/EXTERNAL Roadmap/variants/K006502_K006503_K006504_K006505_4_lane_gembs
BACK
SAMPLE K006502_K006503_K006504_K006505_4_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1164092177 |
788193530 |
67.71 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1164092177 |
100% |
1140988081 |
98.02 % |
23104096 |
1.98 % |
| |
|
|
|
|
|
|
| Passed |
791559851 |
68.00 % |
786157851 |
68.90 % |
5402000 |
0.68 % |
| Filtered |
372532326 |
32.00 % |
354830230 |
31.10 % |
17702096 |
2.24 % |
| |
|
|
|
|
|
|
| q20 |
227297218 |
61.01 % |
220735357 |
62.21 % |
6561861 |
37.07 % |
| qd2 |
75277281 |
20.21 % |
74867233 |
21.10 % |
410048 |
2.32 % |
| mq40 |
29629261 |
7.95 % |
29076777 |
8.19 % |
552484 |
3.12 % |
| q20,qd2 |
19660185 |
5.28 % |
10567233 |
2.98 % |
9092952 |
51.37 % |
| q20,mq40 |
16383444 |
4.40 % |
16046318 |
4.52 % |
337126 |
1.90 % |
| q20,qd2,mq40 |
3587794 |
0.96 % |
2925107 |
0.82 % |
662687 |
3.74 % |
| qd2,mq40 |
666102 |
0.18 % |
612205 |
0.17 % |
53897 |
0.30 % |
| q20,qd2,fs60 |
12633 |
0.00 % |
0 |
0.00 % |
12633 |
0.07 % |
| qd2,fs60 |
8163 |
0.00 % |
0 |
0.00 % |
8163 |
0.05 % |
| fs60 |
4987 |
0.00 % |
0 |
0.00 % |
4987 |
0.03 % |
| qd2,fs60,mq40 |
2927 |
0.00 % |
0 |
0.00 % |
2927 |
0.02 % |
| fs60,mq40 |
1314 |
0.00 % |
0 |
0.00 % |
1314 |
0.01 % |
| q20,qd2,fs60,mq40 |
999 |
0.00 % |
0 |
0.00 % |
999 |
0.01 % |
| q20,fs60 |
13 |
0.00 % |
0 |
0.00 % |
13 |
0.00 % |
| q20,fs60,mq40 |
5 |
0.00 % |
0 |
0.00 % |
5 |
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 |
5733117 |
18.70 % |
| Transition |
G>A |
All |
5971916 |
19.48 % |
| Transition |
T>C |
All |
9668200 |
31.53 % |
| Transition |
C>T |
All |
5407952 |
17.64 % |
| Transversion |
A>C |
All |
332950 |
1.09 % |
| Transversion |
C>A |
All |
590275 |
1.93 % |
| Transversion |
T>G |
All |
363018 |
1.18 % |
| Transversion |
G>T |
All |
589927 |
1.92 % |
| Transversion |
A>T |
All |
746395 |
2.43 % |
| Transversion |
T>A |
All |
721144 |
2.35 % |
| Transversion |
C>G |
All |
274582 |
0.90 % |
| Transversion |
G>C |
All |
259526 |
0.85 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
561555 |
19.61 % |
| Transition |
G>A |
Passed |
422245 |
14.75 % |
| Transition |
T>C |
Passed |
653052 |
22.81 % |
| Transition |
C>T |
Passed |
419681 |
14.66 % |
| Transversion |
A>C |
Passed |
106652 |
3.73 % |
| Transversion |
C>A |
Passed |
99179 |
3.46 % |
| Transversion |
T>G |
Passed |
107436 |
3.75 % |
| Transversion |
G>T |
Passed |
99257 |
3.47 % |
| Transversion |
A>T |
Passed |
79541 |
2.78 % |
| Transversion |
T>A |
Passed |
79175 |
2.77 % |
| Transversion |
C>G |
Passed |
117311 |
4.10 % |
| Transversion |
G>C |
Passed |
117987 |
4.12 % |
| |
|
|
|
|
| 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 |
6.91 |
26781185 |
3877817 |
| Passed |
2.55 |
2056533 |
806538 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |