discrepancy in UCSC and ensembl chrM (mitochondrial chromosome) data

[Neeba Dijo]

Hi Team ,

I compared some co-ordinates of chromosome M in ensembl geneome browser and UCSC genome browser

But both of them showing different result:

Example 1  ChrM :9541:9541:

Ensemble Result:       T
http://www.ensembl.org/Homo_sapiens/Export/Output/Location?db=core;flank3_display=0;flank5_display=0;output=fasta;r=MT:9541-9541;strand=feature;coding=yes;cdna=yes;peptide=yes;utr3=yes;exon=yes;intron=yes;genomic=unmasked;utr5=yes;_format=Text

UCSC result:         C

http://genome.ucsc.edu/cgi-bin/hgTracks?hgHubConnect.destUrl=..%2Fcgi-bin%2FhgTracks&clade=mammal&org=Human&db=hg19&position=chrM%3A9%2C541-9%2C541&hgt.positionInput=chrM%3A9%2C541-9%2C541&hgt.suggestTrack=knownGene&Submit=submit&hgsid=355114247

Example 2: chrM:7338:7338

Ensemble Result:       A

http://www.ensembl.org/Homo_sapiens/Export/Output/Location?db=core;flank3_display=0;flank5_display=0;output=fasta;r=MT:7338-7338;strand=feature;coding=yes;cdna=yes;peptide=yes;utr3=yes;exon=yes;intron=yes;genomic=unmasked;utr5=yes;_format=Text


UCSC result:        G

http://genome.ucsc.edu/cgi-bin/hgTracks?hgHubConnect.destUrl=..%2Fcgi-bin%2FhgTracks&clade=mammal&org=Human&db=hg19&position=chrM%3A7%2C338-7338&hgt.positionInput=chrM%3A7%2C338-7338&hgt.suggestTrack=knownGene&Submit=submit&hgsid=355114473

I saw many examples like this.

So can you please explain what is the reason behind this

--
Thanks & Regards,

Neeba Sebastian

[Brian Lee]

Dear Neeba,

Thank you for using the UCSC Genome Browser and your question about the discrepancy in UCSC and Ensembl in hg19 chrM.

On our hg19/GRCh37 gateway page (http://genome.ucsc.edu/cgi-bin/hgGateway?db=hg19) we display the following note about chrM to help explain why our sequence is different:

"Note on chrM Since the release of the UCSC hg19 assembly, the Homo sapiens mitochondrion sequence (represented as "chrM" in the Genome Browser) has been replaced in GenBank with the record NC_012920. We have not replaced the original sequence, NC_001807, in the hg19 Genome Browser. We plan to use the Revised Cambridge Reference Sequence (rCRS) in the next human assembly release."

Please see this related archived mailing list response for more information: https://groups.google.com/a/soe.ucsc.edu/forum/#!msg/genome/hFp-dGG9gBs/ccniNtFBXtYJ

Thank you again for your inquiry and using the UCSC Genome Browser. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

All the best,

Brian Lee

UCSC Genome Bioinformatics Group

--