Open Access Research article

High-resolution autosomal radiation hybrid maps of the pig genome and their contribution to the genome sequence assembly

Bertrand Servin1*, Thomas Faraut1, Nathalie Iannuccelli1, Diana Zelenika2 and Denis Milan1

Author Affiliations

1 Laboratoire de Génétique Cellulaire, Animal Genetics Division, INRA, Chemin de Borde-Rouge Auzeville, 31326 Castanet-Tolosan, France

2 , Centre National de Génotypage, 91057 Evry, France

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BMC Genomics 2012, 13:585  doi:10.1186/1471-2164-13-585

Published: 15 November 2012

Additional files

Additional file 1:

Radiation hybrid maps of the Illumina pig 60K SNP chip. This text file contains the position (in centiRays) of 38379 SNPs from the Illumina porcineSNP60 SNP chip on radiation hybrid maps. For each SNP, two positions are given, one on the IMpRH panel (pos.rh1) (Yerle et al., 1998) and one on the IMNpRH2 panel (pos.rh2) (Yerle et al., 2002).

Format: TXT Size: 1.1MB Download file

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Additional file 2 :

Characteristics of the RH maps. This table contains detailed characteristics of the RH maps obtained for each chromosome: number of SNPs mapped, number of distinct position for each panel, resolution, average marker distance and retention fraction.

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Additional file 3:

Detailed comparison of RH maps with the build9 assembly and with the build10 assembly. This file contains comprehensive pictures comparing (i) the build9 draft assembly and the RH maps and (ii) the pig genome sequence build10 and the RH maps.

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Additional file 4:

Predicted positions on the pig genome for 2703 SNPs. This file contains a predicted chromosome and location in base pairs for 2703 SNPs currently not assigned a position on the pig genome. We estimate that 95% of these predicted positions lie at less than 1Mb of the true position, with a median at 120Kb. See details in the text.

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Additional file 5:

Predicted positions on the pig genome for 1328 scaffolds. This file contains a predicted chromosome and location in base pairs for 1328 scaffolds currently unplaced on the pig genome. This files contains only the Tentatives scaffolds (see details in the main text).

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Additional file 6:

Validation of the predicted position for scaffold GL894031. This file contains figures and text presenting the validation of the predicted position for the unplaced scaffold GL894031.

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Additional file 7:

Resolution of RH mapping for high density arrays. This file contains theoretical calculations on the resolution of RH panels and the design of RH experiments.

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Additional file 8:

Number of uSNPs with multiple chromosome assignments against similarity score threshold. This file is a figure showing the evolution of the number uSNPs with multiple chromosome assignments as a function of the similarity score threshold.

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