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Table 4 Summary of the SNPs effect prediction in 55K array

From: A new chicken 55K SNP genotyping array

Item Count Percent (%)
Total number of SNPs in the panel 52,184  
Annotation possible 52,108 99.85
intergenic variant 16,106 30.86
intron variant 25,275 48.43
intron variant & noncoding transcript variant 3981 7.63
missense variant 590 1.13
missense variant & splice region variant 13 0.02
synonymous variant 1601 3.07
Splicing 187 0.36
start/stop gained/lost/retained 12 0.02
3 prime UTR variant 1358 2.60
5 prime UTR variant 229 0.44
upstream gene variant (1 kb) 871 1.67
downstream gene variant (1 kb) 1014 1.94
noncoding transcript exon variant 871 1.67