Open Access Highly Accessed Research article

Genomic variation in the vomeronasal receptor gene repertoires of inbred mice

Elizabeth H Wynn, Gabriela Sánchez-Andrade, Keren J Carss and Darren W Logan*

Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK

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BMC Genomics 2012, 13:415 doi:10.1186/1471-2164-13-415

Published: 21 August 2012

Additional files

Additional file 1:

Table S1. Listing the numbers of VRs at each stage of our parsing process, subdivided by receptor class.

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Additional file 2:

Table S2. Listing the SNP distribution in VR repertoires, subdivided by receptor class.

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Additional file 3:

Figure S1. Showing an example of a VR, Vmn2r100, deleted in SPRET/EiJ. (A) Exome sequencing of C3HeB/FeJ indicates the genomic location of the Vmn2r100 gene (black bars) in that strain, by the position of reads mapped to the C57BL/6J reference (blue lines). (B) The mapping of whole genome sequence reads from SPRET/EiJ to the same genomic interval shows a defined gap in read coverage. This is consistent with a genomic deletion in this strain. (C) The mapping of whole genome sequence reads from CAST/EiJ to the same genomic interval shows that reads span the whole region in this strain, and thus suggests the gap in SPRET/EiJ is not due to a read mapping problem.

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Additional file 4:

Figure S2. Showing evidence of a duplication in Vmn2r56 in the CAST/EiJ line. Sequence reads from CAST/EiJ are stacked vertically, mapped to an exon of Vmn2r56 on chromosome 7 of the C56BL/6J reference sequence (bottom, black text). SNPs are indicated in red, with three sites showing ambiguous calls (asterisks: sites where approximately half the reads has one nucleotide and the other half has a different nucleotide). The nucleotides at these sites co-segregate within reads (blue text and green text), consistent with two distinct sequences in CAST/EiJ mapping to the same location.

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Additional file 5:

Lists all the SNPs identified in V1Rs, subdivided by gene and strain.

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Additional file 6:

Lists all the SNPs identified in V2Rs, subdivided by gene and strain.

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Additional file 7:

Lists all the SNPs identified in FPRs, subdivided by gene and strain.

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