src/hg/makeDb/doc/hg19.txt 1.34

Index: src/hg/makeDb/doc/hg19.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/hg19.txt,v
retrieving revision 1.33
retrieving revision 1.34
diff -b -B -U 4 -r1.33 -r1.34
--- src/hg/makeDb/doc/hg19.txt	29 Jul 2009 06:49:17 -0000	1.33
+++ src/hg/makeDb/doc/hg19.txt	29 Jul 2009 18:42:22 -0000	1.34
@@ -7,8 +7,22 @@
 
 #	"$Id$";
 
 #############################################################################
+
+# NOTE FOR NEXT HUMAN ASSEMBLY (2009-07-29 - Brooke): hg19 contains the wrong
+# sequence for chrM. The accession NC_001807 was replaced in GenBank with
+# NC_012920, with the note: "This sequence was removed since the accepted
+# reference sequence for the Homo sapiens mitochondrion is the rCRS/Mitomap
+# sequence, which is now available as the record NC_012920".
+# Also, from http://www.mitomap.org/mitoseq.html:
+# "IMPORTANT:  Do not use NC_001807 as "the rCRS" as it is an African
+# (Yoruban) sequence with over 40 variant nucleotides from the rCRS. As of
+# July 8, 2009 it has been removed from GenBank as a reference sequence but
+# may be found, if needed, as  AF347015, one of 53 African sequence deposited
+# in Genbank by Ingman et al in 2001."
+# Use NC_012920 for the chrM sequence for the next build!
+
 # Download sequence (DONE - 2009-02-04 - Hiram)
     mkdir -p /hive/data/genomes/hg19/download
     cd /hive/data/genomes/hg19/download
     mkdir -p assembled_chromosomes