What is chrom and position values in Wuhan-Hu-1 genome data
Hi,
I have variants from covid samples using gatk and haplotype caller. In the resulted table, for each sample and variant there is two columns named "chrom" and "pos". The chrom value is the same for all rows as "NC_045512.2" but the position is changing. I would like to know what position is this? What format is used in the chromosome? Can I use this position to map the variants to genes?
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NC_045512.2 is the name of the genome at NCBI https://www.ncbi.nlm.nih.gov/nuccore/1798174254
Pos is the position of the variant in the genome so yes, given gene annotations you can map that.
Sorry I am new to this. From where I can get the gene annotations for this genome? Can you explain more.
Gene annotations in GTF and GFF format can be downloaded from: https://ftp.ncbi.nlm.nih.gov/genomes/refseq/viral/Severe_acute_respiratory_syndrome-related_coronavirus/latest_assembly_versions/GCF_009858895.2_ASM985889v3/
NCBI's genome page is here: https://www.ncbi.nlm.nih.gov/genome/86693