Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
, 45 (D1), D1075-D1081

Rice SNP-seek Database Update: New SNPs, Indels, and Queries


Rice SNP-seek Database Update: New SNPs, Indels, and Queries

Locedie Mansueto et al. Nucleic Acids Res.


We describe updates to the Rice SNP-Seek Database since its first release. We ran a new SNP-calling pipeline followed by filtering that resulted in complete, base, filtered and core SNP datasets. Besides the Nipponbare reference genome, the pipeline was run on genome assemblies of IR 64, 93-11, DJ 123 and Kasalath. New genotype query and display features are added for reference assemblies, SNP datasets and indels. JBrowse now displays BAM, VCF and other annotation tracks, the additional genome assemblies and an embedded VISTA genome comparison viewer. Middleware is redesigned for improved performance by using a hybrid of HDF5 and RDMS for genotype storage. Query modules for genotypes, varieties and genes are improved to handle various constraints. An integrated list manager allows the user to pass query parameters for further analysis. The SNP Annotator adds traits, ontology terms, effects and interactions to markers in a list. Web-service calls were implemented to access most data. These features enable seamless querying of SNP-Seek across various biological entities, a step toward semi-automated gene-trait association discovery. URL:


Figure 1.
Figure 1.
Genotype query options (A) and results table (B) with multiple reference genomes alleles. The selected reference genome (Nipponbare) is displayed at the top header row just below the SNP positions. The alleles for the other genomes (Kasalath, DJ 123, IR 64, 93-11) are shown below in the table header. The corresponding positions in the other genomes are displayed in the message box.
Figure 2.
Figure 2.
Genotype matrix with short indels. The table displays deletions (positions in blue) at anchor positions (region): 27698 (27699), 27791 (27792–27794), 27836 (27837–27841). Insertion regions (positions in green) are at 27722.01 27722.04 and 27797.01. For deletion regions, the reference is copied from the reference genome, while for insertions the reference genome is set to gaps.
Figure 3.
Figure 3.
Allele frequency chart with major/minor allele/genotype frequency/count at each SNP position in the queried region for all or each subpopulation.
Figure 4.
Figure 4.
Query capabilities of SNP-Seek. The blocks at the left (rounded) are possible query constraints to the query modules (rectangles). The query results may be stored as a list (parallelograms), and used as constraints in further queries. Lists may also be created by the user as initial constraints. The marker annotator accepts a list of SNP positions, which may be the result from experiments or GWAS studies, to generate constraints for further queries or loop back to the initial constraints, increasing the confidence of the association.

Similar articles

See all similar articles

Cited by 37 articles

See all "Cited by" articles


    1. Sherry S.T., Ward M.H., Kholodov M., Baker J., Phan L., Smigielski E.M., Sirotkin K. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2001;29:308–311. - PMC - PubMed
    1. Tello-Ruiz M.K., Stein J., Wei S., Preece J., Olson A., Naithani S., Amarasinghe V., Dharmawardhana P., Jiao Y., Mulvaney J., et al. Gramene 2016: Comparative plant genomics and pathway resources. Nucleic Acids Res. 2016;44:D1133–D1140. - PMC - PubMed
    1. Zhao H., Yao W., Ouyang Y., Yang W., Wang G., Lian X., Xing Y., Chen L., Xie W. RiceVarMap: a comprehensive database of rice genomic variations. Nucleic Acids Res. 2015;43:D1018–D1022. - PMC - PubMed
    1. The IC4R Consortium. Information Commons for Rice (IC4R) Nucleic Acids Res. 2015;44:D1172–D1180. - PMC - PubMed
    1. Zheng T., Yu H., Zhang H., Wu Z., Wang W., Tai S., Chi L., Ruan J., Wei C., Shi J., et al. Rice functional genomics and breeding database (RFGB)-3K-rice SNP and InDel sub-database. Chinese Sci. Bull. 2015;60:367.

Publication types