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2.5 years ago
irfanwustl
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90
I have downloaded a GENCODE track from UCSC genome browser which has the list of genes and their genomic positions. However, for some genes, I am confused with the chromosome name. For example, I have seen chr15_KI270905v1_alt as a chromosome. I know there is chromosome 15 but what does chr15_KI270905v1_alt mean?
This might be useful: https://gatk.broadinstitute.org/hc/en-us/articles/360041155232-Reference-Genome-Components
_alt"chromosomes" are called alt contigs. These are not really chromosomes; they're contigs (contiguous sequences). The reference genome is made of a bunch of contigs, of which the principal ones are chromosome-wide contigs.