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Enum: HumanGenomeBuild

Human (Homo sapiens) reference genome assemblies. Permissible value names follow the Genome Reference Consortium (GRC) / NCBI assembly names; UCSC database names (hg38, hg19, ...) are given as aliases. Meanings are the INSDC assembly accessions for the base (unpatched) release; patch releases share the same coordinate system.

URI: valuesets:HumanGenomeBuild

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Permissible Values

Value Title Meaning Description Ncbi Assembly Name Refseq Accession Ucsc Name
GRCh38 GRCh38 insdc.gca:GCA_000001405.15 Genome Reference Consortium Human Build 38, released December 2013. Current primary human reference assembly (latest patch GRCh38.p14, GCA_000001405.29). GRCh38 GCF_000001405.26 hg38
GRCh37 GRCh37 insdc.gca:GCA_000001405.1 Genome Reference Consortium Human Build 37, released February 2009. UCSC hg19 is largely equivalent but uses a different mitochondrial sequence (NC_001807 rather than the rCRS NC_012920) and "chr"-prefixed sequence names. GRCh37 GCF_000001405.13 hg19
NCBI36 NCBI36 NCBI Build 36.1 of the human genome, released March 2006. Superseded. NCBI36 GCF_000001405.12 hg18
T2T_CHM13v2 T2T-CHM13v2.0 insdc.gca:GCA_009914755.4 Telomere-to-Telomere Consortium complete gapless assembly of the CHM13 hydatidiform mole cell line, version 2.0 (adds chrY from HG002), released 2022. T2T-CHM13v2.0 GCF_009914755.1 hs1

Slots

Name Description
human_genome_build Reference genome build (assembly) for human sequence coordinates

Identifier and Mapping Information

Annotations

property value
taxon NCBITaxon:9606
stewards https://www.ncbi.nlm.nih.gov/grc

Schema Source

  • from schema: https://w3id.org/valuesets

LinkML Source

name: HumanGenomeBuild
instantiates:
- valuesets_meta:ValueSetEnumDefinition
annotations:
  taxon:
    tag: taxon
    value: NCBITaxon:9606
  stewards:
    tag: stewards
    value: https://www.ncbi.nlm.nih.gov/grc
description: Human (Homo sapiens) reference genome assemblies. Permissible value names
  follow the Genome Reference Consortium (GRC) / NCBI assembly names; UCSC database
  names (hg38, hg19, ...) are given as aliases. Meanings are the INSDC assembly accessions
  for the base (unpatched) release; patch releases share the same coordinate system.
title: Human Genome Build
from_schema: https://w3id.org/valuesets
contributors:
- orcid:0000-0002-6601-2165
- https://github.com/anthropics/claude-code
status: DRAFT
rank: 1000
permissible_values:
  GRCh38:
    text: GRCh38
    description: Genome Reference Consortium Human Build 38, released December 2013.
      Current primary human reference assembly (latest patch GRCh38.p14, GCA_000001405.29).
    meaning: insdc.gca:GCA_000001405.15
    annotations:
      ucsc_name:
        tag: ucsc_name
        value: hg38
      refseq_accession:
        tag: refseq_accession
        value: GCF_000001405.26
      ncbi_assembly_name:
        tag: ncbi_assembly_name
        value: GRCh38
    title: GRCh38
    aliases:
    - hg38
    - GRCh38
    - GRCh38.p14
  GRCh37:
    text: GRCh37
    description: Genome Reference Consortium Human Build 37, released February 2009.
      UCSC hg19 is largely equivalent but uses a different mitochondrial sequence
      (NC_001807 rather than the rCRS NC_012920) and "chr"-prefixed sequence names.
    meaning: insdc.gca:GCA_000001405.1
    annotations:
      ucsc_name:
        tag: ucsc_name
        value: hg19
      refseq_accession:
        tag: refseq_accession
        value: GCF_000001405.13
      ncbi_assembly_name:
        tag: ncbi_assembly_name
        value: GRCh37
    title: GRCh37
    aliases:
    - hg19
    - GRCh37
    - GRCh37.p13
    - b37
  NCBI36:
    text: NCBI36
    description: NCBI Build 36.1 of the human genome, released March 2006. Superseded.
    annotations:
      ucsc_name:
        tag: ucsc_name
        value: hg18
      refseq_accession:
        tag: refseq_accession
        value: GCF_000001405.12
      ncbi_assembly_name:
        tag: ncbi_assembly_name
        value: NCBI36
    title: NCBI36
    aliases:
    - hg18
    - NCBI Build 36
  T2T_CHM13v2:
    text: T2T_CHM13v2
    description: Telomere-to-Telomere Consortium complete gapless assembly of the
      CHM13 hydatidiform mole cell line, version 2.0 (adds chrY from HG002), released
      2022.
    meaning: insdc.gca:GCA_009914755.4
    annotations:
      ucsc_name:
        tag: ucsc_name
        value: hs1
      refseq_accession:
        tag: refseq_accession
        value: GCF_009914755.1
      ncbi_assembly_name:
        tag: ncbi_assembly_name
        value: T2T-CHM13v2.0
    title: T2T-CHM13v2.0
    aliases:
    - T2T-CHM13v2.0
    - CHM13v2.0
    - hs1