S1 File - Uncovering Genomic Features and Maternal Origin of Korean Native Chicken by Whole Genome Sequencing

Supporting figures and tables. Figure S1. Overall process of genome assembly and gene prediction. Table S1. List of GeneBank ID, Location and Type of 75 individuals used in phylogenomic analysis. Table S2. The result summary of Modeltest using 56 models from PAUP. Figure S2. An overview of the phylogenetic analysis process. Table S3. The result summary of read mapping using Bowtie2. Figure S3. Insert size distributions of 5 KNC samples. Figure S4. Distribution of known and novel SNVs in each chromosome. Table S4. The result summary of variant calling using GATK. Figure S5. Ratio of breed specific SNV and the proportion of each breed in breed specific SNVs. Figure S6. Ratio of breed specific InDel and the proportion of each breed in breed specific InDels. Figure S7. Ratio of the number of chromosomal variants to the total number of variant. Figure S8. Ratio of each variant location in three variant types (SNP, InDel and CNV). Table S5. The list of synonymous and non-synonymous variants in common genes of highly variable regions. Table S6. The result summary of Korean Native Chicken genome assembly using IDBA_UD. Table S7. The result summary of remapping unaligned reads to assembled genome using bowtie2. Figure S9. Neighbor joining tree of 75 samples used in this analysis. (DOCX)