Download table for SNPs/variants dataset and alignment files of 3K RG accessions to 16 reference genomes.

Reference Genome*	Acronyms	Internal genome numbering	Assembly (NCBI ID)	3KRG SNPs** (PLINK2.0 format)	PLINK2.0 file size (Gb)	Realignment/alignment files*** (CRAM format)	CRAM total file size (Tb)
GJ-temp: IRGSP	IRGSP	genome1	GCF_001433935.1	Nipponbare IRGSP SNPs and variants	4.49	Nipponbare IRGSP CRAM ; sorted CRAM	2.89 ; 5.74
GJ-subtrp: CHAO MEO	CM	genome15	GCA_009831315.1	Chao Meo SNPs and variants	4.84	Chao Meo CRAM	2.89
GJ-trop1: Azucena	AZ	genome5	GCA_009830595.1	Azucena SNPs and variants	4.64	Azucena CRAM	2.84
GJ-trop2: KETAN NANGKA	KN	genome14	GCA_009831275.1	Ketan Nangka SNPs and variants	4.88	Ketan Nangka CRAM	2.92
cB: ARC 10497	ARC	genome7	GCA_009831255.1	ARC SNPs and variants	4.92	ARC CRAM	2.96
XI-1A: ZhenShan97RS3	ZS97	genome28	GCA_001623345.2	Zhen Shan 97 SNPs and variants	4.78	Zhen Shan 97 CRAM	2.38
XI-1B1: IR 64	IR64	genome6	GCA_009914875.1	IR 64 SNPs and variants	4.75	IR 64 CRAM ; sorted CRAM	2.40 ; 6.03
XI-1B2: PR 106	PR106	genome13	GCA_009831045.1	PR 106 SNPs and variants	4.78	PR 106 CRAM	2.45
XI-2A: GOBOL SAIL	GS	genome16	GCA_009831025.1	Gobol Sail SNPs and variants	4.83	Gobol Sail CRAM	2.59
XI-2B: LARHA MUGAD	LM	genome8	GCA_009831355.1	Larha Mugad SNPs and variants	4.95	Larha Mugad CRAM	2.62
XI-3A: LIMA	LIMA	genome11	GCA_009829395.1	Lima SNPs and variants	4.72	Lima CRAM	2.53
XI-3B1: KHAO YAI GUANG	KYG	genome10	GCA_009831295.1	Khao Yai Guang SNPs and variants	4.76	Khao Yai Guang CRAM	2.52
XI-3B2: LIU XU	LX	genome9	GCA_009829375.1	Liu Xu SNPs and variants	4.89	Liu Xu CRAM	2.72
XI-adm: MH63RS3	MH63	genome27	GCA_001623365.2	MH 63 SNPs and variants	4.79	MH 63 CRAM	2.41
cA1: N22	N22	genome4	GCA_001952365.3	N 22 SNPs and variants	4.74	N 22 CRAM	3.02
cA2: NATEL BORO	NABO	genome12	GCA_009831335.1	Natel Boro SNPs and variants	5.22	Natel Boro CRAM	3.21

* The annotation files and transcriptome data are available on the page:  https://yongzhou2019.github.io/Rice-Population-Reference-Panel/data/

** The SNPs are called from the 3K rice genome project based on the rice population reference panel, i.e. 16 rice genome references using the GATK-HPC pipeline, which is available at wiki page:

https://github.com/IBEXCluster/Rice-Variant-Calling/wiki/  (Zhou Y, Kathiresan N, Yu Z, et al. HPC-based genome variant calling workflow (HPC-GVCW)[J]. bioRxiv, 2023: 2023.06. 25.546420).

The generation of the files required basic bioinformatics skills and tools, e.g., Plink2 (https://www.cog-genomics.org/plink/2.0/)/.

The SNP files in VCF and PLINK2.0 format are also available at the KAUST repository with DOI:https://doi.org/10.25781/KAUST-12WKO .

***The files required basic bioinformatics skills and tools, e.g.,

samtools (http://www.htslib.org/ ), IGV (https://igv.org/), Geneious (https://www.geneious.com/ ),

or Persephone (https://persephonesoft.com/ ), for further operation and visualization.

Citations:

1. 3,000 Rice Genomes Project. The 3,000 rice genomes project[J]. GigaScience, 2014, 3(1): 2047-217X-3-7.

2. Wang W, Mauleon R, Hu Z, et al. Genomic variation in 3,010 diverse accessions of Asian cultivated rice[J]. Nature, 2018, 557(7703): 43-49.

3. Zhou Y, Chebotarov D, Kudrna D, et al. A platinum standard pan-genome resource that represents the population structure of Asian rice[J]. Scientific data, 2020, 7(1): 113.)

4. Zhou Y, Yu Z, Chebotarov D, et al. Pan-genome inversion index reveals evolutionary insights into the subpopulation structure of Asian rice[J]. Nature Communications, 2023, 14(1): 1567.

5. Yu Z, Chen Y, Zhou Y, et al. Rice Gene Index: A comprehensive pan-genome database for comparative and functional genomics of Asian rice[J]. Molecular plant, 2023, 16(5): 798-801.