Calculating human genome covering each segment

Question

[zizigolu]

Hi

I have some genomic ranges like

Chr start         end
1   10583       863511
1   12841835    12854479

I want to know for instance;

The range of 10583 to  863511 on chromosome 1 does cover how much of the genome

People say

tab$range_fraction <- (tab$end - tab$start) / human_genome_size

I am wondering what I should put as human_genome_size

Googling turns that human genome is 3,234.83 Mbp (mega-basepairs) per haploid genome and 6,469.66 Mbp total (diploid). Should I use haploid or diploid genome size as dominator?

Although I am not certain about what google shows

[ATpoint]

Hello A!

It appears that your post has been cross-posted to another site: https://bioinformatics.stackexchange.com/questions/13019/the-percentage-of-genome-with-copy-number

This is typically not recommended as it runs the risk of annoying people in both communities.

Answer 1

[ATpoint]

Genome sizes always refer to the haploid genome. Get the chromSizes files from RefSeq or similar sources to get the sizes of all chromsomes. https://hgdownload-test.gi.ucsc.edu/goldenPath/hg38/bigZips/hg38.chrom.sizes From there it is just (interval size) / (total genome), sure you can implement that.