List of genes and the number of variants in the highly variable regions of SNVs and InDels.

<p>The number of variants was based on the result of multi-sample calling from GATK.</p><p>List of genes and the number of variants in the highly variable regions of SNVs and InDels.</p

Summary of sequencing information and rawdata QC result using trimmomatic.

<p>Coverage was calculated based on the size of reference genome Galgal4(1046.93MB).</p><p>Summary of sequencing information and rawdata QC result using trimmomatic.</p

Manhattan plot showing the rate of SNVs and InDels per 500kbp window for the autosomes and sex chromosome.

<p>The red line denotes the top 1% of empirical distribution.</p

List of commonly predicted genes from assembled sequences of each sample.

<p>List of commonly predicted genes from assembled sequences of each sample.</p

Phylogenetic tree using 75 whole MT genome sequences, including five Korean Native Chickens from this study.

<p>Box a shows the morphology and plumage color of the different KNC strains. Box b shows the legend (sample type and locality) for the phylogenetic tree in c. In the phylogentic tree, values (Bayesian posterior probability <0.8 or bootstrap value <600) were marked with a “-“ symbol.</p

Nucleotide diversity (A and C) and cumulative average of nucleotide diversity (B) for each swine breed.

<p>Nucleotide diversity of 10⁷-bp non-overlapping window is shown. Each pig breed is marked by a colored line; orange for wild boar, blue for Landrace, green for Yorkshire, purple for Yucatan miniature pig and yellow for Duroc.</p

Hierarchical clustering of biological process GO terms associated with genes located in outlier loci (regions) detected by XP-EHH method in comparisons between Yucatan miniature pig and Duroc (A), Landrace (B) and Yorkshire (C).

<p>The gene list of each GO term clustered using DAVID was compared to calculate the distance between the GO terms. For a distance value of > 0.4~0.5, GO terms were re-clustered, and GO term groups are shown in boxes. The representative GO terms manually selected are shown in red. The numbers of genes in the GO terms are in brackets with the corresponding <i>p</i>-values.</p