Supplementary Tables for the manuscript, Quantitative trait loci underlying a speciation phenotype.

Name: Supplementary Tables for the manuscript, Quantitative trait loci underlying a speciation phenotype.
Creator: figshare
Published: 2023-05-18T07:43:36+08:00

DataCite Commons2023-05-18 更新2024-09-03 收录

基因组学

QTL分析

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https://figshare.com/articles/dataset/Supplimentary_Tables_for_the_manuscript_strong_Quantitative_trait_loci_underlying_a_speciation_phenotype_strong_/22921697 数据链接链接失效反馈

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Table S1 | Summary of scaffolds associated with L. kohalensis x L. paranigra pulse rate QTL across studies. Column headers are defined as follows; scaffold: scaffold identity, size: size (in bp) of scaffold, LG: linkage group on which the scaffold falls, start_position: genomic location of start of scaffold, end_position: genomic location of end of scaffold, id_source: study in which the scaffold has been identified, peak_location_reanalysis: location (in cM) of given QTL peak in present study, scaffold_type_reanalysis: indicator of whether the scaffold is the peak scaffold or merely falls within the CI in present study, peak_location_finemap: location (in cM) of given QTL in Xu & Shaw 2019, scaffold_type_reanalysis: indicator of whether the scaffold is the peak scaffold or merely falls within the CI in Xu & Shaw 2019. Table S2 | Annotations and genomic locations of L. kohalensis transcripts (reciprocal best BLAST hits only). Column headers are defined as follows; transcript: transcript identifier, scaffold: scaffold to which the transcript maps, start: genomic location of start of transcript, stop: genomic location of end of transcript, direction: indicator of which direction the transcript is transcribed in, Entry_Name: Uniprot ID assigned to transcript, Protein_Name: Protein name associated with Uniprot_ID, Gene_Name: Gene names associated with Uniprot_ID, Gene_Ontology_IDs: GO IDs associated with Uniprot_ID, pident: percentage of identical matches, length: length (in bp) of sequence overlap, mismatch: number of mismatches, gapopen: number of gap openings, qstart: start of alignment in query, qend: end of alignment in query, sstart: start of alignment in subject, send: end of alignment in subject, evalue: expect value, bitscore: bit score. Table S3 | Annotations and genomic locations of L. paranigra transcripts (reciprocal best BLAST hits only). Column headers are defined as follows; transcript: transcript identifier, scaffold: scaffold to which the transcript maps, start: genomic location of start of transcript, stop: genomic location of end of transcript, direction: indicator of which direction the transcript is transcribed in, Entry_Name: Uniprot ID assigned to transcript, Protein_Name: Protein name associated with Uniprot_ID, Gene_Name: Gene names associated with Uniprot_ID, Gene_Ontology_IDs: GO IDs associated with Uniprot_ID, pident: percentage of identical matches, length: length (in bp) of sequence overlap, mismatch: number of mismatches, gapopen: number of gap openings, qstart: start of alignment in query, qend: end of alignment in query, sstart: start of alignment in subject, send: end of alignment in subject, evalue: expect value, bitscore: bit score. Table S4 | Annotations and genomic locations of L. kohalensis transcripts (all BLAST hits). Column headers are defined as follows; transcript: transcript identifier, scaffold: scaffold to which the transcript maps, start: genomic location of start of transcript, stop: genomic location of end of transcript, direction: indicator of which direction the transcript is transcribed in, Entry_Name: Uniprot ID assigned to transcript, Protein_Name: Protein name associated with Uniprot_ID, Gene_Name: Gene names associated with Uniprot_ID, Gene_Ontology_IDs: GO IDs associated with Uniprot_ID, pident: percentage of identical matches, length: length (in bp) of sequence overlap, mismatch: number of mismatches, gapopen: number of gap openings, qstart: start of alignment in query, qend: end of alignment in query, sstart: start of alignment in subject, send: end of alignment in subject, evalue: expect value, bitscore: bit score. Table S5 | Annotations and genomic locations of L. paranigra transcripts (all BLAST hits). Column headers are defined as follows; transcript: transcript identifier, scaffold: scaffold to which the transcript maps, start: genomic location of start of transcript, stop: genomic location of end of transcript, direction: indicator of which direction the transcript is transcribed in, Entry_Name: Uniprot