Software
Snat: a SNP annotation tool for bovine by integrating various sources of genomic information
Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, P.R. China
BMC Genetics 2011, 12:85 doi:10.1186/1471-2156-12-85
Published: 7 October 2011Additional files
Additional file 1:
411 SNPs involved in Illumina Bovine 50K SNP chip but not included in dbSNP. In Illumina Bovine 50K SNP chip, 52,255 markers are explicitly located in chromosomes based on Btau4.0. However, 411 out of these 52255 SNP markers are not included in dbSNP via position comparison based on Btau4.0. All these 411 SNPs are listed in the table. These SNPs can be annotated through "Any locus" function by Snat.
Format: XLS Size: 58KB Download file
This file can be viewed with: Microsoft Excel Viewer
Additional file 2:
Two examples given to compare Snat with FunctSNP. The examples show the differences between the two tools on features of input data and annotation process.
Format: PDF Size: 515KB Download file
This file can be viewed with: Adobe Acrobat Reader
Additional file 3:
Detailed descriptions on annotation results by Snat. An example is provided to give a detailed explanation on the annotation reports.
Format: PDF Size: 264KB Download file
This file can be viewed with: Adobe Acrobat Reader
Additional file 4:
Information of 20 significant SNPs identified associated with milk yield. This table lists positions of 20 significant SNPs based on Btau4.0 identified associated with milk yield from our recent GWAS results (Jiang et al., 2010).
Format: XLS Size: 21KB Download file
This file can be viewed with: Microsoft Excel Viewer
Additional file 5:
The raw annotation outputs for the 20 significant SNPs using Snat. SNPs within 5k bp region away from these 20 SNPs are annotated by Snat. All the data are printed into the raw text file.
Format: TXT Size: 1019KB Download file
Additional file 6:
A summary of annotation data for the 20 significant SNPs structured in TSV format. The raw annotation outputs of the 20 significant SNPs are further processed to generate a well-structured summary file in TSV format by the program raw2TSV.pl.
Format: TSV Size: 3KB Download file
Additional file 7:
Annotation results of the 20 significant SNPs saved in a worksheet. The summaries of annotation data for the 20 SNPs structured in TSV format are saved in the worksheet for more easily viewing.
Format: XLS Size: 24KB Download file
This file can be viewed with: Microsoft Excel Viewer
Additional file 8:
SNPs involved in dbSNP related to each of the 20 SNPs annotated. The cluster IDs (rs#) of all SNPs harbored within 5k bp regions from each of these 20 SNPs are integrated. This file is extracted by the program raw2TSV.pl from the raw text file.
Format: TSV Size: 4KB Download file
Additional file 9:
Non-redundant UniProt protein information extracted from the raw annotation outputs for the 20 SNPs. The file is generated by the program raw2TSV.pl and contains non-redundant UniProt protein information extracted from the raw annotation outputs for the 20 SNPs.
Format: TSV Size: 6KB Download file
Additional file 10:
Non-redundant GO terms extracted from the raw annotation outputs for the 20 SNPs. The file is generated by the program raw2TSV.pl and contains non-redundant data of GO terms extracted from the raw annotation outputs for the 20 SNPs.
Format: TSV Size: 24KB Download file
Additional file 11:
Non-redundant KEGG Pathway information extracted from the raw annotation outputs for the 20 SNPs. The file is generated by the program raw2TSV.pl and contains non-redundant KEGG Pathway information extracted from the raw annotation outputs for the 20 SNPs.
Format: TSV Size: 9KB Download file
Additional file 12:
The numbers of QTLs and five most relevant traits corresponding to each of the 20 SNPs. The file is generated by the program raw2TSV.pl and contains the data of the numbers of QTLs and five most relevant traits corresponding to each of the 20 SNPs extracted from the raw annotation outputs.
Format: TSV Size: 3KB Download file
Additional file 13:
Information of 105 significant SNPs identified associated with milk production traits based on Btau4.0. This table lists positions of 105 significant SNPs based on Btau4.0 identified associated with milk production traits from our recent GWAS results (Jiang et al., 2010).
Format: XLS Size: 25KB Download file
This file can be viewed with: Microsoft Excel Viewer
