Additional file 1 of Deep whole-genome resequencing sheds light on the distribution and effect of amphioxus SNPs

Additional file 1: Data S1. Protein-coding sequences and annotation of the haploid reference genome. Data S2. Samples for AlphaFold2 analysis. Fig S1. Pie charts of SNPs detected in each type of genomic region in amphioxus of different sexes. Fig S2. Statistics of COG functional classes of top-1000 genes with largest number of synonymous variants (a), missense variants (b), and intron variants (c). A: RNA processing and modification; B: Chromatin structure and dynamics; C: Energy production and conversion; D: Cell cycle control, cell division, chromosome partitioning; E: Amino acid transport and metabolism; F: Nucleotide transport and metabolism; G: Carbohydrate transport and metabolism; H: Coenzyme transport and metabolism; I: Lipid transport and metabolism; J: Translation, ribosomal structure and biogenesis; K: Transcription; L: Replication, recombination and repair; M: Cell wall/membrane/envelope biogenesis; N: Cell motility; O: Posttranslational modification, protein turnover, chaperones; P: Inorganic ion transport and metabolism; Q: Secondary metabolites biosynthesis, transport and catabolism; R: General function prediction only; S: Function unknown; T: Signal transduction mechanisms; U: Intracellular trafficking, secretion, and vesicular transport; V: Defense mechanisms; W: Extracellular structures; X: Unnamed protein; Y: Nuclear structure; Z: Cytoskeleton. Fig S3. Box plot of total pN/pS ratio distribution. Table S1. Number of common SNPs on each chromosome. Table S2. Number of variants affecting each gene calculated via SnpEff. Table S3. Statistics of SNPs detected in each type of genomic region in each amphioxus sample. Table S4. Full tables of GO enrichment results.