/EXTERNAL Roadmap/variants/K006532_K006533_2_lane_gembs
BACK
SAMPLE K006532_K006533_2_lane_gembs
Variant counts
| Type |
Total |
Pass |
% |
| SNPs |
1157229447 |
1080082720 |
93.33 % |
| Multiallelic |
0 |
0 |
0.00 % |
VCF Filtering Stats
| Type |
#Sites |
% |
#Non-Variant Sites |
% |
#Variant Sites |
% |
| All |
1157229447 |
100% |
1149272209 |
99.31 % |
7957238 |
0.69 % |
| |
|
|
|
|
|
|
| Passed |
1080174865 |
93.34 % |
1076025906 |
93.63 % |
4148959 |
0.38 % |
| Filtered |
77054582 |
6.66 % |
73246303 |
6.37 % |
3808279 |
0.35 % |
| |
|
|
|
|
|
|
| mq40 |
46497711 |
60.34 % |
45924378 |
62.70 % |
573333 |
15.05 % |
| q20,mq40 |
15777476 |
20.48 % |
15572874 |
21.26 % |
204602 |
5.37 % |
| q20 |
8182873 |
10.62 % |
8023752 |
10.95 % |
159121 |
4.18 % |
| q20,qd2,mq40 |
2221161 |
2.88 % |
1631055 |
2.23 % |
590106 |
15.50 % |
| q20,qd2 |
1956389 |
2.54 % |
634049 |
0.87 % |
1322340 |
34.72 % |
| qd2 |
1833283 |
2.38 % |
1172759 |
1.60 % |
660524 |
17.34 % |
| qd2,mq40 |
368845 |
0.48 % |
287436 |
0.39 % |
81409 |
2.14 % |
| q20,qd2,fs60 |
95773 |
0.12 % |
0 |
0.00 % |
95773 |
2.51 % |
| fs60 |
80115 |
0.10 % |
0 |
0.00 % |
80115 |
2.10 % |
| q20,fs60 |
16518 |
0.02 % |
0 |
0.00 % |
16518 |
0.43 % |
| fs60,mq40 |
14698 |
0.02 % |
0 |
0.00 % |
14698 |
0.39 % |
| qd2,fs60 |
6749 |
0.01 % |
0 |
0.00 % |
6749 |
0.18 % |
| q20,qd2,fs60,mq40 |
1445 |
0.00 % |
0 |
0.00 % |
1445 |
0.04 % |
| qd2,fs60,mq40 |
1324 |
0.00 % |
0 |
0.00 % |
1324 |
0.03 % |
| q20,fs60,mq40 |
222 |
0.00 % |
0 |
0.00 % |
222 |
0.01 % |
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 |
1872331 |
21.19 % |
| Transition |
G>A |
All |
1148614 |
13.00 % |
| Transition |
T>C |
All |
1872516 |
21.19 % |
| Transition |
C>T |
All |
1159614 |
13.12 % |
| Transversion |
A>C |
All |
277892 |
3.14 % |
| Transversion |
C>A |
All |
428032 |
4.84 % |
| Transversion |
T>G |
All |
277839 |
3.14 % |
| Transversion |
G>T |
All |
434521 |
4.92 % |
| Transversion |
A>T |
All |
411511 |
4.66 % |
| Transversion |
T>A |
All |
399691 |
4.52 % |
| Transversion |
C>G |
All |
275427 |
3.12 % |
| Transversion |
G>C |
All |
279863 |
3.17 % |
| |
|
|
|
|
| Transition |
A>G |
Passed |
818671 |
17.36 % |
| Transition |
G>A |
Passed |
739434 |
15.68 % |
| Transition |
T>C |
Passed |
822266 |
17.44 % |
| Transition |
C>T |
Passed |
740749 |
15.71 % |
| Transversion |
A>C |
Passed |
201946 |
4.28 % |
| Transversion |
C>A |
Passed |
206678 |
4.38 % |
| Transversion |
T>G |
Passed |
200483 |
4.25 % |
| Transversion |
G>T |
Passed |
207026 |
4.39 % |
| Transversion |
A>T |
Passed |
185758 |
3.94 % |
| Transversion |
T>A |
Passed |
184154 |
3.91 % |
| Transversion |
C>G |
Passed |
202703 |
4.30 % |
| Transversion |
G>C |
Passed |
204657 |
4.34 % |
| |
|
|
|
|
| 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 |
2.17 |
6053075 |
2784776 |
| Passed |
1.96 |
3121120 |
1593405 |
| dbSNPAll |
0 |
0 |
0 |
| dbSNPPassed |
0 |
0 |
0 |