# RGD-PIPELINE: ftp-file-extracts
# MODULE: variants-ver-1.0.1
# GENERATED-ON: 2021/04/10
# PURPOSE: non-synonomous variants for rat strains, extracted from RGD database
# CONTACT: rgd.data@mcw.edu
# FORMAT: tab delimited text
#
# SAMPLE: WN/N (MCW)
# SAMPLE-INFO: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
# SEQUENCED-BY: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)<br>Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
# SEQUENCER: SOLiD 4 and 5500
# SECONDARY-ANALYSIS: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
# GRANT-NUMBER: null
# WHERE-BRED: National Institutes of Health
# STRAIN-RGD-ID: 10045
#
# COLUMN INFORMATION:
#
#1  VID	      unique variant id
#2  VAR_TYPE    variant type:'snv','ins','del'
#3  CHROMOSOME  chromosome
#4  POSITION    position on chromosome
#5  REF_NUC     reference nucleotide
#6  VAR_NUC     variant nucleotide
#7  REF_AA      reference amino acid
#8  VAR_AA      variant amino acid
#9  PREDICTION  polyphen prediction
#10 TRANSCRIPT  transcript id
#11 POS_NUC     nucleotide position of variant relative to 1st nucleotide of CDS
#12 POS_AA      aminoacid position of variant relative to protein 1st aminoacid