DOI: 10.6084/m9.figshare.5002562
title: G3/2017/044198

description: Data for publication G3/2017/044198 on Red deer linkage mapping. The pipeline for analysis is archived at https://github.com/susjoh/DeerMapv4. The data provided can be input into the pipeline at script 2.0_Crimap_Run_Initial_a.R and run sequentially.<br>All IDs have been recoded in order to be run in the Crimap software, and so should not be merged with other datasets. They comprise the individuals used for linkage mapping analysis only.<br><br>Deer31_QC.RData is the genotype and sex data in R/GenABEL format for all deer after basic quality control. <br>Pseudoautosomal_SNPs.txt is a list of all SNPs in the pseudoautosomal region on the X chromosome.<br>Pedigree_16-05-02.recoded.txt is the raw pedigree data.<br>3_Deer_Sequences.fa is the flanking sequence information for each SNP locus.<br>Table S1: Rum red deer (\textit{Cervus elaphus}) linkage map after Build 5. Column headers are as follows: SNP.Name = SNP Name, BTA.Chr = cattle chromosome, BTA.Position = cattle base pair position (BTA UMD v3.0), CEL.LG = Deer linkage group, CEL.Order = Marker order on deer linkage group, cMPosition.SexAveraged = sex-averaged linkage map position (cM), cMPosition.Female = female linkage map position (cM), cMPosition.Male = male linkage map position (cM), Skeleton.SNP = indicates if SNP is included in the skeleton map (see main text), PAR = indicates if SNP is in the pseudoautosomal region, Estimated.Mb.Position = the estimated genomic position on the deer genome (see methods), inf.mei = number of informative meioses, inf.mei.PK = number of informative meioses where grandparental phase was known, tot\_f = number of informative meioses in females, tot\_m = number of informative meioses in males, pk\_f = number of informative meioses in females with phase known, pk\_f = number of informative meioses in males with phase known, A1 = major reference allele, A2 = minor reference allele, CallRate = SNP call rate in original dataset (N$_{IDS}$ = 2361), Q.2 = minor allele frequency, PseudoAutosomalSNP = indicates if sex-linked SNPs (CEL34) are in the pseudoautosomal region.<br><br>Table S2: Data for Figure S5, comparison of map positions between Cattle (bp, build vUMD 3.0), Deer (cM, Build 5) and Sheep (bp, build Oar\_v3.1) for the X chromosome. Window.Start = cM position of the start of the window of most likely position, Window.Stop = cM position of the end of the window, CEL.LG = Deer linkage group identifier, SNP.Start = First mapped SNP at the start cM position, SNP.Stop = Last mapped SNP at the end cM position, chunk = chunk identifier, SNP.Start.Of.Chromosome = Indicates if the most likely position is at the beginning of the chromosome, SNP.End.Of.Chromosome = Indicates if the most likely position is at the end of the chromosome, Unmap.SNP.vec = Vector of SNPs within the unmapped chunk.<br>Table S3: Probabilities of crossing over within 1Mb windows in males and females.Column headers are as follows: CEL.LG = Deer linkage group identifier, Window = Window order, Start = Mb position of the start of the window, Stop = Mb position of the end of the window, Locus.Count & Number of loci within the window, Mean.Inf.Count = Mean number of informative loci, cM = Sex-averaged recombination rate, cM.Male = Male recombination rate, cM.Female = Female recombination rate, Window.To.End = Window order from the other end of the chromosomes, FM.Rate = Ratio of female to male recombination rate, adj.cM = Sex-averaged recombination rate adjusted for chromosome size, adj.cM.Male & Male recombination rate adjusted for chromosome size, adj.cM.Female = Female recombination rate adjusted for chromosome size, adj.FM.Rate = Ratio of female to male recombination rate adjusted for chromosome size. <br><br>Table S4: Probabilities of crossing over within 1Mb windows in males and females. Column headers are as follows: CEL.LG & Deer linkage group identifier, Window = Window order, Start = Mb position of the start of the window, Stop = Mb position of the end of the window, Locus.Count = Number of loci within the window, Mean.Inf.Count = Mean number of informative loci, cM = Sex-averaged recombination rate, cM.Male = Male recombination rate, cM.Female = Female recombination rate, Window.To.End = Window order from the other end of the chromosomes, FM.Rate = Ratio of female to male recombination rate, adj.cM = Sex-averaged recombination rate adjusted for chromosome size, adj.cM.Male = Male recombination rate adjusted for chromosome size, adj.cM.Female = Female recombination rate adjusted for chromosome size, adj.FM.Rate = Ratio of female to male recombination rate adjusted for chromosome size.<br>Table S5: BLAST results for SNP flanking sequences in the Deer against the Sheep (Oar\_v3.1) and Cattle (Btau\_4.6.1) genomes in order to determine lineage of origin. Column headers are as follows: Locus\_Name = SNP ID, Species = Reference sequence, Ovis or Bos for sheep and cattle, respectively., bit = Bit score of local alignment., Chr = Reference species chromosome., PCmatch = Percentage match between query and reference sequences., matches = Number of matching bases between query and reference sequences., mismatches = Number of mismatching bases between query and reference sequences., gaps = Number of gaps between query and reference sequences., SeqStart = Query sequence start position., SeqSto = Query sequence stop position., ChrStart = Reference sequence start position., ChrStop = Reference sequence stop position., eval = Expect value (E): the number of hits one can expect to see by chance when searching a database of a particular size., Ncount = Number of unknown bases in the deer query sequence., Informative.Length = Number of known bases in the deer query sequence., PCmatch.Full = Percentage of matches at known bases., Count = Number of independent hits for the query sequence., BTA3Chr = Chromosome on cattle genome version vUMD3.0., BTA3Position = Position on cattle genome version vUMD3.0., CEL.LG = Deer linkage group., cMPosition.run5 = Deer build 5 centimorgan position.<br>Table S6: Raw data and results for binomial tests for the transmission distortion analysis. Alleles were assigned as A or B as the first and second reference allele in the GenABEL files. Column headers are as follows: A.Count & Number of A alleles transmitted from FID to offspring, SNP.Name = SNP ID, Parent = Indicates if FID was the father or mother, Geno.Count = Number of informative transmissions, P.val = P-value from the exact binomial test, CEL.order = The order of SNPs on the linkage group, CEL.LG = Linkage group, Fission = The fission/fusion history of the chromosomes, cMPosition.run5 = Deer build 5 centimorgan position., Dummy.Position = The estimated genomic position on the deer genome, Bin = 1Mb Window in which the SNP falls.