A Compilation of Raw Pig SNP Data (2008)
— Select Candidates for a Pig SNP Chip

1. Compiled SNP data, version 1 (May 21, 2008)

Data Info

Source: ftp://ftp.ncbi.nih.gov/snp/organisms/pig_9823/rs_fasta/rs_chNotOn.fas.gz
Status: 8,427 SNPs were loaded to database (May 11, 2008)
        SNP quality scores developed (May 20, 2008)

2. Compiled SNP data, version 2 (July 31, 2008)

Data statistics (click to expand/ hide)

There are a total of 17704 SNPs in the database

 1. The sequence quality score span:

    The Score range = 25 (min) - 120 (max)

 2. SNP counts by sequence quality score ranges:

    Count   Categr.
    ------  ------
     1716   20-51
     6773   51-80
     2380   81-111
     6835   >112

 3. SNP sequences longer than 69bp:

     9453

 4. SNP counts by chromosome location

   No. of SNPs   Chromosome
   -----------   ----------
       204           X
      1360           1
       764           2
       391           3
      1039           4
       728           5
       480           6
      1487           7
       302           8
       516           9
       290          10
       188          11
       497          12
       463          13
      1267          14
       407          15
       107          16
       460          17
       159          18
   ------------------------
Sum: 11109 SNPs have chromosome locations
      6595 SNPs that don't have chromosome location

 5. SNP counts by additional info (MAF, chr., annotation, etc)

    No. of SNPs   Score_groups
    -----------   -----------
       4347       Score:10
       4381       Score:30
       8728       Score:50
        248       Score:70

 6. SNP counts by data sources:

    Counts  Data / information source
    ------  --------------------------------
     4347    dbSNP
      231    dbSNP; Kwan-suk Kim
       14    dbSNP; Kwan-suk Kim; MARC
      153    dbSNP; MARC
     1077    dbSNP; Martien Groenen
     2306    dbSNP; Miguel Perez (NCBI)
      179    dbSNP; Miguel Perez (NCBI); Kwan-suk Kim
       11    dbSNP; Miguel Perez (NCBI); Kwan-suk Kim; MARC
      109    dbSNP; Miguel Perez (NCBI); MARC
      136    Martien Groenen
      159    Max Rothschild (Du1)
      298    Max Rothschild (Du2)
      435    Max Rothschild (Fan)
     8249    Miguel Perez (PIGGIS)

Data source and process status (click to expand/ hide)

 1. The early stage of the work is to gather all publically available SNPs
    - works are in "prep_data_gethering"
    - results are in "http://www.animalgenome.org/pigs/projects/SNPchip.php"
    - results were forwarded to Martien to continue...
      and the final results were ended in a publication by Ramos et al.:
      "Design of a High Density SNP Genotyping Assay in the Pig Using SNPs
      Identified and Characterized by Next Generation Sequencing Technology.
      PLoS ONE 4(8): e6524. doi:10.1371/journal.pone.0006524 (2009)

 2. The data files in this folder are from Martien:
     - dbSNPsubm_MAF2.rep.txt.gz
     - dbSNPsubm_MAF3.rep.txt.gz
     - PorcineSNP60_SNP_List.README
     - PorcineSNP60_SNP_List.txt.gz
     - snpMap.v8.txt.gz
     - SNPmap.v9.txt.gz

 3. Continued works on the pig SNPs are in ../plotsnp

Data Download (Tab delimited data file with README)

© 2003-2010 NAGRP - Bioinformatics Coordination Program. Contact: NAGRP Bioinformatics Team

March 16, 2010 (Tuesday)