/EXTERNAL BLUEPRINT/variants/K011858_K011880_K011881_K011882_K011883_K011884_K011885_K011886_K011887_K011923_K011924_11_lane_gembs
BACK
SAMPLE K011858_K011880_K011881_K011882_K011883_K011884_K011885_K011886_K011887_K011923_K011924_11_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
911241285 |
7013090 |
0.77 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
911241285 |
100% |
891235032 |
97.80 % |
20006253 |
2.20 % |
| |
|
|
|
|
|
|
| Passed |
16273922 |
1.79 % |
6360553 |
0.71 % |
9913369 |
60.92 % |
| Filtered |
894967363 |
98.21 % |
884874479 |
99.29 % |
10092884 |
62.02 % |
| |
|
|
|
|
|
|
| q20 |
670611267 |
74.93 % |
663675886 |
75.00 % |
6935381 |
68.72 % |
| q20,qd2 |
139568553 |
15.59 % |
137667179 |
15.56 % |
1901374 |
18.84 % |
| q20,mq40 |
58735435 |
6.56 % |
58226746 |
6.58 % |
508689 |
5.04 % |
| q20,qd2,mq40 |
25285408 |
2.83 % |
25149112 |
2.84 % |
136296 |
1.35 % |
| mq40 |
758529 |
0.08 % |
148068 |
0.02 % |
610461 |
6.05 % |
| qd2 |
6197 |
0.00 % |
5956 |
0.00 % |
241 |
0.00 % |
| qd2,mq40 |
1920 |
0.00 % |
1532 |
0.00 % |
388 |
0.00 % |
| qd2,fs60 |
19 |
0.00 % |
0 |
0.00 % |
19 |
0.00 % |
| fs60,mq40 |
17 |
0.00 % |
0 |
0.00 % |
17 |
0.00 % |
| fs60 |
9 |
0.00 % |
0 |
0.00 % |
9 |
0.00 % |
| qd2,fs60,mq40 |
5 |
0.00 % |
0 |
0.00 % |
5 |
0.00 % |
| q20,qd2,fs60,mq40 |
3 |
0.00 % |
0 |
0.00 % |
3 |
0.00 % |
| q20,qd2,fs60 |
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 |
5528654 |
22.46 % |
| Transition |
G>A |
All |
1939974 |
7.88 % |
| Transition |
T>C |
All |
6776478 |
27.52 % |
| Transition |
C>T |
All |
925257 |
3.76 % |
| Transversion |
A>C |
All |
797198 |
3.24 % |
| Transversion |
C>A |
All |
1683506 |
6.84 % |
| Transversion |
T>G |
All |
979106 |
3.98 % |
| Transversion |
G>T |
All |
1506321 |
6.12 % |
| Transversion |
A>T |
All |
1172820 |
4.76 % |
| Transversion |
T>A |
All |
1584702 |
6.44 % |
| Transversion |
C>G |
All |
806572 |
3.28 % |
| Transversion |
G>C |
All |
920263 |
3.74 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
118599 |
18.30 % |
| Transition |
G>A |
Passed |
82207 |
12.68 % |
| Transition |
T>C |
Passed |
184973 |
28.54 % |
| Transition |
C>T |
Passed |
33135 |
5.11 % |
| Transversion |
A>C |
Passed |
24453 |
3.77 % |
| Transversion |
C>A |
Passed |
38494 |
5.94 % |
| Transversion |
T>G |
Passed |
27669 |
4.27 % |
| Transversion |
G>T |
Passed |
23960 |
3.70 % |
| Transversion |
A>T |
Passed |
14340 |
2.21 % |
| Transversion |
T>A |
Passed |
36382 |
5.61 % |
| Transversion |
C>G |
Passed |
26966 |
4.16 % |
| Transversion |
G>C |
Passed |
37038 |
5.71 % |
| |
|
|
|
|
| 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 |
1.61 |
15170363 |
9450488 |
| Passed |
1.83 |
418914 |
229302 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |