apple_REFPOP_progeny_marker_position_data.txt

List of the 10295 SNP loci genotyped with the Illumina Infinium 20K array on the apple REFPOP progeny. The column "Index_20K" indicates the SNP index number on the 20K array that is used as column name in the file apple_REFPOP_progeny_marker_data.txt. The column "Original_Locus_Name" indicates the full name of the SNP; the column "Affymetrix_id" indicates the name of the SNP on the Affymetrix Axiom 480K SNP array (Bianco et al 2016); the columns "chr" and "position" indicate the position of the SNP on GDDH13 v1.1 reference genome (Daccord et al 2017). A value of "0" in column "chr" means the SNP is located on an unmapped portion of GDDH13 v1.1 genome. A value of "19" in column "chr" means the position of the SNP could not be deduced from BLAST results. A value "not robust on 480K" in columns "chr" and "position" means the SNP was not considered robust when genotyped on the Affymetrix Axiom 480K SNP array and thus not used for the apple REFPOP. The column "Used ot not" indicates if the SNP was used in the work on the apple REFPOP by Jung et al (2020). The subset of 10295 robust SNPs was filtered from the 20K genotyping results as described in Howard et al (2020).

本数据集包含利用Illumina Infinium 20K基因分型芯片对苹果REFPOP群体（apple REFPOP progeny）进行基因分型获得的10295个单核苷酸多态性（Single Nucleotide Polymorphism, SNP）位点列表。其中，列"Index_20K"表示该SNP在20K芯片上的位点编号，同时作为文件apple_REFPOP_progeny_marker_data.txt的列名；列"Original_Locus_Name"表示该SNP的完整名称；列"Affymetrix_id"表示该SNP在Affymetrix Axiom 480K SNP芯片中的编号（Bianco等，2016）；列"chr"与"position"分别表示该SNP在GDDH13 v1.1参考基因组（Daccord等，2017）上的染色体编号与物理位置。当列"chr"的值为"0"时，代表该SNP位于GDDH13 v1.1基因组中未完成染色体锚定的区域；当"chr"的值为"19"时，代表无法通过BLAST比对结果推断该SNP的染色体位置；若列"chr"与"position"的取值为"not robust on 480K"，则表示该SNP在Affymetrix Axiom 480K SNP芯片的基因分型实验中未通过稳定性验证，因此未被纳入苹果REFPOP群体的相关研究。列"Used ot not"用于标注该SNP是否被Jung等（2020）开展的苹果REFPOP相关研究采用。本研究筛选得到的10295个可靠SNP位点子集，是按照Howard等（2020）描述的方法从20K芯片的基因分型结果中过滤得到的。