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

Table 1 Variants discovered by breed type

	Fayoumi	Leghorn	^aFayoumi vs. Leghornized reference
Depth of coverage	~24×	~22×	~24×
Assembly coverage	84.5	93.7	84.5
Total variants	4,462,467	4,605,732	3,792,327
Previously uncharacterized variants	3,223,583	3,287,720	3,791,430
Homozygosity	99.9482 %	99.9736 %	99.9330 %
^bTs/Tv (All Variants)	2.371	2.365	2.286
Change rate	1 change every 235 bases	1 change every 227 bases	1 change every 276 bases

Total reads computed using GATK DepthofCoverage. Assembly coverage and Sequence coverage calculated using Samtools and GATK DepthofCoverage. All other data calculated using SnpEff. All data is pre-filter. ^aFayoumi vs. Leghorn only compared using SNV data; indels were excluded along with Chromosomes Z and W. ^bTs/Tv is the ratio of transitions/transversions within each population

ISSN: 1471-2164