# 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: F344/NCrl (ICL) # SAMPLE-INFO: F344/NCrl sequenced by ICL # SEQUENCED-BY: Imperial College London (Prof. Timothy Aitman) # SEQUENCER: Illumina HiSeq 2000 # SECONDARY-ANALYSIS: BWA-0.5.8c, GATK-v1.0.6001, samtools, Picard # GRANT-NUMBER: MRC core funding, BHF Center of Research Excellence (RE/08/002) and Euratrans (HEALTH-F4-2010-241504) # WHERE-BRED: Charles River Laboratories # STRAIN-RGD-ID: 737926 # # 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