Supplementary files: Sequencing Ultraconserved Elements (UCEs) for Marine Population Genomics: A Proof- of-­Concept Using a Deep-­Sea Mussel Species

This study aims to employ UCE target capture sequencing to study the population genetic structure and demographic dynamics of deep-sea mussel, Gigantidas platifrons.
The supplementary files supporting this study are listed herein:

Pseudoreference and annotation: 00.pseudoref_Gpl.fasta and 00.pseudo_annotation.gff.SNP datasets: vcf1.vcf (11807 SNPs) , vcf2.vcf (8936 SNPs), vcf3.vcf (2062 SNPs), vcf4.vcf (1811 SNPs).SNP datasets with annotations: vcf1_annotated.vcf and vcf2_annotated.vcf.population information: population_4R.txt (four regions), population_6p.txt (six populations).scripts (updating): A (annotation steps and python scripts for pseudoreference), B (annotation steps and python scripts for vcf file mapped to pseudoreference), C (selection analysis: calculate pi and fst ratio and plot)A_1_Pseudo-reference_annotation.shA_2_sum_contigs_length.pyA_3_extract_contigs_info_from_blastout.pyA_4_filter_matched_blast_over_criteria.pyA_5_extract_gff_info.pyB_1_vcf_annotation.shB_2_annotate_selected_snps.pyB_3_add_geno_anno2pseudo.pyB_4_delete_column.pyC_pi_fst_selection.py