/EXTERNAL Roadmap/variants/K006537_1_lane_gembs
BACK
SAMPLE K006537_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1144139979 |
769000942 |
67.21 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1144139979 |
100% |
1128547851 |
98.64 % |
15592128 |
1.36 % |
| |
|
|
|
|
|
|
| Passed |
772326711 |
67.50 % |
767173471 |
67.98 % |
5153240 |
0.67 % |
| Filtered |
371813268 |
32.50 % |
361374380 |
32.02 % |
10438888 |
1.35 % |
| |
|
|
|
|
|
|
| q20 |
322181746 |
86.65 % |
319909557 |
88.53 % |
2272189 |
21.77 % |
| q20,qd2 |
23207198 |
6.24 % |
15675718 |
4.34 % |
7531480 |
72.15 % |
| q20,mq40 |
13729691 |
3.69 % |
13630025 |
3.77 % |
99666 |
0.95 % |
| mq40 |
7347311 |
1.98 % |
7152708 |
1.98 % |
194603 |
1.86 % |
| q20,qd2,mq40 |
3001556 |
0.81 % |
2831495 |
0.78 % |
170061 |
1.63 % |
| qd2 |
2280162 |
0.61 % |
2123406 |
0.59 % |
156756 |
1.50 % |
| qd2,mq40 |
60610 |
0.02 % |
51471 |
0.01 % |
9139 |
0.09 % |
| q20,qd2,fs60 |
1332 |
0.00 % |
0 |
0.00 % |
1332 |
0.01 % |
| fs60 |
1217 |
0.00 % |
0 |
0.00 % |
1217 |
0.01 % |
| qd2,fs60 |
911 |
0.00 % |
0 |
0.00 % |
911 |
0.01 % |
| qd2,fs60,mq40 |
779 |
0.00 % |
0 |
0.00 % |
779 |
0.01 % |
| fs60,mq40 |
415 |
0.00 % |
0 |
0.00 % |
415 |
0.00 % |
| q20,qd2,fs60,mq40 |
340 |
0.00 % |
0 |
0.00 % |
340 |
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 |
5750947 |
32.46 % |
| Transition |
G>A |
All |
2123944 |
11.99 % |
| Transition |
T>C |
All |
4846787 |
27.36 % |
| Transition |
C>T |
All |
1851509 |
10.45 % |
| Transversion |
A>C |
All |
250581 |
1.41 % |
| Transversion |
C>A |
All |
544385 |
3.07 % |
| Transversion |
T>G |
All |
327805 |
1.85 % |
| Transversion |
G>T |
All |
531006 |
3.00 % |
| Transversion |
A>T |
All |
503439 |
2.84 % |
| Transversion |
T>A |
All |
535569 |
3.02 % |
| Transversion |
C>G |
All |
240409 |
1.36 % |
| Transversion |
G>C |
All |
209923 |
1.18 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
486259 |
18.58 % |
| Transition |
G>A |
Passed |
410521 |
15.69 % |
| Transition |
T>C |
Passed |
542792 |
20.74 % |
| Transition |
C>T |
Passed |
413261 |
15.79 % |
| Transversion |
A>C |
Passed |
100812 |
3.85 % |
| Transversion |
C>A |
Passed |
95619 |
3.65 % |
| Transversion |
T>G |
Passed |
100855 |
3.85 % |
| Transversion |
G>T |
Passed |
95564 |
3.65 % |
| Transversion |
A>T |
Passed |
70315 |
2.69 % |
| Transversion |
T>A |
Passed |
69893 |
2.67 % |
| Transversion |
C>G |
Passed |
115287 |
4.41 % |
| Transversion |
G>C |
Passed |
115988 |
4.43 % |
| |
|
|
|
|
| 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 |
4.64 |
14573187 |
3143117 |
| Passed |
2.42 |
1852833 |
764333 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |