Open Access Highly Accessed Research article

Whole-Genome sequencing and genetic variant analysis of a quarter Horse mare

Ryan Doan1, Noah D Cohen2, Jason Sawyer34, Noushin Ghaffari5, Charles D Johnson5 and Scott V Dindot16*

Author Affiliations

1 Department of Veterinary Pathobiology, Texas A&M University College of Veterinary Medicine and Biomedical Sciences, College Station, TX, USA

2 Department of Large Animal Clinical Sciences, Texas A&M University College of Veterinary Medicine, College Station, TX, USA

3 Texas AgriLife Research Center, McGregor, TX, USA

4 Department of Animal Science, Texas A&M University, College Station, TX, USA

5 AgriLife Genomics and Bioinformatics Center, College Station, TX, USA

6 Department of Molecular and Cellular Medicine, Texas A&M Health Science Center College of Medicine, College Station, TX, USA

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BMC Genomics 2012, 13:78  doi:10.1186/1471-2164-13-78

Published: 17 February 2012

Additional files

Additional file 1:

Distribution of paired-end sequencing library insert length. Figure indicating distribution of library insert length and number of sequence reads generated per length.

Format: TIFF Size: 437KB Download file

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Additional file 2:

Sequencing reaction statistics. Table of raw summary statistics of each lane of Illumina sequencing.

Format: XLSX Size: 11KB Download file

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Additional file 3:

Detailed overview of mapping results. Table of total sequence reads (paired and single end), the number of mapped reads and bp to assembled and unassembled chromosomes.

Format: XLSX Size: 12KB Download file

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Additional file 4:

Average depth of coverage of assembled chromosomes. Figure of average mapping read coverage of each chromosome.

Format: TIFF Size: 1MB Download file

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Additional file 5:

5X filtered SNPs and INDELS identified by whole genome sequencing. Table listing chromosomal coordinates of SNPs and INDELs identified using a minimum sequence read depth coverage of 5X.

Format: ZIP Size: 19.4MB Download file

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Additional file 6:

10X filtered SNPs and INDELS identified by whole genome sequencing. Table listing chromosomal coordinates of SNPs and INDELs identified using a minimum sequence read depth coverage of 10X.

Format: ZIP Size: 14MB Download file

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Additional file 7:

Loss of SNPs by post-filtering. Table describing the number of SNPs and INDELs removed by post-filtering.

Format: XLSX Size: 8KB Download file

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Additional file 8:

Comparison of minimum depth of coverage SNP filters. Total number of (A) SNPs and (B) non-synonymous SNP remaining after increasing the minimum sequence read depth of coverage. Proportion of homozygous and heterozygous (C) SNPs and (D) non-synonymous SNPs lost by increasing minimum sequence read depth of coverage.

Format: TIFF Size: 568KB Download file

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Additional file 9:

Annotation of SNPs with minimum read depth coverage of 5X. Table describing the genic annotation of SNPs identified at 5X coverage.

Format: XLSX Size: 20KB Download file

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Additional file 10:

Annotation of SNPs with minimum read depth coverage of 5X relative to the Ensembl gene annotation. Table describing the intergenic and genic location of SNPs identified at 5X coverage.

Format: XLSX Size: 21KB Download file

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Additional file 11:

Genes affected by SNPs with minimum read depth coverage of 5X. Table describing the number of genes identified with SNPs, including the annotation of the SNPs within the genetic elements.

Format: XLSX Size: 13KB Download file

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Additional file 12:

Overview of SNP annotation with minimum read depth coverage of 5X. Table summarizing the number and annotation of SNPs with minimum read depth coverage of 5X.

Format: XLSX Size: 10KB Download file

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Additional file 13:

Annotation of SNPs with minimum read depth coverage of 6X. Table describing the genic annotation of SNPs identified with minimum read depth coverage of 6X coverage.

Format: XLSX Size: 20KB Download file

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Additional file 14:

Annotation of SNPs with minimum read depth coverage of 6X relative to the Ensembl gene annotation. Table describing the intergenic and genic location of SNPs identified with minimum read depth coverage of 6X coverage.

Format: XLSX Size: 21KB Download file

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Additional file 15:

Annotation of SNPs with minimum read depth coverage of 7X. Table describing the genic annotation of SNPs identified with minimum read depth coverage of 7X coverage.

Format: XLSX Size: 20KB Download file

Open Data

Additional file 16:

Annotation of SNPs with minimum read depth coverage of 7X relative to the Ensembl gene annotation. Table describing the intergenic and genic location of SNPs identified with minimum read depth coverage of 7X coverage.

Format: XLSX Size: 21KB Download file

Open Data

Additional file 17:

Annotation of SNPs with minimum read depth coverage of 8X. Table describing the genic annotation of SNPs identified with minimum read depth coverage of 8X coverage.

