Changes between Version 46 and Version 47 of UTGBMedaka/Track

Timestamp:

09/05/07 13:50:18 (18 years ago)

Author:

ssksn

Comment:

--

UTGBMedaka/Track

@@ -128 +128 @@
 
 This track displays all the polymorphisms regions between medaka Hd-rR and HNI strain. 
+
+In addition to the genome of the Hd-rR medaka inbred strain,
+the genome of another inbred strain HNI was also sequenced to produce the draft 648-Mb HNI genome.
+Inbred strains Hd-rR and HNI originated in the southern and northern Japanese populations, respectively.
+They can mate and produce healthy offspring,
+although they are estimated to have diverged about 4 million years ago,
+and their genome sequences have diverged by approximately 3.42%.
+The alignment of the two medaka genomes identified
+about 16.4 million single nucleotide polymorphisms (SNPs), from which 2,401 SNPs were selected
+and mapped genetically onto medaka chromosomes using a backcross panel between these two inbred strains. 
+
+The alignment of the Hd-rR and HNI genomes revealed 16,519,460 SNPs and 2,859,905 insertions/deletions (indels),
+and the locations of individual SNPs and indels are given in the web database.
+Pink indicates matched bases, while mismatches are highlighted by green, yellow, blue, and red that represent A, C, G, and T, respectively, in the HNI genome.
+Cyan indicates the two possibilities, deletions from the HNI genome or insertions into the Hd-rR genome,
+though the settlement requires comparison with the genome of an outgroup of Hd-rR and HNI.
+Gray means the failure of the alignment because of low quality bases in either of the two genomes or lack of HNI reads in the region.
+
 The details of this track is described here: http://medaka3.utgenome.org/~ssksn/HNI_SNPs/common/HNI_SNPs_description.html