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

Table 5 Classification of SNVs used for validation

Class	Fayoumi SNVs	Leghorn SNVs	Common SNVs	Total	Classification description
A	5	0	0	5	Segregating in population only
B	14	0	0	14	Fayoumi and Leghorn different (one segregating, one not segregating), and segregating in controls
C	2	0	0	2	Fayoumi, Leghorn, and controls mix of homozygous for reference or alternate allele, but no heterozygotes
D	4	10	0	14	Failed
E	11	24	2	37	Evidence of duplication
F	1	2	0	3	Only Homozygous (Fayoumi and Leghorn homozygous for different alleles, segregating in controls)
Total	37	36	2	75
					Pass rate = 81.3 % (75–14)/75

Table shows the results of wet-lab validation of 100 uncharacterized SNVs. The data from validation was used to inform the additional filtering steps used in downstream analysis (strict-filter) of the within-line variation

ISSN: 1471-2164