19 research outputs found

    RAD_baimaii_BLAT

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    BLAT results against the A. dirus draft genom (https://olive.broadinstitute.org/genomes/anop_diru_wrair2.1). Contains results from both RAD landscape genomics loci and the linkage map. Loci denoted with a "u" means the loci are unique to the linkage map

    RAD_baimaii_filtered_SNPs

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    This file contains all bi-allelic SNPs with a minimum allele frequency>0.1 from the RAD sequence data set: RAD_baimaii_filtered_fullsequence.tsv. The first part of the locus name give the RAD locus and the second part (after ".") gives the position of the SNP (starting from 1) along the 96 bp sequence. 3828 loci and 184 individuals

    RAD_baimaii_RAW_numbers

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    This file contains RAW data from the software STACKS containing stack depths for the RAD genotypes for Anopheles baimaii. The file "RAD_baimaii_RAW_alleles" contains the corresponding alleles. These two files provided the raw data for quality filtering of the RAD sequence data set as described in the original paper. See also STACKs documentation for more details

    RAD_baimaii_filtered

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    Contains the filtered Anopheles baimaii RAD sequence data set. (184 individuals and 3008 RAD loci). The rad sequence here contains only sites that were polymorphic in the RAW data (e.g. file "RAD_baimaii_RAW_alleles.tsv"). Monomorphic loci have alleles called "consensus"

    RAD_baimaii_RAW_alleles

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    This file contains RAW data from the software STACKS containing the RAD genotypes. The file "RAD_baimaii_RAW_numbers" contains the corresponding stack depths for each allele and these provided the raw data for quality filtering of the RAD sequence data set as described in the original paper. See also STACKs documentation for more details

    RAD_baimaii_Rqtl

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    RData file that contains all necessary information for the Anopheles baimaii linkage map. See documentation for the R-package 'qtl' for more info
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