Format: XLSX Size: 20KB Download file

Open Data

Additional file 18:

Annotation of SNPs with minimum read depth coverage of 8X relative to the Ensembl gene annotation. Table describing the intergenic and genic location of SNPs identified with minimum read depth coverage of 8X coverage.

Format: XLSX Size: 21KB Download file

Open Data

Additional file 19:

Annotation of SNPs with minimum read depth coverage of 9X. Table describing the genic annotation of SNPs identified with minimum read depth coverage of 9X coverage.

Format: XLSX Size: 19KB Download file

Open Data

Additional file 20:

Annotation of SNPs with minimum read depth coverage of 9X relative to the Ensembl gene annotation. Table describing the intergenic and genic location of SNPs identified with minimum read depth coverage of 9X coverage.

Format: XLSX Size: 20KB Download file

Open Data

Additional file 21:

Annotation of SNPs with minimum read depth coverage of 10X. Table describing the genic annotation of SNPs identified with minimum read depth coverage of 10X coverage.

Format: XLSX Size: 19KB Download file

Open Data

Additional file 22:

Annotation of SNPs with minimum read depth coverage of 10X relative to the Ensembl gene annotation. Table describing the intergenic and genic location of SNPs identified with minimum read depth coverage of 10X coverage.

Format: XLSX Size: 20KB Download file

Open Data

Additional file 23:

Genes affected by SNPs with minimum read depth coverage of 10X. Table describing the number of genes identified with SNPs, including the annotation of the SNPs within the genetic elements.

Format: XLSX Size: 13KB Download file

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Additional file 24:

Imprinted genes containing SNPs in coding regions. List of known imprinted genes in humans containing coding SNPs in Quarter Horse.

Format: XLSX Size: 22KB Download file

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Additional file 25:

Annotation of INDELs with minimum read depth coverage of 5X.

Format: XLSX Size: 24KB Download file

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Additional file 26:

Annotation of INDELs with minimum read depth coverage of 10X. Table describing genic annotation and location of INDELs with minimum read depth coverage of 10X.

Format: XLSX Size: 22KB Download file

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Additional file 27:

Distribution of total number of INDELs by length. Plot showing the number of INDELS by length identified with minimum read depth coverage of 10X.

Format: TIFF Size: 784KB Download file

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Additional file 28:

Coordinates of CNVs. Table describing the location of CNVs identified by analysis of read depth.

Format: XLSX Size: 51KB Download file

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Additional file 29:

Identification of a loss within an olfactory gene cluster by sequencing read-depth. Plot of read depth indicating a copy number loss within olfactory gene cluster.

Format: TIFF Size: 302KB Download file

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Additional file 30:

Identification of a homozygous deletion by read-depth coverage. Plot of read depth indicating a homozygous deletion.

Format: TIFF Size: 235KB Download file

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Additional file 31:

Biological process enrichments and associated p-values for SNPs, INDELS, and CNVs with minimum read depth coverage of 10X. Statistical analyses of biological process enrichments for SNP, INDELS, and CNVs with minimum read depth coverage of 10X.

Format: XLSX Size: 11KB Download file

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Additional file 32:

Biological process enrichment analysis of conserved and radical non-synonymous SNPs. Statistical analyses of biological process enrichments for conserved and radical SNPs with minimum read depth coverage of 10X.

Format: TIFF Size: 953KB Download file

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Additional file 33:

Annotation of SNPs in the reference Thoroughbred genome. Table describing genic annotation and location of known SNPs in the reference Thoroughbred genome.

Format: XLSX Size: 12KB Download file

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Additional file 34:

Comparison of biological processes affected by SNPs in the Quarter Horse and Thoroughbred genomes. (A) BP enrichment of non-synonymous homozygous SNPs and (B) heterozygous SNPs in the Quarter Horse genome. (C) BP enrichment of non-synonymous heterozygous SNPs in the Thoroughbred genome. (D) Number of genes containing non-synonymous SNPs within each BP pathway.

Format: TIFF Size: 1.4MB Download file

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Additional file 35:

Biological process enrichments and associated p-values for SNP comparison between Quarter Horse and reference Thoroughbred with minimum coverage of 10 reads. Comparison and statistical analysis of biological process enrichments between Quarter Horse and reference Thoroughbred.

Format: XLSX Size: 10KB Download file

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Additional file 36:

Statistical analysis of enriched genes in the Quarter Horse and reference Thoroughbred. Statistical analysis of comparison between enriched genes in the Quarter Horse and reference Thoroughbred.

Format: XLSX Size: 10KB Download file

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Additional file 37:

Biological process terms and classification. All terms used for biological processes enrichment and their associated category.

Format: XLSX Size: 30KB Download file

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