[ensembl-dev] hg19 - GRCh37

Hiram Clawson hiram at soe.ucsc.edu
Wed Feb 22 16:13:35 GMT 2012

Good Morning Nick:

There is one slight difference between the Ensembl display of GRCh37
and the hg19/GRCh37 display at UCSC.  The chrM - Mt mitochondrian
sequence is different.  When GRCh37 was released, there was no specification
of what sequence to use for chrM.  At the time UCSC constructed
the hg19 genome browser, the sequence NC_001807 was the accepted chrM.
Later, the sequence NC_012920 was selected as the reference chrM.

Note the discussion of GRCh37 and chrM sequence at the gateway page:


----- Original Message -----
From: "Nick Fankhauser" <lists at nyk.ch>
To: "dev" <dev at ensembl.org>
Sent: Wednesday, February 22, 2012 6:37:32 AM
Subject: [ensembl-dev] hg19 - GRCh37


are the coordinates in GRCh37 really identical to the hg19 coordinates?

I ask because I have iCLIP peaks mapped to hg19 and plan to find
intersections to the positions of all known genes, which I'm retrieving
through the ENSEMBL API.


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