/EXTERNAL BLUEPRINT/variants/K006376_15_lane_gembs
BACK
SAMPLE K006376_15_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1156132260 |
1058350156 |
91.54 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1156132260 |
100% |
1145584016 |
99.09 % |
10548244 |
0.91 % |
| |
|
|
|
|
|
|
| Passed |
1059080552 |
91.61 % |
1055835320 |
92.17 % |
3245232 |
0.31 % |
| Filtered |
97051708 |
8.39 % |
89748696 |
7.83 % |
7303012 |
0.69 % |
| |
|
|
|
|
|
|
| q20 |
64416125 |
66.37 % |
63801952 |
71.09 % |
614173 |
8.41 % |
| q20,mq40 |
12847602 |
13.24 % |
12738106 |
14.19 % |
109496 |
1.50 % |
| q20,qd2 |
9968396 |
10.27 % |
3936397 |
4.39 % |
6031999 |
82.60 % |
| mq40 |
4497260 |
4.63 % |
4298776 |
4.79 % |
198484 |
2.72 % |
| q20,qd2,mq40 |
3031400 |
3.12 % |
2851697 |
3.18 % |
179703 |
2.46 % |
| qd2 |
2241042 |
2.31 % |
2081951 |
2.32 % |
159091 |
2.18 % |
| qd2,mq40 |
48350 |
0.05 % |
39817 |
0.04 % |
8533 |
0.12 % |
| qd2,fs60,mq40 |
722 |
0.00 % |
0 |
0.00 % |
722 |
0.01 % |
| fs60,mq40 |
350 |
0.00 % |
0 |
0.00 % |
350 |
0.00 % |
| qd2,fs60 |
216 |
0.00 % |
0 |
0.00 % |
216 |
0.00 % |
| fs60 |
142 |
0.00 % |
0 |
0.00 % |
142 |
0.00 % |
| q20,qd2,fs60,mq40 |
76 |
0.00 % |
0 |
0.00 % |
76 |
0.00 % |
| q20,qd2,fs60 |
26 |
0.00 % |
0 |
0.00 % |
26 |
0.00 % |
| q20,fs60,mq40 |
1 |
0.00 % |
0 |
0.00 % |
1 |
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 |
3768161 |
30.91 % |
| Transition |
G>A |
All |
976290 |
8.01 % |
| Transition |
T>C |
All |
3735143 |
30.64 % |
| Transition |
C>T |
All |
994062 |
8.16 % |
| Transversion |
A>C |
All |
226030 |
1.85 % |
| Transversion |
C>A |
All |
505165 |
4.14 % |
| Transversion |
T>G |
All |
227793 |
1.87 % |
| Transversion |
G>T |
All |
501514 |
4.11 % |
| Transversion |
A>T |
All |
424467 |
3.48 % |
| Transversion |
T>A |
All |
417678 |
3.43 % |
| Transversion |
C>G |
All |
205820 |
1.69 % |
| Transversion |
G>C |
All |
206848 |
1.70 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
628941 |
16.97 % |
| Transition |
G>A |
Passed |
608849 |
16.43 % |
| Transition |
T>C |
Passed |
630310 |
17.01 % |
| Transition |
C>T |
Passed |
614716 |
16.59 % |
| Transversion |
A>C |
Passed |
155412 |
4.19 % |
| Transversion |
C>A |
Passed |
163006 |
4.40 % |
| Transversion |
T>G |
Passed |
156250 |
4.22 % |
| Transversion |
G>T |
Passed |
163738 |
4.42 % |
| Transversion |
A>T |
Passed |
138511 |
3.74 % |
| Transversion |
T>A |
Passed |
138247 |
3.73 % |
| Transversion |
C>G |
Passed |
153567 |
4.14 % |
| Transversion |
G>C |
Passed |
153780 |
4.15 % |
| |
|
|
|
|
| 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 |
3.49 |
9473656 |
2715315 |
| Passed |
2.03 |
2482816 |
1222511 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |