Table 1 Summary of functional annotation of SNP and INDEL variants from layer and broiler chicken lines
Category | SNP Count | SNP % | INDEL Count | INDEL % |
|---|---|---|---|---|
Total no of variants | 13,449,339 | Â | 1,335,889 | Â |
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 |
1Â kb downstream | 1,274,658 | 8.37 | 123,378 | 8.22 |
1Â 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 |