Dataset for "High intraspecies allelic diversity in Arabidopsis NLR immune receptors is associated with distinct genomic and epigenomic features "
Authors/Creators
- 1. Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA 94720
- 2. Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA 94720
- 3. Department of Plant Sciences, University of California Davis, Davis, CA, USA 95616
Description
Data generated associated with understanding the features of NLRs in Arabidopsis Col-0.
Contains:
-all_gene_table.xslx: %CG gene body methylation, log2(TPM), distance to nearest TE, Pi (normalized by bp and by effective site), Tajima's D for all genes
-working_table.xslx: cluster status, N-terminal domain class, and genome position of NLRs
-Athaliana_NLR_entropy: Shannon entropy calculated per sequence of Athaliana NLRs
-egglib_window_stats: Pi and D calculated over 300bp windows, 75bp step of all NLRs
-popgen_per_domain: Pi, D, PiS, and PiN calculated by domain of all NLRs
-positive_selection: proportion of sites under positive selection estimated by MEME and FEL at a posterior probability > 0.95, corrected for multiple hypothesis testing
-nlr_aa_annotation: alignment position based annotation of domains
-nlrome_IDs.txt: IDs of accessions used to make VCF files for whole genome popgen analysis
-The CHH, CHG, and CG bigwig files
-Simulated RNAseq reads generated using Polyester
-iTOL annotation files
Files
egglib_window_stats.csv
Files
(2.8 GB)
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