Data from: A dense linkage map of Lake Victoria cichlids improved the Pundamilia genome assembly and revealed a major QTL for sex-determination

Feulner PGD, Schwarzer J, Haesler MP, Meier JI, Seehausen O

Date Published: May 17, 2018

DOI: https://doi.org/10.5061/dryad.59q56g6

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Title marker position Pundamilia linkage map
Downloaded 9 times
Description Text file giving the position of 1,597 loci on the Pundamilia linkage map and the respective positions on Pundamilia and Oreochromis references
Download P_cross.MarkerPositions.txt (170.6 Kb)
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Title chain file converting P_nyererei_v1 to v2
Downloaded 3 times
Description Chain files to convert position between original (v1.0) and new reference (v2.0) of Pundamilia
Download P_nyererei_v1.To.P_nyererei_v2.chain (574.0 Kb)
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Title chain file converting P_nyererei_v2 to v1
Downloaded 2 times
Description Chain files to convert position between new reference (v2.0) and original (v1.0) of Pundamilia
Download P_nyererei_v2.To.P_nyererei_v1.chain (574.0 Kb)
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Title P_nyererei_v2 annotation
Downloaded 8 times
Description Annotation file matching reference v2.0 position based on NCBI annotation release 101
Download P_nyererei_v2.gff.gz (12.25 Mb)
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Title recombination rates Pundamilia
Downloaded 7 times
Description Text file giving the extrapolated recombination rates along Pundamilia reference genome
Download P_nyererei_v2.RecRates.txt (103.0 Kb)
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Title genotype file Pundamilia
Downloaded 52 times
Description vcf file containing 7401 genotypes of 224 Pundamilia individuals
Download P_cross.224ids.7401pos.vcf (57.03 Mb)
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Title phenotypes for Pundamilia cross
Downloaded 26 times
Description phenotypes for 224 Pundamilia individuals containing id, sex, size, and family id
Download P_cross.Pheno.txt (4.208 Kb)
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Title P_nyererei reference v2
Downloaded 6 times
Description Fasta file of the improved Pundamilia reference genome (v2.0)
Download P_nyererei_v2.fasta.gz (220.1 Mb)
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When using this data, please cite the original publication:

Feulner PGD, Schwarzer J, Haesler MP, Meier JI, Seehausen O (2018) A dense linkage map of Lake Victoria cichlids improved the Pundamilia genome assembly and revealed a major QTL for sex-determination. G3: Genes - Genomes - Genetics 8(7): 2411-2420. https://doi.org/10.1534/g3.118.200207

Additionally, please cite the Dryad data package:

Feulner PGD, Schwarzer J, Haesler MP, Meier JI, Seehausen O (2018) Data from: A dense linkage map of Lake Victoria cichlids improved the Pundamilia genome assembly and revealed a major QTL for sex-determination. Dryad Digital Repository. https://doi.org/10.5061/dryad.59q56g6
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