/EXTERNAL BLUEPRINT/variants/K006356_10_lane_gembs
BACK
SAMPLE K006356_10_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1121655148 |
681879675 |
60.79 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1121655148 |
100% |
1109163018 |
98.89 % |
12492130 |
1.11 % |
| |
|
|
|
|
|
|
| Passed |
683566302 |
60.94 % |
680409962 |
61.34 % |
3156340 |
0.46 % |
| Filtered |
438088846 |
39.06 % |
428753056 |
38.66 % |
9335790 |
1.37 % |
| |
|
|
|
|
|
|
| q20 |
379037319 |
86.52 % |
377598071 |
88.07 % |
1439248 |
15.42 % |
| q20,qd2 |
35104954 |
8.01 % |
27724184 |
6.47 % |
7380770 |
79.06 % |
| q20,mq40 |
13399697 |
3.06 % |
13304079 |
3.10 % |
95618 |
1.02 % |
| mq40 |
5685172 |
1.30 % |
5537370 |
1.29 % |
147802 |
1.58 % |
| q20,qd2,mq40 |
3023383 |
0.69 % |
2842668 |
0.66 % |
180715 |
1.94 % |
| qd2 |
1771986 |
0.40 % |
1693513 |
0.39 % |
78473 |
0.84 % |
| qd2,mq40 |
61837 |
0.01 % |
53171 |
0.01 % |
8666 |
0.09 % |
| q20,qd2,fs60 |
1401 |
0.00 % |
0 |
0.00 % |
1401 |
0.02 % |
| fs60 |
948 |
0.00 % |
0 |
0.00 % |
948 |
0.01 % |
| qd2,fs60,mq40 |
850 |
0.00 % |
0 |
0.00 % |
850 |
0.01 % |
| qd2,fs60 |
518 |
0.00 % |
0 |
0.00 % |
518 |
0.01 % |
| q20,qd2,fs60,mq40 |
393 |
0.00 % |
0 |
0.00 % |
393 |
0.00 % |
| fs60,mq40 |
387 |
0.00 % |
0 |
0.00 % |
387 |
0.00 % |
| q20,fs60 |
1 |
0.00 % |
0 |
0.00 % |
1 |
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 |
3153197 |
22.02 % |
| Transition |
G>A |
All |
2638501 |
18.42 % |
| Transition |
T>C |
All |
3032303 |
21.17 % |
| Transition |
C>T |
All |
2552778 |
17.83 % |
| Transversion |
A>C |
All |
223251 |
1.56 % |
| Transversion |
C>A |
All |
578846 |
4.04 % |
| Transversion |
T>G |
All |
233314 |
1.63 % |
| Transversion |
G>T |
All |
568295 |
3.97 % |
| Transversion |
A>T |
All |
479828 |
3.35 % |
| Transversion |
T>A |
All |
477922 |
3.34 % |
| Transversion |
C>G |
All |
194296 |
1.36 % |
| Transversion |
G>C |
All |
188243 |
1.31 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
400497 |
18.51 % |
| Transition |
G>A |
Passed |
365249 |
16.88 % |
| Transition |
T>C |
Passed |
400275 |
18.49 % |
| Transition |
C>T |
Passed |
363857 |
16.81 % |
| Transversion |
A>C |
Passed |
86227 |
3.98 % |
| Transversion |
C>A |
Passed |
77215 |
3.57 % |
| Transversion |
T>G |
Passed |
85855 |
3.97 % |
| Transversion |
G>T |
Passed |
77150 |
3.56 % |
| Transversion |
A>T |
Passed |
54733 |
2.53 % |
| Transversion |
T>A |
Passed |
54707 |
2.53 % |
| Transversion |
C>G |
Passed |
98959 |
4.57 % |
| Transversion |
G>C |
Passed |
99525 |
4.60 % |
| |
|
|
|
|
| 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 |
3.86 |
11376779 |
2943995 |
| Passed |
2.41 |
1529878 |
634371 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |