# 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: LEC/Tj (KyushuU) # SAMPLE-INFO: Target capture sequencing of exons and conserved non-coding sequences. Provided by: Dr. Mikita Suyama (Kyushu University) and Dr. Takashi Kuramoto (Kyoto University) # SEQUENCED-BY: Kyushu University (Dr. Mikita Suyama)
Kyoto University (Dr. Takashi Kuramoto) # SEQUENCER: Illumina NextSeq 500 # SECONDARY-ANALYSIS: BWA (v0.7.4), SAMtools (v.0.1.12a), Picard tools (v.1.87), GATK (v.2.5.2) # GRANT-NUMBER: supported in part by the Cooperative Research Project Program of the Medical Institute of Bioregulation, Kyushu University, and the Genome Information Upgrading Program of the National BioResource Project, Japan Agency for Medical Research and Development # WHERE-BRED: NBRP-Rat/Kyoto University # STRAIN-RGD-ID: 1302721 # # 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