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What are GL*.* values in chr column of rna seq counts?

This RNA-seq counts file that I came across contains some values in the chromosome column ranging from values ranging GL000191.1:GL000247.1

The regular 1-22, X, Y, MT are in the column too

Are these GL. values used to facilitate use of hg19? Or are they something else?

reference sequencing rna-seq rna
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updated by GenoMax GenoMax • written by LayneSadler LayneSadler

1 answer

Those are unlocalized genomic contigs. Here is one example of an example record that is now deprecated: https://www.ncbi.nlm.nih.gov/nuccore/GL000191.1?report=genbank

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written by GenoMax GenoMax

thank you. hmm, so they found evidence that this sequence exists but do not yet know where it resides in the genome?

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written by LayneSadler LayneSadler

That was the case with previous genome assembly hg19 when this was a valid accession. Since that time this sequence likely made it into main assembly for GRCh38 so this accession has been retired.

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written by GenoMax GenoMax

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