24 research outputs found
Miller & Coltman HFC Study Database
Population specific effect size and g2 estimates, along with covariates
BLAST results
Top BLAST results of consensus contigs extracted from the .bam file. blastx+ 2.2.27 was used with an e-value threshold of 0.000001 against a custom database of RefSeq eutherian protein sequences
Trimmed Un-mapped Data assembly
Resultant BAM file from a pool of rRNA-depleted, non-normalized cDNA of six white-tailed deer from the University of Saskatchewan's Specialized Livestock Research Facility that was assembled de novo in CLC Genomics Workbench 6.0.1
White-tailed deer SNPs (VCF file)
We detected SNPs using CLC’s quality-based variant detection algorithm (min. average quality of five flanking bases on either side of SNP = 15; min. quality of central base = 20; min. coverage = 20; max. coverage = 1000; min. variant frequency = 15%; min. variant count = 4), discarding all reads with non-specific alignments. Multiallelic SNPs were discarded as they may result from incorrect alignment of reads from paralogous genes in the transcriptome data. All SNPs have been submitted to dbSNP and will be available online in the October 2013 update. This VCF file is available in the interim
dbSNP ss Accession Numbers
List of SNP ss accession numbers detected in the assembly using CLC Genomics Workbench 6.0.1. These SNPs will be available online in the next dbSNP update, currently scheduled for Oct. 2013
pedigree
Description: Pedigree of the population of bighorn sheep (Ovis canadensis), located at Ram Moutnain, Alberta, Canada(52°8’N, 115°8’W, elevation 1082 to 2173 m). NA is used for missing values
Columns:
Id: id of the animal
dam: id of the dam
sire: id of the sir
phenotypic data
Description: Phenotypic measurement and covariates used for animal model and for estimation of the genetic covariance of trait with fitness. The population of bighorn sheep (Ovis canadensis) is located at Ram Moutnain, Alberta, Canada(52°8’N, 115°8’W, elevation 1082 to 2173 m). Measurements where taken between 1973 and 2013. Animals aged 13 and older where grouped for analysis due to small sample size. Animals translocated from the Cadomin population where excluded. NA is used for missing values
Columns:
ID: unique identifier for each animal.
yr: year of measurement.
age: age at measurement.
sex: sex of animal(1=male, 0=female).
cohort: year of birth.
hlM: horn length of males aged 2 to 5 in cm adjusted to 15 September.
hlF: horn length of females aged 2 to 5 in cm adjusted to 15 September.
Avhb114M: horn base of males aged 2 to 5 in cm adjusted to 15 September.
Avhb114F: horn base of females in cm adjusted to 15 September.
relLongM: relative longevity of males. Longevity divided by the mean longevity of males of the same cohort.
relLongF: relative longevity of females. Longevity divided by the mean longevity of females of the same cohort
Janes et. al. (2015). Heredity - Polygamy and fine-scale structure of mountain pine beetle
This file contains individual, population, geographic, sex and life stage information for samples. The alleles for each SNP and a corresponding 200 base sequence for each are provided also. Accession numbers for SNPs previously used in Janes et al. (2014). How the mountain pine beetle (Dendroctonus ponderosae) breached the Canadian Rocky Mountains. Molecular Biology and Evolution. 31(7):1803-1815 are supplied in the dbSNP format
nacanids_unrel_42Ksnps_CoatColor_wYNP_n33_white.tfam
PLINK formatted TFAM file with coat color genotype for each of 33 wolves. Individuals coded as a 2 are white, individuals coded as a 1 are not white (can be black or gray)