Single nucleotide variant discovery of highly inbred Leghorn and Fayoumi chicken breeds using pooled whole genome resequencing data reveals insights into phenotype differences

Table 2 Comparison of variant changes for each line

Type	Total	Homozygous	Heterozygous
Fayoumi vs. RJF^b
SNV	4,146,394	3,638,803	507,591
INS^c	180,752	158,256	22,496
DEL^d	135,321	125,514	9,807
TOTAL	4,462,467	3,922,573	539,894
Leghorn vs. RJF
SNV	4,271,399	4,010,609	260,790
INS	189,494	177,474	12,020
DEL	144,839	142,181	2,658
TOTAL	4,605,732	4,330,264	275,468
Fayoumi vs. Leghorn: reference^a
SNV	3,792,327	3,094,177	698,150
TOTAL	3,792,327	3,094,177	698,150

Fayoumi and Leghorn vs. RJF and Fayoumi vs. the Leghornized reference genome. ^aFayoumi vs. the Leghornized reference genome analysis done on SNVs only
^b RJF Red Jungle Fowl, ^c INS insertion variants, ^d DEL deletion variants

ISSN: 1471-2164