Cattle reference genome ARS-UCD2.0

Question

[am29]

Hi,

I am trying to find out about the overall number of variants, especially SNPs and indels in a new cattle reference genome ARS-UCD2.0 (GCA_002263795.4).

I couldn't find anything neither in NCBI, ENSEMBL, or dbSNP. The latest info on ENSEMBL is regarding ARS-UCD1.3.

Please help me.

[1769mkc]

add more details about the sample(coverage etc) and pipelines used so that others can give you more input

[am29]

I didn't do any experiments with this assembly, I am simply interested in the number of SNPs and indels in the new reference genome (for my paper).

For example, the previous reference assembly had 96,494,428 SNPs and indels, according to Ensembl https://www.ensembl.org/Bos_taurus/Info/Annotation

For the current assembly, there is no information on Ensembl, only a bit on NCBI https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_002263795.3/ but this is not what I am looking for.

Answer 1

[Michael]

I think there is a misunderstanding here. A reference genome doesn't "have" any variants, except for the differences between haplotypes in haplotype-resolved assemblies. Variant positions are annotated based on the re-sequencing of other individuals. Therefore, the number of variant loci in the cattle genome based on (not "in") the new assembly will be nearly identical to that based on the old assembly. The only difference will be in regions that are not directly mappable between those two which are likely minuscule. A process like LiftOver could convert the positions of the variants to the coordinates of the new assembly. Over time, variants might be detected in regions missing from the old assembly or better mappable in the new assembly. When working with variants, you must ensure you are working within the compatible coordinate system of the assembly and annotation they are given.