2026-10-11 https://api.researchdata.se/oai-pmh

oai:researchdata.se:doi-10-17044-scilifelab-22817410/0 2024-03-28 subject:ssif:3 subject:ssif:10609 subject:ssif:106 subject:ssif:1 subject:ssif:10611 principal:slug:uppsala-university

info:eu-repo/semantics/other http://purl.org/dc/dcmitype/Dataset https://doi.org/10.17044/SCILIFELAB.22817410 7. Ecological genomics of the Northern krill: Genome-scale comparisons of adaptive divergence https://orcid.org/0000-0002-9081-9663 Per Unneberg Medical and Health Sciences Medicin och hälsovetenskap Genetics and Genomics Genetik och genomik Biological Sciences Biologi Ecology Ekologi This item holds multiple tar archives with genome-scale comparisons of divergence between Northern krill populations, including estimated allele-frequencies and divergence (e.g. FST) , and extended haplotype signatures (XP-nSL estimates). Many analyses were performed in "chunks" (160 in total across both gene-rich and gene-poor sequences), which are described in a previous item. Population definitions Population definitions are the same as desribed in a different item: - "at vs. me" = Atlantic Ocean samples (n=67) vs. the Mediterranean (i.e. Barcelona) samples (n=7). - "we vs. ea" = South-West North Atlantic Ocean (n=20) vs. North-East North Atlantic Ocean (n=47). In files using this contrast, sometimes the label "wa" is used instead of "we" for the South-West North Atlantic Ocean samples. Contents: - allele_freqs_fst.gene_rich_sequences.at_vs_me.tar, contains per-SNP estimates of allele frequencies and FST between "at" and "me" groups along gene-rich sequences. - allele_freqs_fst.gene_rich_sequences.we_vs_ea.tar, as above but between "we" and "ea" groups. - allele_freqs_fst.gene_poor_sequences.at_vs_me.tar, contains per-SNP estimates of allele frequencies and FST between "at" and "me" groups along gene-poor sequences. - allele_freqs_fst.gene_poor_sequences.we_vs_ea.tar, as above but for "we" and "ea" groups. - allele_freqs_fst.merged_sequences.at_vs_me.csv.gz, contains per-SNP estimates of allele frequencies and FST between "at" and "me" merged into a single TSV file. - allele_freqs_fst.merged_sequences.we_vs_ea.csv.gz, as above but for "we" and "ea". - allele_freqs_fst.gene_rich_sequences_windows.at_vs_me.tar.gz, contains per-window estimates of FST between "at" and "me" groups along gene-rich sequences. - allele_freqs_fst.gene_rich_sequences_windows.we_vs_ea.tar.gz, as above but for "we" and "ea" groups. - allele_freqs_fst.gene_poor_sequences_windows.at_vs_me.tar.gz, contains per-window estimates of FST between "at" and "me" groups along gene-poor sequences. - allele_freqs_fst.gene_poor_sequences_windows.we_vs_ea.tar.gz, as above but for "we" and "ea" groups. - selscan_xpnsl.gene_rich_sequences.tar.gz, contains per-SNP cross-population XP-nSL statistics for gene-rich sequences. - selscan_xpnsl.gene_poor_sequences.tar.gz, contains per-SNP cross-population XP-nSL statistics for gene-poor sequences. - selscan_xpnsl.gene_rich_sequences_windows.tar.gz, contains per-window cross-population XP-nSL statistics for gene-rich sequences. - selscan_xpnsl.gene_poor_sequences_windows.tar.gz, as above but for gene-poor sequences. - fst_vs_xpnsl.per_snp.at_vs_me.csv.gz, contains per-SNP FST, genomic region and XP-nSL values in a single file for the "at vs. me" contrast. - fst_vs_xpnsl.per_snp.we_vs_ea.csv.gz, contains per-SNP FST, genomic region and XP-nSL values in a single file for the "we vs. ea" contrast. - fst_vs_xpnsl_vs_diversity_vs_regions.merged_sequences.at_vs_me.tsv.tar.gz, integrates window-based statistics into a single file for the "at vs. me" contrast. - fst_vs_xpnsl_vs_diversity_vs_regions.merged_sequences.we_vs_ea.tsv.tar.gz, as above but for the "we vs. ea" contrast. allele_freqs_fst.gene_(rich|poor)_sequences.(at_vs_me|we_vs_ea).tar The TSV files in these archives contain per-SNP estimates of allele frequencies and FST, along with SNP annotations. There are nine main fields/columns with overlapping/redundant information to accommodate flexible parsing. Large fields have nested subfields that are separated by "|" (first level) or ":" (second level). - name of sequence (e.g. "seq_s_1") - position of SNP (e.g. "448878") - reference allele (e.g. "A") - alternate allele (e.g. "G") - major column with FST value and allele frequency and other data for each population. It is described below. - type of SNP (e.g. intron, synonymous, missense, intergenic, ...) and label of associated gene (e.g. missense|REF_STRG_1_4_XLOC_012878) - FST tag and value (e.g. fst|0.0653) - region, type of SNP and gene label (e.g. region|missense|REF_STRG_1_4_XLOC_012878) - gene annotation derived from EnTAP annotations and Drosophila homologs, which are described below. Uses comma-separated sub-fields. Subfields in field 5: Example: at/me:0.0653:148:1.0000:1.0000:1.0000|at,134,133.0000,1.0000,0.9925,0.0075|me,14,13.0000,1.0000,0.9286,0.0714 This field splits into three major subfields on "|": one about the pairwise comparison and two with metadata about each population. 1st subfield (at/me:0.0653:148:1.0000:1.0000:1.0000) - name of contrast (at/me) - FST of SNP (0.0653) - Sample size (148) - Proportion of observed data given overall sample size (1.0000), https://creativecommons.org/licenses/by/4.0/ Uppsala University Uppsala universitet 2024-03-27T00:00:00Z