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Table 1 Summary of functional annotation of SNP and INDEL variants from layer and broiler chicken lines

From: Genome-wide characterization of genetic variants and putative regions under selection in meat and egg-type chicken lines

Category SNP Count SNP % INDEL Count INDEL %
Total no of variants 13,449,339   1,335,889  
Total annotation 15,223,947 100 1,500,714 100
Alternative annotation 1,774,608 11.66 164,825 10.98
Intergenic 5,866,525 38.53 590,736 39.36
Intronic 6,409,486 42.10 644,103 42.92
Exonic 175,258 1.15 2555 0.17
1 kb downstream 1,274,658 8.37 123,378 8.22
1 kb upstream 1,306,400 8.58 116,815 7.78
UTR3’ 142,796 0.94 17,587 1.17
UTR5’ 26,064 0.17 2462 0.16
Splicing 20,703 0.14 2866 0.19
ncRNA 1814 0.012 164 0.01
miRNA 243 0.002 48 0.003
Exonic categories
 Synonymous 122,502 69.90
 Non-synonymous 52,219 29.80
 Stopgain 424 0.24
 Stoploss/retained 88 0.05
 Frameshift 1381 54.01
 Non-frameshift 1094 42.82
 Coding unknown 25 0.01 80 3.13