/EXTERNAL Roadmap/variants/K012802_1_lane_gembs
BACK
SAMPLE K012802_1_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1121308242 |
17622324 |
1.57 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1121308242 |
100% |
1096200256 |
97.76 % |
25107986 |
2.24 % |
| |
|
|
|
|
|
|
| Passed |
27667626 |
2.47 % |
17079489 |
1.56 % |
10588137 |
38.27 % |
| Filtered |
1093640616 |
97.53 % |
1079120767 |
98.44 % |
14519849 |
52.48 % |
| |
|
|
|
|
|
|
| q20 |
997419402 |
91.20 % |
990034129 |
91.74 % |
7385273 |
50.86 % |
| q20,qd2 |
67152274 |
6.14 % |
60389658 |
5.60 % |
6762616 |
46.57 % |
| q20,mq40 |
19863246 |
1.82 % |
19733766 |
1.83 % |
129480 |
0.89 % |
| q20,qd2,mq40 |
8941351 |
0.82 % |
8861203 |
0.82 % |
80148 |
0.55 % |
| mq40 |
242611 |
0.02 % |
83435 |
0.01 % |
159176 |
1.10 % |
| qd2 |
12594 |
0.00 % |
11471 |
0.00 % |
1123 |
0.01 % |
| qd2,mq40 |
9045 |
0.00 % |
7105 |
0.00 % |
1940 |
0.01 % |
| qd2,fs60,mq40 |
48 |
0.00 % |
0 |
0.00 % |
48 |
0.00 % |
| fs60,mq40 |
21 |
0.00 % |
0 |
0.00 % |
21 |
0.00 % |
| qd2,fs60 |
15 |
0.00 % |
0 |
0.00 % |
15 |
0.00 % |
| fs60 |
5 |
0.00 % |
0 |
0.00 % |
5 |
0.00 % |
| q20,qd2,fs60,mq40 |
3 |
0.00 % |
0 |
0.00 % |
3 |
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 |
7767350 |
27.95 % |
| Transition |
G>A |
All |
1351974 |
4.87 % |
| Transition |
T>C |
All |
4133424 |
14.88 % |
| Transition |
C>T |
All |
1421800 |
5.12 % |
| Transversion |
A>C |
All |
663243 |
2.39 % |
| Transversion |
C>A |
All |
2376503 |
8.55 % |
| Transversion |
T>G |
All |
1248636 |
4.49 % |
| Transversion |
G>T |
All |
2142060 |
7.71 % |
| Transversion |
A>T |
All |
2433538 |
8.76 % |
| Transversion |
T>A |
All |
2854933 |
10.27 % |
| Transversion |
C>G |
All |
867797 |
3.12 % |
| Transversion |
G>C |
All |
526193 |
1.89 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
89166 |
16.09 % |
| Transition |
G>A |
Passed |
59560 |
10.75 % |
| Transition |
T>C |
Passed |
66862 |
12.07 % |
| Transition |
C>T |
Passed |
63646 |
11.49 % |
| Transversion |
A>C |
Passed |
33366 |
6.02 % |
| Transversion |
C>A |
Passed |
35142 |
6.34 % |
| Transversion |
T>G |
Passed |
36907 |
6.66 % |
| Transversion |
G>T |
Passed |
35087 |
6.33 % |
| Transversion |
A>T |
Passed |
32332 |
5.84 % |
| Transversion |
T>A |
Passed |
33041 |
5.96 % |
| Transversion |
C>G |
Passed |
35361 |
6.38 % |
| Transversion |
G>C |
Passed |
33599 |
6.06 % |
| |
|
|
|
|
| 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 |
1.12 |
14674548 |
13112903 |
| Passed |
1.02 |
279234 |
274835 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |