The sequence region names in the GENCODE annotation files are a mixture of UCSC names (reference chromosomes) and GenBank accessions (unplaced and unlocalized scaffolds, patches and haplotypes). In the files in this directory, all the sequence region names correspond to the UCSC style.

The equivalences between GenBank accessions and UCSC names were extracted from the following file:

ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/vertebrate_mammalian/Homo_sapiens/all_assembly_versions/GCA_000001405.27_GRCh38.p12/GCA_000001405.27_GRCh38.p12_assembly_report.txt