---
title: Which reference genome is being used to align the reads?
description: Reference genomes hg19 and hg38 are used for standard chromosomes. The preferred reference genome can always be selected when launching a new analysis. The following alternate loci were removed from h
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# Which reference genome is being used to align the reads?
#### **Reference genome**
Reference genomes hg19 and hg38 are used for standard chromosomes. The preferred reference genome can always be selected when launching a new analysis.
The following alternate loci were removed from hg19 :
- chr4\_ctg9\_hap1
- chr6\_apd\_hap1
- chr6\_cox\_hap2
- chr6\_dbb\_hap3
- chr6\_mann\_hap4
- chr6\_mcf\_hap5
- chr6\_qbl\_hap6
- chr6\_ssto\_hap7
- chr17\_ctg5\_hap1
Please, note that we do not handle ALT contigs of the hg38 reference genome version at the moment.
#### **Mitochondrial genome**
With regard to the mitochondrial genome, in [VarSome Clinical](https://varsome.com/varsome-editions/varsome-clinical/) when the analysis is launched from fastq sample(s), using either **hg19** or **hg38**, any mitochondrial sequences will be aligned to the [standard mitochondrial](https://www.mitomap.org/foswiki/bin/view/MITOMAP/MitoSeqs) genome (GenBank number: [NC\_120920.1)](https://www.ncbi.nlm.nih.gov/nuccore/NC_012920.1), which is included in the **hg38** human genome. For more details please see the [Mitochondrial genome versions](https://docs.varsome.com/mito-genome-versions?hsLang=en).
#### **Pseudoautosomal regions**
The pseudoautosomal regions of chromosome Y have been masked in both hg19.
For hg38, the masked regions are:
- chromosome:GRCh38:Y:10001 - 2781479 is shared with X: 10001 - 2781479 (PAR1)
- chromosome:GRCh38:Y:56887903 - 57217415 is shared with X: 155701383 - 156030895 (PAR2)
Should I use hg19 or hg38?
- When starting your analysis from VCF: the reference genome must be the same as the one it was used in the mapping and variant calling pipeline that generated the VCF files.
- If you are using a specific assay, please make sure the assay version is available for the reference genome you want to select. Please, contact [support](mailto:support@varsome.com) if you are not sure about this.
- If you don't know which genome should you select, the recommended option is hg38. This is a corrected and improved version of hg19. You should use the newer and better assembly.
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