Where do people get the position of GRCh38 alternative loci?
I've found multiple sources, and they seem to give different positions of some alternative loci.
If I download the patch 9 dataset from http://www.ebi.ac.uk/ena/data/view/GCA_000001405.24 (by clicking "regions" in the top right corner), I will for get that the alternative locus KI270915 is positioned on chr 19:54698377-54869056:
LRC_KIR KI270915.1 170665 1-170665 19 54698377-54869056
However, If I download patch 9 from ncbi (ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_000001405.24_GRCh38.p9), the same alternative locus is positioned on chr 19:54025634-55084318
LRC_KIR 19 54025634 55084318 alt-scaffold KI270915.1 NT_187669.1 ALT_REF_LOCI_21
Please correct me if I have misunderstood the format of these files.
I have not checked all the alternative loci, but most of them seem to have identical coordinates between the two sources, apart from a few.
Does anyone know why these would be different?
Also, does anyone know how the position of these alternative loci are decided (see this unanswered question: How are the GRC alt locus to primary assembly alignments generated? )?