/EXTERNAL BLUEPRINT/variants/K010540_1_lane_gembs
BACK
SAMPLE K010540_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1014722505 |
217634217 |
21.45 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1014722505 |
100% |
1005906197 |
99.13 % |
8816308 |
0.87 % |
| |
|
|
|
|
|
|
| Passed |
220305940 |
21.71 % |
217023702 |
21.57 % |
3282238 |
1.49 % |
| Filtered |
794416565 |
78.29 % |
788882495 |
78.43 % |
5534070 |
2.51 % |
| |
|
|
|
|
|
|
| q20 |
690236547 |
86.89 % |
688509934 |
87.28 % |
1726613 |
31.20 % |
| q20,qd2 |
80280042 |
10.11 % |
76743363 |
9.73 % |
3536679 |
63.91 % |
| q20,mq40 |
17338086 |
2.18 % |
17266897 |
2.19 % |
71189 |
1.29 % |
| q20,qd2,mq40 |
5526460 |
0.70 % |
5449647 |
0.69 % |
76813 |
1.39 % |
| mq40 |
749748 |
0.09 % |
645122 |
0.08 % |
104626 |
1.89 % |
| qd2 |
259456 |
0.03 % |
245793 |
0.03 % |
13663 |
0.25 % |
| qd2,mq40 |
25433 |
0.00 % |
21739 |
0.00 % |
3694 |
0.07 % |
| qd2,fs60,mq40 |
234 |
0.00 % |
0 |
0.00 % |
234 |
0.00 % |
| q20,qd2,fs60,mq40 |
170 |
0.00 % |
0 |
0.00 % |
170 |
0.00 % |
| fs60,mq40 |
149 |
0.00 % |
0 |
0.00 % |
149 |
0.00 % |
| qd2,fs60 |
98 |
0.00 % |
0 |
0.00 % |
98 |
0.00 % |
| q20,qd2,fs60 |
86 |
0.00 % |
0 |
0.00 % |
86 |
0.00 % |
| fs60 |
56 |
0.00 % |
0 |
0.00 % |
56 |
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 |
2952920 |
27.92 % |
| Transition |
G>A |
All |
585791 |
5.54 % |
| Transition |
T>C |
All |
2918239 |
27.59 % |
| Transition |
C>T |
All |
576478 |
5.45 % |
| Transversion |
A>C |
All |
207086 |
1.96 % |
| Transversion |
C>A |
All |
807294 |
7.63 % |
| Transversion |
T>G |
All |
213878 |
2.02 % |
| Transversion |
G>T |
All |
786662 |
7.44 % |
| Transversion |
A>T |
All |
560753 |
5.30 % |
| Transversion |
T>A |
All |
557757 |
5.27 % |
| Transversion |
C>G |
All |
208350 |
1.97 % |
| Transversion |
G>C |
All |
201975 |
1.91 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
151148 |
18.88 % |
| Transition |
G>A |
Passed |
142528 |
17.81 % |
| Transition |
T>C |
Passed |
151088 |
18.88 % |
| Transition |
C>T |
Passed |
142097 |
17.75 % |
| Transversion |
A>C |
Passed |
27470 |
3.43 % |
| Transversion |
C>A |
Passed |
26086 |
3.26 % |
| Transversion |
T>G |
Passed |
27092 |
3.38 % |
| Transversion |
G>T |
Passed |
25829 |
3.23 % |
| Transversion |
A>T |
Passed |
15722 |
1.96 % |
| Transversion |
T>A |
Passed |
15792 |
1.97 % |
| Transversion |
C>G |
Passed |
37751 |
4.72 % |
| Transversion |
G>C |
Passed |
37827 |
4.73 % |
| |
|
|
|
|
| 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 |
1.98 |
7033428 |
3543755 |
| Passed |
2.75 |
586861 |
213569 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |