The rice_3K_genomes_feb2015_reffix.vcf.gz is a corrected version of the file rice_3K_genomes_feb2015_reffix.vcf.gz, which corresponds to a VCF conversion that Gramene did from the 3kRG 400k CoreSNP Dataset (PLINK format) downloaded from OryzaSNP at http://oryzasnp-atcg-irri-org.s3-website-ap-southeast-1.amazonaws.com/  The PLINK file description indicated that it was mapped to the MSU7/IRGSP1.0 genome.  However, looks like the PLINK recode step had introduced a systematic mapping error by picking the 2nd allele (of possibly a random sample) as the reference base.  Our Ensembl Genome collaborators identified the problem and have corrected it in the resulting _reffix VCF file.