/EXTERNAL Roadmap/variants/K006487_K006488_2_lane_gembs
BACK
SAMPLE K006487_K006488_2_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1142320032 |
605356502 |
52.99 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1142320032 |
100% |
1120780131 |
98.11 % |
21539901 |
1.89 % |
| |
|
|
|
|
|
|
| Passed |
608011978 |
53.23 % |
603675586 |
53.86 % |
4336392 |
0.71 % |
| Filtered |
534308054 |
46.77 % |
517104545 |
46.14 % |
17203509 |
2.83 % |
| |
|
|
|
|
|
|
| q20 |
439806528 |
82.31 % |
433600369 |
83.85 % |
6206159 |
36.07 % |
| q20,qd2 |
44914974 |
8.41 % |
34886949 |
6.75 % |
10028025 |
58.29 % |
| qd2 |
23695069 |
4.43 % |
23374288 |
4.52 % |
320781 |
1.86 % |
| q20,mq40 |
15938030 |
2.98 % |
15743362 |
3.04 % |
194668 |
1.13 % |
| mq40 |
5942792 |
1.11 % |
5755055 |
1.11 % |
187737 |
1.09 % |
| q20,qd2,mq40 |
3839377 |
0.72 % |
3614653 |
0.70 % |
224724 |
1.31 % |
| qd2,mq40 |
150132 |
0.03 % |
129869 |
0.03 % |
20263 |
0.12 % |
| q20,qd2,fs60 |
6614 |
0.00 % |
0 |
0.00 % |
6614 |
0.04 % |
| qd2,fs60 |
5866 |
0.00 % |
0 |
0.00 % |
5866 |
0.03 % |
| qd2,fs60,mq40 |
3956 |
0.00 % |
0 |
0.00 % |
3956 |
0.02 % |
| fs60 |
2719 |
0.00 % |
0 |
0.00 % |
2719 |
0.02 % |
| fs60,mq40 |
999 |
0.00 % |
0 |
0.00 % |
999 |
0.01 % |
| q20,qd2,fs60,mq40 |
985 |
0.00 % |
0 |
0.00 % |
985 |
0.01 % |
| q20,fs60 |
8 |
0.00 % |
0 |
0.00 % |
8 |
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 |
6827243 |
21.11 % |
| Transition |
G>A |
All |
9246744 |
28.59 % |
| Transition |
T>C |
All |
5574879 |
17.24 % |
| Transition |
C>T |
All |
7516789 |
23.24 % |
| Transversion |
A>C |
All |
298699 |
0.92 % |
| Transversion |
C>A |
All |
562514 |
1.74 % |
| Transversion |
T>G |
All |
355719 |
1.10 % |
| Transversion |
G>T |
All |
551798 |
1.71 % |
| Transversion |
A>T |
All |
456246 |
1.41 % |
| Transversion |
T>A |
All |
446471 |
1.38 % |
| Transversion |
C>G |
All |
273621 |
0.85 % |
| Transversion |
G>C |
All |
234149 |
0.72 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
441769 |
19.00 % |
| Transition |
G>A |
Passed |
321885 |
13.84 % |
| Transition |
T>C |
Passed |
681273 |
29.30 % |
| Transition |
C>T |
Passed |
321973 |
13.85 % |
| Transversion |
A>C |
Passed |
74808 |
3.22 % |
| Transversion |
C>A |
Passed |
67045 |
2.88 % |
| Transversion |
T>G |
Passed |
74146 |
3.19 % |
| Transversion |
G>T |
Passed |
68346 |
2.94 % |
| Transversion |
A>T |
Passed |
47227 |
2.03 % |
| Transversion |
T>A |
Passed |
46729 |
2.01 % |
| Transversion |
C>G |
Passed |
89493 |
3.85 % |
| Transversion |
G>C |
Passed |
90597 |
3.90 % |
| |
|
|
|
|
| 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 |
9.17 |
29165655 |
3179217 |
| Passed |
3.16 |
1766900 |
558391 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |