Open Access Research article

Dissecting structural and nucleotide genome-wide variation in inbred Iberian pigs

Anna Esteve-Codina124*, Yogesh Paudel3, Luca Ferretti1, Emanuele Raineri4, Hendrik-Jan Megens3, Luis Silió5, María C Rodríguez5, Martein AM Groenen3, Sebastian E Ramos-Onsins1 and Miguel Pérez-Enciso126*

Author Affiliations

1 Center for Research in Agricultural Genomics (CRAG), Campus UAB, Bellaterra, 08193, Spain

2 Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain

3 Animal Breeding and Genomics Centre, Wageningen University, De Elst 1, Wageningen, 6708 WD, The Netherlands

4 Centre Nacional d'Anàlisi Genòmica (CNAG), Barcelona, Spain

5 Departamento de Mejora Genética Animal, INIA, Madrid, 28040, Spain

6 Institut Català de Recerca i Estudis Avançats (ICREA), Carrer de Lluís Companys 23, Barcelona, 08010, Spain

For all author emails, please log on.

BMC Genomics 2013, 14:148  doi:10.1186/1471-2164-14-148

Published: 5 March 2013

Additional files

Additional file 1:

Simulated power against depth. Power was computed as the number of SNP called by SNAPE software divided by the total number of real SNPs in the pool. Depth corresponds to the average depth in the pooled data. Bottom: Power against MAF (minor allele frequency in the pool).

Format: JPEG Size: 38KB Download file

Open Data

Additional file 2:

Variability (Wattersons's estimate, per bp) inside multicopy regions vs. variability of windows containing multicopy regions but outside the multicopy region units?

Format: PDF Size: 200KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 3:

Genes within multicopy regions and extreme selection tests’ windows. MCR genes: genes within multicopy regions; Lowest theta shared autosomes: genes within extreme low θ in autosomes and X pseudoautosomal region (PAR) common in the individual and the pool; Lowest theta shared non-pseudoautosomal region (NPAR): genes within extreme low θ in X NPAR region common in the individual and the pool; Largest theta pool: genes within extreme high θ regions in the pool; Largest theta individual: genes within extreme high θ regions in the individual; Lowest combined test: genes with lowest values of the combined Tajima’s D- Fay&Wu’s H and θ test; ΗΚΑ excess of differentiation autosomes+PAR: genes within HKA excess of differentiation in autosomes and X PAR region; ΗΚΑ vexcess of polymorphism autosomes+PAR: genes within HKA excess of polymorphism in autosomes and X PAR region; ΗΚΑ excess of polymorphism NPAR: genes within HKA excess of polymorphism in X NPAR region.

Format: ZIP Size: 823KB Download file

Open Data

Additional file 4:

Correlation across 200 kb windows between Tajima’s D and Fay - Wu’s H statistics in pooled data. Regression line is shown in red.

Format: PDF Size: 730KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data