1.5k Pilot SNP Array Design

The details of the 1,536 sheep SNPs on the 1.5k SNP chip are provided in an Excel file. The SNPs were identified as part of the ISGC pilot resequencing project that was performed at the AGRF. Two types of targets were resequenced, BAC end sequences and ESTs. The table below contains summary information of the criteria used for target selection and the number of SNPs of each type on the chip.

The majority of targets have been mapped to the Virtual Sheep Genome (VSG) and can be visualised in VSG context via hyperlinks (column 2 of the spreadsheet) to the VSG. The Excel file contains the VSG predicted chromosome and coordinate details for all SNPs with the exception of 29 EST targets, 1 BES target and a Y chromosome SNP.

Criteria for Target selection Number of SNPs
Minor allele frequency (MAF) from resequenced sheep at least 0.2, and Illumina score at least 0.6 (best target list) 1,085
SNPs predicted to map to comparative genome contigs (CGCs) that are not represented in the best target list 197
SNPs predicted to bridge gaps on the VSG 114
Additional SNPs on large CGCs 90
Additional EST-based SNPs 22
Targets also present on RH panels 15
Targets to address over-clustering issues in virtual genome build 12
Y-chromosome SNP 1