Asking the meaning of the reference sequence
I'm running an alignment job and found some interesting reference sequences, like "chrY_KI270740v1_random", etc. I'm curious about the exact meaning of those sequences. Those sequences are like "chrrandom", "chralt", "chrfix", "chUn", and are mostly "GL000" or "KI270*". Can anyone tell me what's their exact meaning?
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GenoMax
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Pallondyle •
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1 answer
See: https://genome.ucsc.edu/FAQ/FAQdownloads#downloadAlt
MHC and LHC Haplotypes (GL,KI): https://www.ncbi.nlm.nih.gov/grc/help/faq/#assembly-regions
You will find this post by Heng Li interesting: https://lh3.github.io/2017/11/13/which-human-reference-genome-to-use
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