The effects of all bi-allelic SNPs (low, medium and high effects) on the genome were determined based on the pre-built release 7.0 annotation from the Rice Genome Annotation Project (http://rice.plantbiology.msu.edu/) using SnpEff51 (link) release 4.1l, with parameters -v -noLog -canon rice7. Using sequence ontology terms, a low-effect SNP was classified as ‘synonymous_variant’, ‘splice_region_variant’, ‘initiator_codon_variant’, ‘5_prime_UTR_premature_start_codon_gain_variant’ or ‘stop_retained_variant’. A moderate-effect SNP was identified as a ‘missense_variant’ and a high-effect SNP as a ‘start_lost’, ‘stop_gained’, ‘stop_lost’, ‘splice_donor_variant’ or ‘splice_acceptor_variant’. For indel effects, only indels with lengths that were not multiples of three were counted and SNPs overlapped with protein-coding regions (CDSs of RGAP 715 (link) genes) were considered as the most disruptive effects on genes. Results of the SNP and indel effect analysis are given in Supplementary Data 2 Tables 3, 4. We computed the SNP numbers (proportions) of rare SNPs and homozygous singletons for a ‘typical genome’ of a subpopulation as the median SNP number (proportion) of the SNPs in a given category among those genomes for that subpopulation (Supplementary Data 2 Table 5).
Wang W., Mauleon R., Hu Z., Chebotarov D., Tai S., Wu Z., Li M., Zheng T., Fuentes R.R., Zhang F., Mansueto L., Copetti D., Sanciangco M., Palis K.C., Xu J., Sun C., Fu B., Zhang H., Gao Y., Zhao X., Shen F., Cui X., Yu H., Li Z., Chen M., Detras J., Zhou Y., Zhang X., Zhao Y., Kudrna D., Wang C., Li R., Jia B., Lu J., He X., Dong Z., Xu J., Li Y., Wang M., Shi J., Li J., Zhang D., Lee S., Hu W., Poliakov A., Dubchak I., Ulat V.J., Borja F.N., Mendoza J.R., Ali J., Li J., Gao Q., Niu Y., Yue Z., Naredo M.E., Talag J., Wang X., Li J., Fang X., Yin Y., Glaszmann J.C., Zhang J., Li J., Hamilton R.S., Wing R.A., Ruan J., Zhang G., Wei C., Alexandrov N., McNally K.L., Li Z, & Leung H. (2018). Genomic variation in 3,010 diverse accessions of Asian cultivated rice. Nature, 557(7703), 43-49.
Corresponding Organization : Shanghai Center For Bioinformation Technology
Other organizations :
Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, International Rice Research Institute, BGI Group (China), Agricultural Genomics Institute at Shenzhen, Shanghai Jiao Tong University, China Agricultural University, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, University of Arizona, Joint Genome Institute, Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Genetic Improvement and Adaptation of Mediterranean and Tropical Plants
All bi-allelic SNPs (low, medium and high effects)
dependent variables
Effects of bi-allelic SNPs on the genome
control variables
Pre-built release 7.0 annotation from the Rice Genome Annotation Project
SnpEff release 4.1l, with parameters -v -noLog -canon rice7
Annotations
Based on most similar protocols
Etiam vel ipsum. Morbi facilisis vestibulum nisl. Praesent cursus laoreet felis. Integer adipiscing pretium orci. Nulla facilisi. Quisque posuere bibendum purus. Nulla quam mauris, cursus eget, convallis ac, molestie non, enim. Aliquam congue. Quisque sagittis nonummy sapien. Proin molestie sem vitae urna. Maecenas lorem.
As authors may omit details in methods from publication, our AI will look for missing critical information across the 5 most similar protocols.
About PubCompare
Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.
We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.
However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.
Ready to
get started?
Sign up for free.
Registration takes 20 seconds.
Available from any computer
No download required
