Does reference genome contains alleles?

[KyuzoSeq]

Hi,

I'm really confused about this; we have two almost same copy of genes (alleles) so when sequencing the genome that means there must be two location for same gene right? Therefore, in an example of hg19 sequence am i right about those two alleles represents and that means same genes shown in twice? or is there any trick that I dont know?

[wdecoster]

No, the reference genome is haploid. Things get more complicated when taking alternative haplotypes into account in hg38, but don't worry about that part

[KyuzoSeq]

No, the reference genome is haploid. Things get more complicated when taking alternative haplotypes into account in hg38, but don't worry about that part

So, how to decide which sets of chromosomes are taken?

[wdecoster]

So, how to decide which sets of chromosomes are taken?

Both homologous chromosomes are collapsed in a haploid reference genome. You have a maternal and paternal chr1 but those are just one reference chr1

[KyuzoSeq]

Both homologous chromosomes are collapsed in a haploid reference genome. You have a maternal and paternal chr1 but those are just one reference chr1

Do you know any source to help me about understanding this situation? I cannot imagine how chromosomal structure organized in digital sequence. Maternal and paternal chromosomes stay there ok but when we getting digital sequence how this information is organized in the data; in other words there are maternal and paternal chr1s yes but how just one reference chr1 can be made?

[dpryan]

The two chromosomes are almost completely identical, so in practice the resulting haploid genome ends up being a mix of both. To really confuse you, the human reference genome is comprised from multiple people, so different parts will end up representing the paternal allele from person A and the next part of the genome perhaps the maternal allele from person B.

[mbblack]

The public consortium human genome reference sequence is explicitly a consensus sequence (actually stated as such in the 2001 Science paper) of five individual humans used to produce the plasmid clones. It was never intended to represent anything more than a generic feature reference of the genome.

The Celera human genome was mainly (but not exclusively) a single person's genomic sequence. J. Craig Venter's person genome was published as a diploid individual human genome build in 2007 and is available in GenBank.