Supplementary Data of "Introgression between highly divergent sea squirt genomes: an adaptive breakthrough?"

<strong>Datasets used in the analyses (see Table S5 for a detailed description).</strong> ► Dataset #1: phased SNPs with offspring.<br> joint_bwa_mem_mdup_IR_recal_variants_refine_HQ_denovo_Oad18ad31ad2.clean.biallelic.noindels_filter_phased_phasedBeagle.vcf<br> ► Dataset #2: all SNPs with missing data.<br> joint_bwa_mem_mdup_IR_recal_variants_refine_HQ_denovo_Oad18ad31ad2.clean.biallelic.noindels_filter_parents_oNA5.vcf<br> ► Dataset #3a: phased SNPs.<br> joint_bwa_mem_mdup_IR_recal_variants_refine_HQ_denovo_Oad18ad31ad2.clean.biallelic.noindels_filter_phased_phasedBeagle_parents.vcf<br> ► Dataset #3b: CDS version of “phased SNPs”.<br> joint_bwa_mem_mdup_IR_recal_variants_refine_HQ_denovo_Oad18ad31ad2.clean.biallelic.noindels_filter_phased_phasedBeagle_parents_SNP_CHRall.orf.cds<br> ► Dataset #3c: FASTA version of “phased SNPs”.<br> joint_bwa_mem_mdup_IR_recal_variants_refine_HQ_denovo_Oad18ad31ad2.clean.biallelic.noindels_filter_phased_phasedBeagle_parents_SNP_chr5.sub_${START}-${END}.fasta<br> ► Dataset #4: ancestry informative phased SNPs.<br> joint_bwa_mem_mdup_IR_recal_variants_refine_HQ_denovo_Oad18ad31ad2.clean.biallelic.noindels_filter_phased_phasedBeagle_parents.frq.fixed.vcf<br> ► Dataset #5: all SNPs.<br> joint_bwa_mem_mdup_IR_recal_variants_refine_HQ_denovo_Oad18ad31ad2.clean.biallelic.noindels_filter_parents_oNA.vcf<br> ► Dataset #6: all polarized SNPs.<br> joint_bwa_mem_mdup_IR_recal_variants_refine_HQ_denovo_Oad18ad31ad2.clean.biallelic.noindels_filter_parents_raw_refine_HQ_edwardsi_oNA3_polar.vcf<br> ► Dataset #7: unfiltered mapping files.<br> ciona_bwa-mapping_${IND}_bwa_mem_mdup_IR_chromosome5:700000-1500000_sorted_nodup.bam