1,555
edits
Changes
From Genome Analysis Wiki
Jump to navigationJump to searchno edit summary
== Assay Design Rates ==
== Assay Design Rates ==
{| border="1" align="center" cellpadding="1" cellspacing="1" summary="Summarizes the Number of SNPs in Each Category That Passed Assay Design. Note that Categories Overlap."
{| align="left" cellpadding="2" cellspacing="1" summary="Summarizes the Number of SNPs in Each Category That Passed Assay Design. Note that Categories Overlap."
|+ Illumina Assay Design Summary
|+ Illumina Assay Design Summary
|-
|-
! scope="col" | SNP Set
! scope="col" | SNP Set
! scope="col" | Number of <br>Candidates
! scope="col" align = "center" | Number of <br>Candidates
! scope="col" | Number of <br>Successful Designs
! scope="col" align = "center" | Number of <br>Successful Designs
! scope="col" | Additional <br>Notes
! scope="col" align = "center" | Additional Notes
|-
|-
! scope="row" | Coding Content
! scope="row" | Coding Content
| 275,165
| align="right" | 275,165
| 243,094
| align="right" | 243,094
| An additional set of 8,242 SNPs that were unique to the 1000 Genomes Project and populations under-represented in the design was added.
| An additional set of 8,242 SNPs that were unique to the 1000 Genomes Project and populations under-represented in the design was added.
|-
|-
! scope="row" | GWAS Tag SNPs
! scope="row" | GWAS Tag SNPs
| 5,763
| align="right" | 5,763
| 5,325
| align="right" | 5,325
|
|
|-
|-
! scope="row" | Grid of Common Variants
! scope="row" | Grid of Common Variants
| 5,710
| align="right" | 5,710
| 5,286
| align="right" | 5,286
|
|
|-
|-
! scope="row" | Randonly Selected Synonymous SNPs
! scope="row" | Randonly Selected Synonymous SNPs
| 5,000
| align="right" | 5,000
| 4,651
| align="right" | 4,651
| For 1,000 SNPs, assays were generated on both strands - to faciliate QC efforts and future development of methods for genotyping of rare variants.
| For 1,000 SNPs, assays were generated on both strands - to faciliate QC efforts and future development of methods for genotyping of rare variants.
|-
|-
! scope="row" | AIM - African Ancestry
! scope="row" | AIM - African Ancestry
| 3,388
| align="right" | 3,388
| 3,241
| align="right" | 3,241
|
|
|-
|-
! scope="row" | AIM - Native American Ancestry
! scope="row" | AIM - Native American Ancestry
| 1,000
| align="right" | 1,000
| 998
| align="right" | 998
|
|
|-
|-
! scope="row" | HLA Tags
! scope="row" | HLA Tags
| 2,536
| align="right" | 2,536
| 2,459
| align="right" | 2,459
|
|
|-
|-
! scope="row" | ESP Requests
! scope="row" | ESP Requests
| 1,003
| align="right" | 1,003
| 843
| align="right" | 843
|
|
|-
|-
! scope="row" | Fingerprint SNPs
! scope="row" | Fingerprint SNPs
| 285
| align="right" | 285
| 259
| align="right" | 259
|
|
|-
|-
! scope="row" | MicroRNA Target Sites
! scope="row" | MicroRNA Target Sites
| 285
| align="right" | 285
| 270
| align="right" | 270
|
|
|-
|-
! scope="row" | Mitochondrial Variants
! scope="row" | Mitochondrial Variants
| 246
| align="right" | 246
| 246
| align="right" | 246
|
|
|-
|-
! scope="row" | Chromosome Y
! scope="row" | Chromosome Y
| 188
| align="right" | 188
| 128
| align="right" | 128
|
|
|-
|-
! scope="row" | Indels
! scope="row" | Indels
| 181
| align="right" | 181
| 181
| align="right" | 181
|
|}
|}
