[ensembl-dev] GRCh37 chrY sequence ?

[Hiram Clawson]

Good Morning Ensembl:

A user reported to UCSC that the GRCh37/hg19 chrY sequence at UCSC is
different from the chrY sequence at Ensembl.  I picked up the v67
chrY sequence from Ensembl and compared it to the UCSC chrY and
the GRCh37 chrY sequence and Ensembl has a different sequence.
I checked previous versions of chrY from Ensembl and they remain
the same, so it isn't a patched sequence.  Anyone know what
the story is here ?

--Hiram

faCount composition measure of chrY sequence from genbank, UCSC and Ensembl:

#seq           len     A       C       G       T       N       cpg
CM000686.1 59373566 7667625 5099171 5153288 7733482 33720000 217906
hg19.chrY  59373566 7667625 5099171 5153288 7733482 33720000 217906
Y.v67      59373566 6965778 4475138 4518436 7025177 36389037 163434