ID assigned to transcript, Protein_Name: Protein name associated with Uniprot_ID, Gene_Name: Gene names associated with Uniprot_ID, Gene_Ontology_IDs: GO IDs associated with Uniprot_ID, pident: percentage of identical matches, length: length (in bp) of sequence overlap, mismatch: number of mismatches, gapopen: number of gap openings, qstart: start of alignment in query, qend: end of alignment in query, sstart: start of alignment in subject, send: end of alignment in subject, evalue: expect value, bitscore: bit score. Table S6 | Annotations, genomic locations, and QTL associations of L. kohalensis transcripts expressed on QTL scaffolds. Column headers are defined as follows; scaffold: scaffold identity, transcript: transcript identifier, start: genomic location of start of transcript, stop: genomic location of end of transcript, direction: indicator of which direction the transcript is transcribed in, Entry_Name: Uniprot ID assigned to transcript, Protein_Name: Protein name associated with Uniprot_ID, Gene_Name: Gene names associated with Uniprot_ID, pident: percentage of identical matches, length: length (in bp) of sequence overlap, mismatch: number of mismatches, gapopen: number of gap openings, qstart: start of alignment in query, qend: end of alignment in query, sstart: start of alignment in subject, send: end of alignment in subject, evalue: expect value, bitscore: bit score, size: size (in bp) of scaffold, LG: linkage group on which the scaffold falls, start_position: genomic location of start of scaffold, end_position: genomic location of end of scaffold, id_source: study in which the scaffold has been identified, peak_location_reanalysis: location (in cM) of given QTL peak in present study, scaffold_type_reanalysis: indicator of whether the scaffold is the peak scaffold or merely falls within the CI in present study, peak_location_finemap: location (in cM) of given QTL in Xu & Shaw 2019, scaffold_type_reanalysis: indicator of whether the scaffold is the peak scaffold or merely falls within the CI in Xu & Shaw 2019. Table S7 | Annotations, genomic locations, and QTL associations of L. paranigra transcripts expressed on QTL scaffolds. Column headers are defined as follows; scaffold: scaffold identity, transcript: transcript identifier, start: genomic location of start of transcript, stop: genomic location of end of transcript, direction: indicator of which direction the transcript is transcribed in, Entry_Name: Uniprot ID assigned to transcript, Protein_Name: Protein name associated with Uniprot_ID, Gene_Name: Gene names associated with Uniprot_ID, pident: percentage of identical matches, length: length (in bp) of sequence overlap, mismatch: number of mismatches, gapopen: number of gap openings, qstart: start of alignment in query, qend: end of alignment in query, sstart: start of alignment in subject, send: end of alignment in subject, evalue: expect value, bitscore: bit score, size: size (in bp) of scaffold, LG: linkage group on which the scaffold falls, start_position: genomic location of start of scaffold, end_position: genomic location of end of scaffold, id_source: study in which the scaffold has been identified, peak_location_reanalysis: location (in cM) of given QTL peak in present study, scaffold_type_reanalysis: indicator of whether the scaffold is the peak scaffold or merely falls within the CI in present study, peak_location_finemap: location (in cM) of given QTL in Xu & Shaw 2019, scaffold_type_reanalysis: indicator of whether the scaffold is the peak scaffold or merely falls within the CI in Xu & Shaw 2019. Table S8 | Genes associated with enriched GO terms in pulse rate QTL. Column headers are defined as follows; Go Term: Gene Ontology term, Species: species from which the reads came, Transcript: Transcript ID, Uniprot ID: Uniprot code associated with transcript, Protein Name: Protein name associated with Uniprot ID, scaffold: scaffold identity, LG: linkage group on which the scaffold falls.

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figshare

创建时间：

2023-05-18

搜集汇总

数据集介绍

Supplementary Tables for the manuscript, <strong>Quantitative trait loci underlying a speciation phenotype.</strong> 数据集图片

背景与挑战

背景概述

该数据集为论文《Quantitative trait loci underlying a speciation phenotype》的补充表格，包含9个表格，主要提供了L. kohalensis和L. paranigra两种物种的脉冲率数量性状位点（QTL）相关支架信息、转录本注释和基因组位置数据，以及基因本体论（GO）术语富集分析结果。数据集发布于2023年，聚焦于行为遗传学和分子进化领域，支持RNAseq实验和QTL研究，使用CC BY 4.0开放许可。

以上内容由遇见数据集搜集并总结生成

Supplementary Tables for the manuscript, <strong>Quantitative trait loci underlying a speciation phenotype.</strong>

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