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

Question

[LayneSadler]

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?

Answer 1

[GenoMax]

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

[LayneSadler]

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

[GenoMax]

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.