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

Table 3 Variant annotations and counts by effect type for each line

Effect Type	Fayoumi	Leghorn	Chi-Square Statistic
Codon_Change_Plus_Codon_Deletion	16	24
Codon_Change_Plus_Codon_Insertion	23	34
Codon_Deletion	40	53
Codon_Insertion	46	63
Downstream	401,163	440,064	P < 0.0001
Exon	418	473
Frame_Shift	384	504	P < 0.0001
Intergenic	2,344,623	2,430,279	P < 0.0001
Intron	2,205,047	2,264,238	P < 0.0001
Non_Synonymous_Coding	14,335	16,924	P < 0.0001
Non_Synonymous_Start	5	2
Splice_Site_Acceptor	229	236
Splice_Site_Donor	196	251	P < 0.01
Start_Gained	1,015	1,185	P < 0.01
Start_Lost	35	41
Stop_Gained	107	121
Stop_Lost	16	18
Synonymous_Coding	37,502	41,860	P < 0.0001
Synonymous_Stop	9	12
Upstream	397,941	438,052	P < 0.0001
Utr_3_Prime	48,430	52,433	P < 0.0001
Utr_5_Prime	6,445	7,802	P < 0.0001

Table shows variant annotations and counts for Fayoumi and Leghorn populations vs. RJF by effect type. The “effect type” is the sequence ontology meaning for example that the variant hits an intron or causes a frameshift. A Pearson’s chi-square goodness-of-fit test was used for comparison (P < 0.01)

ISSN: 1471-2164