/EXTERNAL Roadmap/variants/K012800_1_lane_gembs
BACK
SAMPLE K012800_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1154228541 |
725025179 |
62.81 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1154228541 |
100% |
1133122457 |
98.17 % |
21106084 |
1.83 % |
| |
|
|
|
|
|
|
| Passed |
728499915 |
63.12 % |
722798381 |
63.79 % |
5701534 |
0.78 % |
| Filtered |
425728626 |
36.88 % |
410324076 |
36.21 % |
15404550 |
2.11 % |
| |
|
|
|
|
|
|
| q20 |
382361410 |
89.81 % |
379527640 |
92.49 % |
2833770 |
18.40 % |
| q20,qd2 |
21053970 |
4.95 % |
9090235 |
2.22 % |
11963735 |
77.66 % |
| q20,mq40 |
14710254 |
3.46 % |
14584166 |
3.55 % |
126088 |
0.82 % |
| q20,qd2,mq40 |
3817822 |
0.90 % |
3674344 |
0.90 % |
143478 |
0.93 % |
| qd2 |
2067695 |
0.49 % |
1947828 |
0.47 % |
119867 |
0.78 % |
| mq40 |
1684486 |
0.40 % |
1474147 |
0.36 % |
210339 |
1.37 % |
| qd2,mq40 |
32244 |
0.01 % |
25716 |
0.01 % |
6528 |
0.04 % |
| qd2,fs60,mq40 |
434 |
0.00 % |
0 |
0.00 % |
434 |
0.00 % |
| fs60,mq40 |
143 |
0.00 % |
0 |
0.00 % |
143 |
0.00 % |
| qd2,fs60 |
100 |
0.00 % |
0 |
0.00 % |
100 |
0.00 % |
| q20,qd2,fs60,mq40 |
28 |
0.00 % |
0 |
0.00 % |
28 |
0.00 % |
| fs60 |
25 |
0.00 % |
0 |
0.00 % |
25 |
0.00 % |
| q20,qd2,fs60 |
13 |
0.00 % |
0 |
0.00 % |
13 |
0.00 % |
| q20,fs60 |
1 |
0.00 % |
0 |
0.00 % |
1 |
0.00 % |
| q20,fs60,mq40 |
1 |
0.00 % |
0 |
0.00 % |
1 |
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 |
8517552 |
37.29 % |
| Transition |
G>A |
All |
1576033 |
6.90 % |
| Transition |
T>C |
All |
6860688 |
30.04 % |
| Transition |
C>T |
All |
1673648 |
7.33 % |
| Transversion |
A>C |
All |
268293 |
1.17 % |
| Transversion |
C>A |
All |
838040 |
3.67 % |
| Transversion |
T>G |
All |
356185 |
1.56 % |
| Transversion |
G>T |
All |
776133 |
3.40 % |
| Transversion |
A>T |
All |
635832 |
2.78 % |
| Transversion |
T>A |
All |
688758 |
3.02 % |
| Transversion |
C>G |
All |
367754 |
1.61 % |
| Transversion |
G>C |
All |
283241 |
1.24 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
578912 |
19.09 % |
| Transition |
G>A |
Passed |
464421 |
15.31 % |
| Transition |
T>C |
Passed |
518860 |
17.11 % |
| Transition |
C>T |
Passed |
471976 |
15.56 % |
| Transversion |
A>C |
Passed |
123190 |
4.06 % |
| Transversion |
C>A |
Passed |
132481 |
4.37 % |
| Transversion |
T>G |
Passed |
125541 |
4.14 % |
| Transversion |
G>T |
Passed |
132682 |
4.38 % |
| Transversion |
A>T |
Passed |
119318 |
3.93 % |
| Transversion |
T>A |
Passed |
119723 |
3.95 % |
| Transversion |
C>G |
Passed |
122835 |
4.05 % |
| Transversion |
G>C |
Passed |
122596 |
4.04 % |
| |
|
|
|
|
| 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 |
4.42 |
18627921 |
4214236 |
| Passed |
2.04 |
2034169 |
998366 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |