Additional file 6 of Uncovering the architecture of production-driven introgression in Cinisara cattle breed

Additional file 6. Table S1-List of introgressed SNPs identified in the Cinisara cattle breed. For each SNP, the following information is given: the bovine chromosome, the position of the SNP, the flanking region, the proportion of introgression given by each reference population and the target population. Table S2-List of introgressed SNPs identified in the Cinisara cattle breed. For each SNP, the following information is given: the bovine chromosome, the position of the SNP, the flanking region, the proportion of introgression given by each reference population and the target population. Table S3 - Mean FROH, average individual introgression from HOL and BRW as calculated with lai analysis, and mean total length of IBD sharing with HOL and BRW of CIN_A and CIN_B individuals. Table S4 - List of introgressed SNPs identified in the 99th percentile in the Cinisaracattle breed. For each SNP, the following information is given: the bovine chromosome, the position of the SNP, the flanking region, the proportion of introgression given by each reference population and target population. Table S5 - List of genes located on highly introgressed SNP of Cinisara Ausing Holstein as reference population. The bovine chromosomeon which the SNP and genes are located, the positionsfor SNP start and SNP end, the positionsfor gene start and gene end and the gene names are given. Table S6 - List of genes located on the highly introgressed SNP of Cinisara Ausing Brown Swiss as reference population. The bovine chromosomeon which the SNP and genes are located, the positionsfor SNP start and SNP end, the positionsfor gene start and gene end and the gene names are given. Table S7 - List of the highly introgressed SNP identified in CIN_A using Holstein as reference population located on the quantitative traits loci. The chromosome and start and end position of SNPs, the chromosome, start and end position and the description of QTL are given. Table S8 - List of the highly introgressed SNP identified in CIN_A using Brown Swiss as reference population located on the quantitative traits loci. The chromosome and start and end position of SNPs, the chromosome, start and end position and the description of QTL are given. Table S9 - List of introgressed SNPs identified in the 99th percentile in the Cinisaracattle breed. For each SNP, the following information is given: the bovine chromosome, the position of the SNP, the flanking region, the proportion of introgression given by each reference population and target population. Table S10 - List of genes located on the candidate regions of Cinisara Ausing Holstein as reference population. The bovine chromosomeon which the SNP and genes are located, the positionsfor SNP start and SNP end, the positionsfor gene start and gene end and the gene names are given. Table S11 - List of genes located on the candidate regions of Cinisara Ausing Brown Swiss as reference population. The bovine chromosomeon which the SNP and genes are located, the positionsfor SNP start and SNP end, the positionsfor gene start and gene end and the gene names are given. Table S12 - List of the highly introgressed SNP identified in CIN_B using Holstein as reference population located on the quantitative traits loci. The chromosome and start and end position of SNPs, the chromosome, start and end position and the description of QTL are given. Table S13 - List of the highly introgressed SNP identified in CIN_B using Brown Swiss as reference population located on the quantitative traits loci. The chromosome and start and end position of SNPs, the chromosome, start and end position and the description of QTL are given. Table S14 - List of genes in common between CIN_A and CIN_B in the highly introgressive SNPs from HOL. The bovine chromosomeon which the SNP and genes are located, the positionsfor SNP start and SNP end, the positionsfor gene start and gene end and the gene names are given. Table S15 - List of genes in common between CIN_A and CIN_B in the highly introgressive SNPs from BRW. The bovine chromosomeon which the SNP and genes are located, the positionsfor SNP start and SNP end, the positionsfor gene start and gene end and the gene names are given.附加文件6。表S1：辛尼萨拉牛（Cinisara cattle）中鉴定到的渐渗型单核苷酸多态性（Single Nucleotide Polymorphism, SNP）列表。每条SNP包含以下信息：牛染色体编号、SNP的物理位置、侧翼序列、各参考群体与目标群体计算得到的渐渗比例。表S2：辛尼萨拉牛中鉴定到的渐渗型SNP列表，每条SNP包含以下信息：牛染色体编号、SNP的物理位置、侧翼序列、各参考群体与目标群体计算得到的渐渗比例。表S3：CIN_A与CIN_B个体的平均FROH、通过lai分析计算得到的来自荷斯坦（Holstein, HOL）与布朗瑞士牛（Brown Swiss, BRW）的个体平均渐渗水平，以及与荷斯坦、布朗瑞士牛共享的同源同祖片段（Identity By Descent, IBD）总平均长度。表S4：辛尼萨拉牛中鉴定到的处于99th百分位的渐渗型SNP列表，每条SNP包含以下信息：牛染色体编号、SNP的物理位置、侧翼序列、各参考群体与目标群体计算得到的渐渗比例。表S5：以荷斯坦为参考群体时，辛尼萨拉牛A亚群（Cinisara A, CIN_A）高渐渗型SNP区域内的基因列表。包含以下信息：SNP与基因所在的牛染色体编号、SNP起始与终止位置、基因起始与终止位置，以及基因名称。表S6：以布朗瑞士牛为参考群体时，辛尼萨拉牛A亚群高渐渗型SNP区域内的基因列表。包含以下信息：SNP与基因所在的牛染色体编号、SNP起始与终止位置、基因起始与终止位置，以及基因名称。表S7：以荷斯坦为参考群体时，在CIN_A中鉴定到的、位于数量性状基因座（Quantitative Trait Locus, QTL）上的高渐渗型SNP列表。包含以下信息：SNP所在染色体编号、SNP起始与终止位置，以及QTL所在染色体编号、QTL起始与终止位置和QTL描述信息。表S8：以布朗瑞士牛为参考群体时，在CIN_A中鉴定到的、位于数量性状基因座上的高渐渗型SNP列表。包含以下信息：SNP所在染色体编号、SNP起始与终止位置，以及QTL所在染色体编号、QTL起始与终止位置和QTL描述信息。表S9：辛尼萨拉牛中鉴定到的处于99th百分位的渐渗型SNP列表，每条SNP包含以下信息：牛染色体编号、SNP的物理位置、侧翼序列、各参考群体与目标群体计算得到的渐渗比例。表S10：以荷斯坦为参考群体时，辛尼萨拉牛A亚群候选区域内的基因列表。包含以下信息：SNP与基因所在的牛染色体编号、SNP起始与终止位置、基因起始与终止位置，以及基因名称。表S11：以布朗瑞士牛为参考群体时，辛尼萨拉牛A亚群候选区域内的基因列表。包含以下信息：SNP与基因所在的牛染色体编号、SNP起始与终止位置、基因起始与终止位置，以及基因名称。表S12：以荷斯坦为参考群体时，在CIN_B中鉴定到的、位于数量性状基因座上的高渐渗型SNP列表。包含以下信息：SNP所在染色体编号、SNP起始与终止位置，以及QTL所在染色体编号、QTL起始与终止位置和QTL描述信息。表S13：以布朗瑞士牛为参考群体时，在CIN_B中鉴定到的、位于数量性状基因座上的高渐渗型SNP列表。包含以下信息：SNP所在染色体编号、SNP起始与终止位置，以及QTL所在染色体编号、QTL起始与终止位置和QTL描述信息。表S14：来自荷斯坦的高渐渗型SNP区域中，CIN_A与CIN_B共享的基因列表。包含以下信息：SNP与基因所在的牛染色体编号、SNP起始与终止位置、基因起始与终止位置，以及基因名称。表S15：来自布朗瑞士牛的高渐渗型SNP区域中，CIN_A与CIN_B共享的基因列表。包含以下信息：SNP与基因所在的牛染色体编号、SNP起始与终止位置、基因起始与终止位置，以及基因名称。