The Metadata about the Magic-16 rice lines.
| COLUMN | VARIABLE | DESCRIPTION | LITERATURE |
| A | MAGIC16_No | "MAGIC16" -- 15 selections representing the 15 subpopulations from analysis of the 3K rice genome project including one entry from the XI-adm (a very large subset of the 3K rice genomes due to the criteria of unambiguous assignment to a subpopulation. This set of 16 lines will be used to generate populations: NAM (RILs), a 16-way MAGIC, and CSSLs | Zhong et al 2020 |
| B | Genetic_Stock_Accession | The IRGC accession of the seed used for source tissue for the WGS, RNA-Seq, Iso-Seq | |
| C | Genetic_Stock_Varname | The IRGC designation (variety name) of the genetic_stock_accession | |
| D | Country_Origin | Country of origin of the source accession from which the genetic stocks were derived | |
| E | 3K_Assay_ID | the assay ID in the 3K RGP (used in SNP-Seek) | Wang et al 2018 |
| F | OryzaSNP as closest | 20 diverse accessions in OryzaSNP set; SSD purified genetic stocks used for SNP discovery by Affymetrix tiling arrays | McNally et al 2009 |
| G | HDRA_assay_id | the HDRA (High-Density Rice Array) assay ID used in SNP-Seek; also RICE-RP id | McCouch et al, 2016; Wang, D et al 2018) |
| H | K15_subpops_Nature | Admixture-derived subpopulations for the 3K RGP at K=15 where: XI-1A is Xian/indica subpopulation 1A XI-1B-1 is Xian/indica subpopulation 1B-1 XI-1B-2 is Xian/indica subpopulation 1B-2 XI-2A is Xian/indica subpopulation 2A XI-2B is Xian/indica subpopulation 2B XI-3A is Xian/indica subpopulation 3A XI-3B1 is Xian/indica subpopulation 3B1 XI-3B2 is Xian/indica subpopulation 3B2 XI-adm is Xian/indica admixed types between two or more XI subpopulations GJ-adm is Geng/japonica admixed types between two or more GJsubpopulations GJ-trp is Geng/japonica tropical subpopulation GJ-sbtrp is Geng/japonica subtropical subpopulation GJ-tmp Geng/japonica temperate subpopulation cA or Aus is centrum-Aus population cB or Bas is centrum-Basmati population admix is admixed between any two or more of the XI, GJ, cA (Aus), cB (Bas) populations |
Zhong et al 2020 |
| I | K15_subpops_common | More common subpopulation terms | |
| J | K5_groups | Collapse subpopulations to indica, aus, aromatic, tropical japonica, and temperate japonica | |
| K | PacBio_Build | the build name as *.fa or GB accession | Zhang et al 2016; Stein et al 2018; Zhong et al 2020, |
| L | PacBio source | Who contributed source plant/seed materials for the PacBio sequencing | |
| M | Notes | More information |