/EXTERNAL Roadmap/variants/K012820_1_lane_gembs
BACK
SAMPLE K012820_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1157672841 |
1008353732 |
87.10 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1157672841 |
100% |
1138191723 |
98.32 % |
19481118 |
1.68 % |
| |
|
|
|
|
|
|
| Passed |
1009824166 |
87.23 % |
1005468051 |
88.34 % |
4356115 |
0.43 % |
| Filtered |
147848675 |
12.77 % |
132723672 |
11.66 % |
15125003 |
1.50 % |
| |
|
|
|
|
|
|
| q20 |
102590738 |
69.39 % |
101237578 |
76.28 % |
1353160 |
8.95 % |
| q20,qd2 |
19908202 |
13.47 % |
7165163 |
5.40 % |
12743039 |
84.25 % |
| q20,mq40 |
14222396 |
9.62 % |
14062380 |
10.60 % |
160016 |
1.06 % |
| qd2 |
3954748 |
2.67 % |
3597418 |
2.71 % |
357330 |
2.36 % |
| mq40 |
3714963 |
2.51 % |
3426768 |
2.58 % |
288195 |
1.91 % |
| q20,qd2,mq40 |
3408599 |
2.31 % |
3196150 |
2.41 % |
212449 |
1.40 % |
| qd2,mq40 |
48025 |
0.03 % |
38215 |
0.03 % |
9810 |
0.06 % |
| qd2,fs60,mq40 |
564 |
0.00 % |
0 |
0.00 % |
564 |
0.00 % |
| fs60,mq40 |
235 |
0.00 % |
0 |
0.00 % |
235 |
0.00 % |
| qd2,fs60 |
111 |
0.00 % |
0 |
0.00 % |
111 |
0.00 % |
| fs60 |
44 |
0.00 % |
0 |
0.00 % |
44 |
0.00 % |
| q20,qd2,fs60,mq40 |
40 |
0.00 % |
0 |
0.00 % |
40 |
0.00 % |
| q20,qd2,fs60 |
7 |
0.00 % |
0 |
0.00 % |
7 |
0.00 % |
| q20,fs60,mq40 |
2 |
0.00 % |
0 |
0.00 % |
2 |
0.00 % |
| q20,fs60 |
1 |
0.00 % |
0 |
0.00 % |
1 |
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 |
8108770 |
38.34 % |
| Transition |
G>A |
All |
1712833 |
8.10 % |
| Transition |
T>C |
All |
6276334 |
29.68 % |
| Transition |
C>T |
All |
1756829 |
8.31 % |
| Transversion |
A>C |
All |
255476 |
1.21 % |
| Transversion |
C>A |
All |
580196 |
2.74 % |
| Transversion |
T>G |
All |
293965 |
1.39 % |
| Transversion |
G>T |
All |
556674 |
2.63 % |
| Transversion |
A>T |
All |
523837 |
2.48 % |
| Transversion |
T>A |
All |
542463 |
2.56 % |
| Transversion |
C>G |
All |
288227 |
1.36 % |
| Transversion |
G>C |
All |
254228 |
1.20 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
863701 |
21.65 % |
| Transition |
G>A |
Passed |
601387 |
15.08 % |
| Transition |
T>C |
Passed |
705142 |
17.68 % |
| Transition |
C>T |
Passed |
608656 |
15.26 % |
| Transversion |
A>C |
Passed |
151867 |
3.81 % |
| Transversion |
C>A |
Passed |
157339 |
3.94 % |
| Transversion |
T>G |
Passed |
154448 |
3.87 % |
| Transversion |
G>T |
Passed |
157729 |
3.95 % |
| Transversion |
A>T |
Passed |
140361 |
3.52 % |
| Transversion |
T>A |
Passed |
140542 |
3.52 % |
| Transversion |
C>G |
Passed |
154529 |
3.87 % |
| Transversion |
G>C |
Passed |
152926 |
3.83 % |
| |
|
|
|
|
| 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 |
5.42 |
17854766 |
3295066 |
| Passed |
2.30 |
2778886 |
1209741 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |