<p>Generally a single allele is used. This may be arbitrary or match the major allele frequency of the species. For sex chromosomes, usually both/all are included, so for mammals both X and Y are part of the reference genome.</p>

CC BY-SA 4.0
2019-11-06T10:04:39.947Z
In order to do so, do they perform "haplotype phasing" ? So, if you have something similar to sexual chromosome on another pair (really big divergent regions), one of them will be left out, as it is not recognise as a particular pair ?
LauraR
CC BY-SA 4.0
2019-11-06T10:05:38.150Z
There is usually nothing special done in this regard unless it's a more finished genome (mouse, human, etc.).
Devon Ryan
CC BY-SA 4.0
2019-11-06T09:54:41.963Z
2019-11-06T09:54:41.963Z
Devon Ryan
<p>this is a very general question about diploid genome assembly. I am wondering how people deal with heterozygous region in a genome when assembling ?
Do they pick one of the haplotype to be in the referene and leave out the other ?
I am particularly thinking about situation similar to mammalian chromosome Y. 
Do you put Y or X in the assembly ? An hybrid ?</p>

<p>Thanks</p>

<reference-genome><genome-sequencing>
How do researchers account for heterozygosity in genome assembly?
# How do researchers account for heterozygosity in genome assembly?

(Asked by: username_0 on 2019-11-06)

this is a very general question about diploid genome assembly. I am wondering how people deal with heterozygous region in a genome when assembling ?
Do they pick one of the haplotype to be in the referene and leave out the other ?
I am particularly thinking about situation similar to mammalian chromosome Y.
Do you put Y or X in the assembly ? An hybrid ?

Thanks

**Tags:** reference-genome, genome-sequencing

---

## 1 answers

### Answer by username_1 on 2019-11-06. Score: 1 | Accepted answer

Generally a single allele is used. This may be arbitrary or match the major allele frequency of the species. For sex chromosomes, usually both/all are included, so for mammals both X and Y are part of the reference genome.

> **Comments:**
> **username_0**: In order to do so, do they perform "haplotype phasing" ? So, if you have something similar to sexual chromosome on another pair (really big divergent regions), one of them will be left out, as it is not recognise as a particular pair ?  
> **username_1**: There is usually nothing special done in this regard unless it's a more finished genome (mouse, human, etc.).  

---

