What is chrom and position values in Wuhan-Hu-1 genome data

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20 months ago

Nemo • 0

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?

alignemnt variant gatk covid hisat2 • 731 views

ADD COMMENT • link updated 20 months ago by GenoMax 141k • written 20 months ago by Nemo • 0

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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.

ADD REPLY • link 20 months ago by ATpoint 82k

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Sorry I am new to this. From where I can get the gene annotations for this genome? Can you explain more.

ADD REPLY • link 20 months ago by Nemo • 0

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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

ADD REPLY • link 20 months ago by GenoMax 141k

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