Hi Archie, This page on assembly terminology might help: http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/info/definitions.shtml
If that doesn't help, we suggest contacting the Genome Reference Consortium: http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/contact.shtml Also, one our engineers had this to add about our naming scheme: chr*_random - are called "unlocalized" sequences. The chromosome is known, but not the location on the chromosome. chrUn_* - are called "unplaced" sequences. They probably belong to the sequenced genome, but placement is unknown at this time. The GL numbers (or other types of numbers) in these names are the genbank identification numbers which can be used in a nucleotide search at Entrez. For example: chr1_GL456211_random - unlocalized sequence belonging to chr1, NCBI identification: GL456211 chrUn_JH584304 - unplaced sequence, NCBI identification JH584304 I hope this helps to clarify things for you. If you have further questions, please contact the list. Vanessa Kirkup Swing UCSC Genome Bioinformatics Group ---------- Forwarded message ---------- From: Archie Russell <[email protected]> Date: Tue, Mar 20, 2012 at 1:46 PM Subject: Re: [Genome] chr Un, random, gl, etc To: Vanessa Kirkup Swing <[email protected]> Cc: [email protected] Thanks Vanessa Do you have guidance on what these contigs represent? Why aren't they mappable? -Archie On Tue, Mar 20, 2012 at 1:41 PM, Vanessa Kirkup Swing <[email protected]> wrote: > Hi Archie, > > Information on the chromosomes are found on the gateway pages > (http://genome.ucsc.edu/cgi-bin/hgGateway) for each assembly. Select the > assembly that you are interested in using the drop downs and then scroll > down the page. For hg19, there is a section called "Chromosome naming > scheme" which should have all the information to answer your questions. > > If you have further questions, please email the list: [email protected]. > > Vanessa Kirkup Swing > UCSC Genome Bioinformatics Group > > > ---------- Forwarded message ---------- > From: Archie Russell <[email protected]> > Date: Tue, Mar 20, 2012 at 11:57 AM > Subject: [Genome] chr Un, random, gl, etc > To: [email protected] > > > Hi, > > Can you tell me what the difference is between "random", "Un", and > "gl*" chromosomes? > > "Un" seems to be "unknown" but then what is "random"? What > would be a good way to describe chrUn_gl000211? > > Are these chromosomes alternate assemblies due to actually genetic > differences > between individuals, or would they exist even if just one person were > sequenced? > > Thanks, > Archie > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
