Research article
Whole-genome resequencing shows numerous genes with nonsynonymous SNPs in the Japanese native cattle Kuchinoshima-Ushi
- † Equal contributors
1 Genome Research Center, NODAI Research Institute, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
2 Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
3 Department of Bioscience, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
BMC Genomics 2011, 12:103 doi:10.1186/1471-2164-12-103
Published: 10 February 2011Additional files
Additional file 1:
Reads for all chromosomes of repeat masked and unmasked genome assembly. In each chromosome, left columns show the reads mapped to the assembly without repeat masking and right columns show those to the repeat-masked assembly. Among the reads that were mapped to the reference genome sequence, most were mapped in pairs (blue column in each chromosome). However, in some read pairs, only one was mapped (red column). Additionally, some read pairs were mapped, but the distances or directions were not adequate (green columns). Length of the chromosomes is shown in the yellow line. High number of reads mapped to BTA13 of the assembly without repeat masking (left column) was removed in the repeat-masked assembly (right column).
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Additional file 2:
Length of the regions that are covered by reads for each chromosome. Length of the regions that are covered by reads for each chromosome. The length of chromosomes is shown in the blue columns, and that of the regions covered by reads is shown in the red columns. The percentage of the regions that are covered by reads in each chromosome is indicated by the green line. On an average, 93% of the genome is covered by reads.
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Additional file 3:
The number of identified SNPs and indels for each chromosome. SNPs are shown in the blue columns, and indels are shown in the red columns. Length of chromosomes is indicated by the green line.
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Additional file 4:
SNP distribution on each chromosome. SNP density (SNPs per 1 kbp) is plotted by physical position. Relative length of the chromosomes was correlated with the length of each chromosome without repeat regions.
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Additional file 5:
Distribution of the size of indels. We identified 284,007 insertions (positive values) and 345,249 deletions (negative values).
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Additional file 6:
The list of genes containing nsSNPs. The list of genes containing nsSNPs along with the accession numbers (ss number).
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Additional file 7:
GO terms which were over-represented in nsSNP-containing genes.
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Additional file 8:
The list of genes containing nsSNPs that were reported as trait-associated in other cattle breeds.
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Additional file 9:
The number of SNPs and indels with various filters. Detected SNPs and indels were filtered with additional filters and the number of homozygous and heterozygous SNPs and indels was compared. Parameters for the filters were (1) Depth: the number of reads mapped to the SNP sites, (2) SNPs: the number of reads calling SNP at the SNP site, and (3) Mutation: the cutoff value of percent aligned reads calling the SNP per total mapped reads at the SNP sites. Cut off value was 30% in all filters. In the table, "%" means the reduced percentage of the number of SNPs/indels compared with basic parameters (i.e., Depth≥ 3, SNPs≥ 2, and Mutation≥ 30).
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Additional file 10:
List of species examined in this study.
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Additional file 11:
Summary of the genes sequenced for the phylogenetic reconstruction. List of the genes and their accession numbers which were used for the phylogenetic analysis.
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