DOI: 10.6084/m9.figshare.12180027
title: Supplementary tables for: Effect of population size and selection on Toll-like receptor diversity in populations of Galápagos mockingbirds

description: The files contain supporting data for a manuscript about Toll-like receptor diversity in Galapagos mockingbirds. In this project we sequenced three Toll-like receptors (TLR1B, TLR4 and TLR15) by pair-end Illumina amplicon sequencing and the files presented here contain information about the sequence quality, genotyping and refined genotypes of individual mockingbirds. More details about methods can be found in the manuscript that will be published soon. <br> Description of the files: <strong>Supporting information 1 - sequences of preliminary TLR screening by Sanger sequencing</strong> <br> Variants of TLR genes ascribed by preliminary sanger sequencing. The file is in genbank format. <br> <strong>Supporting information 2 - amplicon statistics.tsv</strong><br> This file contains various statistics of sequencing data presented per each amplicon (PCR_ID). The columns contain: number of raw sequencing reads (Raw_read_pairs), number of read pairs that survived trimmomatic filtering (both_survived), percentage of those reads from total (bs_perc), number of forward only reads that survived trimmomatic filtering (F_survived), their percentage (Fs_perc), number of reverse only reads that survived trimmomatic filtering (R_survived), their percentage (Rs_perc), number of reads that did not pass quality filtering (dropped), percentage of dropped reads( drop_perc), average sequence length (avg_sequence_length) and its range (Length_range), total number of refined sequences (Total Sequences), GC content (%GC). <br> <strong>Supporting information 3 - amplicon frequency.tsv</strong> The file presents number of unique haplotypes per each TLR amplicon (AMPLICON_ID). The frequency of the five most frequent haplotypes shown (Frequency_{1..5}). If the ratio of frequencies of second to first haplotype (ratio_second_first) was higher then 1/3 we considered the locus heterozygous. <br> <strong>Supporting information 4 - genebank accession numbers.tsv</strong> The file contains link between accession number in Genebank database and haplotype name (Allele name) used in genotype table (next file). <br> <strong>Supporting information 5 - individuals and their genotypes.tsv</strong> This file contains TLR genotypes for each individual (sample name) belonging to particular island (population). Information about genotype (TLR1Ballele-1, TLR1Ballele-2, etc.) together with haplotype sequences stored in Genebank data can be used for recovery of the population level dataset. <br> <br> <strong>Supporting information 6 multiqc_report.html</strong><br> Multiqc report of amplicon dataset after trimmomatic filtering. <br> <strong>Supporting information 7 - Segregating aminoacids in TLR4 and their physicochemical properties.tsv</strong> <br> Tables with four indices of amino acid physicochemical properties for segregating amino acids in TLR4. <br> <strong>Supporting information 8 - Segregating aminoacids in TLR1B and their physicochemical properties.tsv</strong> <br> Tables with four indices of amino acid physicochemical properties for segregating amino acids in TLR1B. <br> <strong>Supporting information 9 - Segregating aminoacids in TLR15 and their physicochemical properties.ts</strong>v <br> Tables with four indices of amino acid physicochemical properties for segregating amino acids in TLR15. <br> <strong>Supporting information 10 - models of protein strucuture for TLR4 variants.zip</strong> <br> Results of modelling protein strucuture for all variants of TLR4 gene in program ittaser. <br> <strong>Supporting information 11 - models of protein strucuture for TLR15 variants.zip</strong> <br> Results of modelling protein strucuture for all variants of TLR15 gene in program ittaser. <br> <strong>Supporting information 12 - surface charge analysis in PIPSA.zip</strong> <br> Results of surface charge analysis by program PIPSA. The zip file contains results for each TLR. <br> <strong>Supporting information 13 - RMSD matrices for TLR1B, TLR4 and TLR15.zip</strong> <br> Root-mean-square deviation of atomic positions (RMSD) among protein variants for all three toll-like receptors. <br> <br> <br>