Magic-16 Metadata

The Metadata about the Magic-16 rice lines.

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
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