.00 % |
11 |
0.00 % |
| fs60 |
9 |
0.00 % |
0 |
0.00 % |
9 |
0.00 % |
| qd2,fs60,mq40 |
7 |
0.00 % |
0 |
0.00 % |
7 |
0.00 % |
| q20,qd2,fs60 |
2 |
0.00 % |
0 |
0.00 % |
2 |
0.00 % |
| q20,qd2,fs60,mq40 |
1 |
0.00 % |
0 |
0.00 % |
1 |
0.00 % |
| q20,fs60 |
0 |
0.00 % |
0 |
0.00 % |
0 |
0.00 % |
| q20,fs60,mq40 |
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 |
6125747 |
22.08 % |
| Transition |
G>A |
All |
2252383 |
8.12 % |
| Transition |
T>C |
All |
7852410 |
28.30 % |
| Transition |
C>T |
All |
1036087 |
3.73 % |
| Transversion |
A>C |
All |
946676 |
3.41 % |
| Transversion |
C>A |
All |
1807717 |
6.51 % |
| Transversion |
T>G |
All |
1117362 |
4.03 % |
| Transversion |
G>T |
All |
1616331 |
5.83 % |
| Transversion |
A>T |
All |
1267879 |
4.57 % |
| Transversion |
T>A |
All |
1777164 |
6.40 % |
| Transversion |
C>G |
All |
896936 |
3.23 % |
| Transversion |
G>C |
All |
1051455 |
3.79 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
109419 |
16.54 % |
| Transition |
G>A |
Passed |
86573 |
13.08 % |
| Transition |
T>C |
Passed |
192646 |
29.12 % |
| Transition |
C>T |
Passed |
42703 |
6.45 % |
| Transversion |
A>C |
Passed |
27427 |
4.15 % |
| Transversion |
C>A |
Passed |
34248 |
5.18 % |
| Transversion |
T>G |
Passed |
28779 |
4.35 % |
| Transversion |
G>T |
Passed |
21993 |
3.32 % |
| Transversion |
A>T |
Passed |
14982 |
2.26 % |
| Transversion |
T>A |
Passed |
34614 |
5.23 % |
| Transversion |
C>G |
Passed |
29526 |
4.46 % |
| Transversion |
G>C |
Passed |
38743 |
5.86 % |
| |
|
|
|
|
| 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 |
1.65 |
17266627 |
10481520 |
| Passed |
1.87 |
431341 |
230312 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |