We detected a total of 2,771,201 SNPs from the germline genome, 91% of which are present in dbSNP (release 129).
Synonymous SNVs and variants present in dbSNP (release 130) were removed due to their low likelihood of being driver mutations.
About half (151,280) of these SNPs were detected in at least two of the breeds and 55,190 were already present in dbSNP release 122.
The MAF is 26% in Hispanics, 18% in African Americans and 5% in European Americans [ 19].> -wrap-foot> SNP information is based on dbSNP, release 138.
All chicken SNPs available in dbSNP release 122 were downloaded and submitted to Illumina for design score calculation, which was performed with Illumina's Assay Design Tool for Infinium.
Using VarScan [ 42] with default parameters, we performed a systematic mutation analysis of our lncRNAs and found a total of 9,713 novel candidate mutations within exonic regions of these lncRNAs after filtering out all known polymorphisms from dbSNP (release 142).
Twenty polymorphic sites were found, of which 16 are predicted to change an amino acid, and only 5 are present in dbSNP release 126 (rs16995685, rs12624954, rs2738047, rs16995668, rs1800957 - please see NCBI webpage in Availability and requirements section).
The probes avoided repetitive elements listed in the REPBASE database (http://www.girinst.org/repbase/index.html) and avoided SNPs present in dbSNP (release 123), the latter of which should minimize a bias due to polymorphisms in restriction enzyme sites.
Of the 30,938 sites that we identified from the RNA-seq data and that passed all of our filters, only 3.1% (967) did not have an assigned rsID in dbSNP release 138.
The ANNOVAR program was used to filter out mutations present in dbSNP (release 130) in order to remove mutations known to be polymorphic, therefore unlikely to be cancer driver mutations [ 40].
