/EXTERNAL Roadmap/variants/K012797_1_lane_gembs
BACK
SAMPLE K012797_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1135202916 |
42808379 |
3.77 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1135202916 |
100% |
1111634112 |
97.92 % |
23568804 |
2.08 % |
| |
|
|
|
|
|
|
| Passed |
52588612 |
4.63 % |
41847923 |
3.76 % |
10740689 |
20.42 % |
| Filtered |
1082614304 |
95.37 % |
1069786189 |
96.24 % |
12828115 |
24.39 % |
| |
|
|
|
|
|
|
| q20 |
1015222677 |
93.78 % |
1008533437 |
94.27 % |
6689240 |
52.15 % |
| q20,qd2 |
41416098 |
3.83 % |
35619024 |
3.33 % |
5797074 |
45.19 % |
| q20,mq40 |
18893493 |
1.75 % |
18785421 |
1.76 % |
108072 |
0.84 % |
| q20,qd2,mq40 |
6762814 |
0.62 % |
6692948 |
0.63 % |
69866 |
0.54 % |
| mq40 |
289510 |
0.03 % |
130134 |
0.01 % |
159376 |
1.24 % |
| qd2 |
17959 |
0.00 % |
16017 |
0.00 % |
1942 |
0.02 % |
| qd2,mq40 |
11571 |
0.00 % |
9208 |
0.00 % |
2363 |
0.02 % |
| qd2,fs60,mq40 |
89 |
0.00 % |
0 |
0.00 % |
89 |
0.00 % |
| qd2,fs60 |
42 |
0.00 % |
0 |
0.00 % |
42 |
0.00 % |
| fs60,mq40 |
39 |
0.00 % |
0 |
0.00 % |
39 |
0.00 % |
| q20,qd2,fs60,mq40 |
6 |
0.00 % |
0 |
0.00 % |
6 |
0.00 % |
| fs60 |
5 |
0.00 % |
0 |
0.00 % |
5 |
0.00 % |
| q20,qd2,fs60 |
1 |
0.00 % |
0 |
0.00 % |
1 |
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 |
8622034 |
33.14 % |
| Transition |
G>A |
All |
1313437 |
5.05 % |
| Transition |
T>C |
All |
4697769 |
18.05 % |
| Transition |
C>T |
All |
1464197 |
5.63 % |
| Transversion |
A>C |
All |
566168 |
2.18 % |
| Transversion |
C>A |
All |
1862058 |
7.16 % |
| Transversion |
T>G |
All |
1135602 |
4.36 % |
| Transversion |
G>T |
All |
1557483 |
5.99 % |
| Transversion |
A>T |
All |
1535695 |
5.90 % |
| Transversion |
T>A |
All |
1998159 |
7.68 % |
| Transversion |
C>G |
All |
804522 |
3.09 % |
| Transversion |
G>C |
All |
462508 |
1.78 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
156967 |
15.79 % |
| Transition |
G>A |
Passed |
119814 |
12.05 % |
| Transition |
T>C |
Passed |
129553 |
13.03 % |
| Transition |
C>T |
Passed |
127570 |
12.83 % |
| Transversion |
A>C |
Passed |
56253 |
5.66 % |
| Transversion |
C>A |
Passed |
59957 |
6.03 % |
| Transversion |
T>G |
Passed |
59806 |
6.01 % |
| Transversion |
G>T |
Passed |
60458 |
6.08 % |
| Transversion |
A>T |
Passed |
52734 |
5.30 % |
| Transversion |
T>A |
Passed |
52384 |
5.27 % |
| Transversion |
C>G |
Passed |
60595 |
6.09 % |
| Transversion |
G>C |
Passed |
58299 |
5.86 % |
| |
|
|
|
|
| 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 |
1.62 |
16097437 |
9922195 |
| Passed |
1.16 |
533904 |
460486 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |