I found location like chr1_KI270761v1_alt:75599-75749 and chr1_KI270892v1_alt:71977-72127 while remapping hg19 genomic coordinates to hg38 using NCBI remap. What does 'KI270761v1_alt and KI270892v1_alt' refer to? I tried but could not find good explaining for it.
1 answer
http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/info/faq.shtml#FAQ2
Alternate Locus
A sequence that provides an alternate representation of a locus found in a largely haploid assembly. These sequences don't represent a complete chromosome sequence although there is no hard limit on the size of the alternate locus; currently these are less than 1 Mb. Previously these sequences have been referred to as "partial chromosomes", "alternate alleles", and "alternate haplotypes". However, these terms are confusing because they contain terms that have biological implications. Diploid assemblies (which by definition are from a single individual) should not have alternate loci representations. Multiple scaffolds from different loci that are considered to be part of the same haplotype should be grouped into alternate locus groups (e.g. mouse 129/Sv group). Note: an alternate locus group was previously considered an alternate partial assembly.
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