/EXTERNAL Roadmap/variants/K012808_1_lane_gembs
BACK
SAMPLE K012808_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1168003718 |
992346211 |
84.96 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1168003718 |
100% |
1136610804 |
97.31 % |
31392914 |
2.69 % |
| |
|
|
|
|
|
|
| Passed |
995335981 |
85.22 % |
988511782 |
86.97 % |
6824199 |
0.69 % |
| Filtered |
172667737 |
14.78 % |
148099022 |
13.03 % |
24568715 |
2.47 % |
| |
|
|
|
|
|
|
| q20 |
113576445 |
65.78 % |
111322884 |
75.17 % |
2253561 |
9.17 % |
| q20,qd2 |
27230681 |
15.77 % |
6161104 |
4.16 % |
21069577 |
85.76 % |
| q20,mq40 |
18161513 |
10.52 % |
17964501 |
12.13 % |
197012 |
0.80 % |
| mq40 |
7708928 |
4.46 % |
7303594 |
4.93 % |
405334 |
1.65 % |
| q20,qd2,mq40 |
3352228 |
1.94 % |
3043851 |
2.06 % |
308377 |
1.26 % |
| qd2 |
2583907 |
1.50 % |
2260475 |
1.53 % |
323432 |
1.32 % |
| qd2,mq40 |
52978 |
0.03 % |
42613 |
0.03 % |
10365 |
0.04 % |
| qd2,fs60,mq40 |
484 |
0.00 % |
0 |
0.00 % |
484 |
0.00 % |
| fs60,mq40 |
280 |
0.00 % |
0 |
0.00 % |
280 |
0.00 % |
| qd2,fs60 |
183 |
0.00 % |
0 |
0.00 % |
183 |
0.00 % |
| fs60 |
53 |
0.00 % |
0 |
0.00 % |
53 |
0.00 % |
| q20,qd2,fs60,mq40 |
46 |
0.00 % |
0 |
0.00 % |
46 |
0.00 % |
| q20,qd2,fs60 |
8 |
0.00 % |
0 |
0.00 % |
8 |
0.00 % |
| q20,fs60,mq40 |
3 |
0.00 % |
0 |
0.00 % |
3 |
0.00 % |
| q20,fs60 |
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 |
14550144 |
43.95 % |
| Transition |
G>A |
All |
1782267 |
5.38 % |
| Transition |
T>C |
All |
11656496 |
35.21 % |
| Transition |
C>T |
All |
1962538 |
5.93 % |
| Transversion |
A>C |
All |
263971 |
0.80 % |
| Transversion |
C>A |
All |
535852 |
1.62 % |
| Transversion |
T>G |
All |
313223 |
0.95 % |
| Transversion |
G>T |
All |
497780 |
1.50 % |
| Transversion |
A>T |
All |
472635 |
1.43 % |
| Transversion |
T>A |
All |
513337 |
1.55 % |
| Transversion |
C>G |
All |
295137 |
0.89 % |
| Transversion |
G>C |
All |
262882 |
0.79 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
1228632 |
24.96 % |
| Transition |
G>A |
Passed |
682337 |
13.86 % |
| Transition |
T>C |
Passed |
921526 |
18.72 % |
| Transition |
C>T |
Passed |
694698 |
14.11 % |
| Transversion |
A>C |
Passed |
175960 |
3.57 % |
| Transversion |
C>A |
Passed |
180264 |
3.66 % |
| Transversion |
T>G |
Passed |
179430 |
3.64 % |
| Transversion |
G>T |
Passed |
181404 |
3.68 % |
| Transversion |
A>T |
Passed |
158374 |
3.22 % |
| Transversion |
T>A |
Passed |
157779 |
3.20 % |
| Transversion |
C>G |
Passed |
181999 |
3.70 % |
| Transversion |
G>C |
Passed |
180513 |
3.67 % |
| |
|
|
|
|
| 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 |
9.49 |
29951445 |
3154817 |
| Passed |
2.53 |
3527193 |
1395723 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |