Open Access Research article

Development and characterisation of an expressed sequence tags (EST)-derived single nucleotide polymorphisms (SNPs) resource in rainbow trout

Mekki Boussaha1*, René Guyomard1, Cédric Cabau2, Diane Esquerré3 and Edwige Quillet1

Author Affiliations

1 INRA, UMR 1313 Génétique Animale et Biologie Intégrative, 78350, Jouy-en-Josas, France

2 INRA, SIGENAE UR83 Recherches Avicoles, 37380, Nouzilly, France

3 INRA, UMR 444 Laboratoire de Génétique Cellulaire Plateforme GET, Castanet, Tolosan, France

For all author emails, please log on.

BMC Genomics 2012, 13:238  doi:10.1186/1471-2164-13-238

Published: 13 June 2012

Additional files

Additional file 1:

Minor sequence frequencies, heterozygosity and PIC values were indicated for all SNPs in the INRA Sigenae database (worksheet 1) and for the validation panel (worksheet 2). Allele frequencies were calculated by direct count of sequence depth for each allele, expected heterozygosities per locus (He) were estimated by He = 2pq and PIC values were estimated by PIC = H-2p2q2, where p and q are the sequence frequencies of the two alternate alleles.

Format: XLS Size: 8.9MB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 2:

Illumina quality design scores for the validation panel.

Format: XLS Size: 466KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 3:

SNP allele frequencies. Allele frequencies for both alleles and minor allele frequencies (MAF) were shown for DH clonal lines (worksheet 1), INRA-SY (worksheet 2), INRA-SP (worksheet 3), NCCCWA (worksheet 4), all 3 populations (worksheet 5) and for true SNPs (worksheet 6). Allele frequencies were calculated by direct count in the raw genotype data file, expected heterozygosities per locus (He) were estimated by He = 2pq and PIC values were estimated by PIC = H-2p2q2, where p and q are the allele frequencies of the two alternate alleles.

Format: XLS Size: 548KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 4:

Best k analysis. Results were shown for the five independent runs using a bur-in of 50,000 and 200,000 iterations. The best K value was determined using the non parametric test as previously described [29].

Format: XLS Size: 35KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 5:

SNP functional annotations. BlastX search results using EST contig (workseet 1) and SNP (worksheet 2) sequences as well as synonymous/non-synonymous SNP prediction results (workseet 3) were summerized.

Format: XLS Size: 278KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 6:

INRA rainbow trout linkage maps. Newly integrated SNPs were highlighted in red.

Format: PDF Size: 730KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 7:

List of duplicated markers and markers assigned in duplicated region.

Format: XLS Size: 113KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data