Supplementary tables for: Natural selection outweighs genetic drift at Toll-like receptor (TLR) genes in the populations of Galápagos mockingbirds

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:Supporting information 2 - amplicon statistics.tsv<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>Supporting information 3 - amplicon frequency.tsvThe 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>Supporting information 4 - genebank accession numbers.tsvThe file contains link between accession number in Genebank database and haplotype name (Allele name) used in genotype table (next file). <br>Supporting information 5 - individuals and their genotypes.tsvThis 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>Supporting information 6 multiqc_report.html<br>Multiqc report of amplicon dataset after trimmomatic filtering.本数据集包含一篇关于加拉帕戈斯嘲鸫（Galapagos mockingbirds）Toll样受体（Toll-like receptor, TLR）多样性的学术手稿的辅助实验数据。本研究通过双端Illumina扩增子测序技术，对3种Toll样受体（TLR1B、TLR4及TLR15）进行了测序，本次提交的文件包含各嘲鸫个体的序列质量、基因分型结果及优化后基因型的相关信息。更多实验方法细节可参阅即将正式发表的该手稿。 ### 文件说明： 1. 辅助信息2 - amplicon statistics.tsv 本文件包含每个扩增子（PCR_ID）对应的测序数据各项统计指标，各列信息如下：原始测序读对数量（Raw_read_pairs）、经Trimmomatic过滤后保留的读对数量（both_survived）、该类读对占总读对的百分比（bs_perc）、经过滤后保留的单端正向读段数量（F_survived）及其占比（Fs_perc）、经过滤后保留的单端反向读段数量（R_survived）及其占比（Rs_perc）、未通过质量过滤的读段数量（dropped）及其占比（drop_perc）、平均序列长度（avg_sequence_length）及长度范围（Length_range）、优化后序列总数量（Total Sequences）以及GC含量（%GC）。 2. 辅助信息3 - amplicon frequency.tsv 本文件记录了每个Toll样受体扩增子（AMPLICON_ID）对应的独特单倍型数量，并展示了5种频率最高的单倍型的占比（Frequency_{1..5}）。若第二高频单倍型与第一高频单倍型的频率比（ratio_second_first）高于1/3，则判定该基因座为杂合型。 3. 辅助信息4 - GenBank accession numbers.tsv 本文件建立了GenBank数据库中的登录号与后续基因型表格中使用的单倍型名称（等位基因名称）之间的对应关系。 4. 辅助信息5 - individuals and their genotypes.tsv 本文件包含隶属于特定岛屿种群的每个个体（样本名）的Toll样受体基因型信息。基因型相关信息（如TLR1Ballele-1、TLR1Ballele-2等）与存储于GenBank的单倍型序列结合，可用于重建种群水平数据集。 5. 辅助信息6 multiqc_report.html 本文件为经Trimmomatic过滤后的扩增子数据集的MultiQC质控报告。