The genome sequencing data of 1614 B. juncea accessions were all mapped to the reference genome T84-66.V2.0 (Yang et al., 2021). After genotype imputation and quality control (MAF > 0.05, missing < 0.1, Heterozygosity rate < 0.5), 7,068,964 SNPs and 1,800,892 InDels were obtained. Users can query variations and access detailed information such as allele frequency and annotation in this module. Additionally, it also provides an evaluation of the effects of variants/haplotypes on phenotypes and gene expression levels by combining phenotypes and gene expression data in the "Single-locus model" . Moreover, the "Variations" module includes a "Multi-locus model" interface to examine genetic interactions between loci and their effects on phenotypes and gene expression levels.

References
1. Yang, J., Wang, J., Li, Z., Li, X., He, Z., Zhang, L., Sha, T., Lyu, X., Chen, S., Gu, Y. et al. (2021). Genomic signatures of vegetable and oilseed allopolyploid Brassica juncea and genetic loci controlling the accumulation of glucosinolates. Plant Biotechnol. J. 19: 2619-2628.