# 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: SHR/OlaIpcv (ICL)
# SAMPLE-INFO: SHR/OlaIpcv sequenced by ICL, UBC 
# SEQUENCED-BY: Imperial College London (Prof. Timothy Aitman)<br>University of British Columbia (Dr. Steven Jones) 
# SEQUENCER: Illumina Hiseq 2000 and GAII 
# SECONDARY-ANALYSIS: BWA-0.5.8c, GATK-v1.0.6001, samtools, Picard 
# GRANT-NUMBER: LSHG-CT-2005-019015, HEALTH-F4-2010-241504 
# WHERE-BRED: Institute of Physiology, Academy of Sciences of the Czech Republic, Prague 
# STRAIN-RGD-ID: 631848
#
# 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