Difference in Human reference build p.10 and p.13

Question

[bioinfo_ga]

Hi, For Human analysis as there has been update in the reference genome (GRCh38)build version from p10 to p13, i observed a drastic change in terms of the genome size as p.10 was 3 GB whereas p13 is 60 GB, what is the reason?

Thanks.

[GenoMax]

i observed a drastic change in terms of the genome size as p.10 was 3 GB whereas p13 is 60 GB,

That is because you are mixing up "primary" assembly with one that contains "alternate haplotypes".

---------
TOPLEVEL
---------
These files contains all sequence regions flagged as toplevel in an Ensembl schema. This includes chromsomes, regions not assembled into chromosomes and N padded haplotype/patch regions.

--------------
PRIMARY ASSEMBLY
-----------------
Primary assembly contains all toplevel sequence regions excluding haplotypes and patches. This file is best used for performing sequence similarity searches where patch and haplotype sequences would confuse analysis.

[bioinfo_ga]

ohh i see, ok let me see both the files. Thanks for the help.

[Bastien Hervé]

From where do you want to take your Human Reference Genome ? Because on NCBI the GRCh38.p10.fna compressed is 911MB and the GRCh38.p13.fna is 920MB

Patch differences from the previous one are inside README_patch_release.txt

ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_000001405.28_GRCh38.p13/

[bioinfo_ga]

From Ensembl database : [http://www.ensembl.org/Homo_sapiens/Info/Index]

[Bastien Hervé]

The Homo_sapiens.GRCh38.dna.toplevel.fa.gz for GRCh38.p13 is 1.0GB

Also, Ensembl releases come from The Genome Reference Consortium