Human Pangenome Reference Consortium

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The Human Pangenome Reference Consortium aims to sequence 300 individuals, producing a pangenome of 600 haplotypes by around 2024. In the recent preprint publication, a first draft human pangenome reference is presented. The study consists of 47 phased, diploid assemblies from a cohort of genetically diverse individuals.

Ensembl annotation of the human assemblies has been produced via a new mapping pipeline:

Genomes and annotations are made available via our FTP site (see table below) and through the UCSC HPRC Assembly Hub

Assembly name Population Accession Assembly submitted by Annotation Proteins Transcripts Variants Other data View in browser
T2T-CHM13v2.0 GCA_009914755.4 T2T Consortium GTF, GFF3 FASTA FASTA ClinVar VCF Gnomad VCF FTP dumps rapid.ensembl.org
HG02257.alt.pat.f1_v2 African Caribbean In Barbados GCA_018466835.1 UCSC Genomics Institute GTF, GFF3 FASTA FASTA ClinVar VCF Gnomad VCF FTP dumps rapid.ensembl.org
HG02257.pri.mat.f1_v2 African Caribbean In Barbados GCA_018466845.1 UCSC Genomics Institute GTF, GFF3 FASTA FASTA ClinVar VCF Gnomad VCF FTP dumps rapid.ensembl.org
HG02559.alt.pat.f1_v2 African Caribbean In Barbados GCA_018466855.1 UCSC Genomics Institute GTF, GFF3 FASTA FASTA ClinVar VCF Gnomad VCF FTP dumps rapid.ensembl.org
HG02559.pri.mat.f1_v2 African Caribbean In Barbados GCA_018466985.1 UCSC Genomics Institute GTF, GFF3 FASTA FASTA ClinVar VCF Gnomad VCF FTP dumps rapid.ensembl.org
HG02486.alt.pat.f1_v2 African Caribbean In Barbados GCA_018467005.1 UCSC Genomics Institute GTF, GFF3 FASTA FASTA ClinVar VCF Gnomad VCF FTP dumps rapid.ensembl.org
HG02486.pri.mat.f1_v2 African Caribbean In Barbados GCA_018467015.1 UCSC Genomics Institute GTF, GFF3 FASTA FASTA ClinVar VCF Gnomad VCF FTP dumps rapid.ensembl.org
HG01891.pri.mat.f1_v2 African Caribbean In Barbados GCA_018467155.1 UCSC Genomics Institute GTF, GFF3 FASTA FASTA ClinVar VCF Gnomad VCF FTP dumps rapid.ensembl.org
HG01891.alt.pat.f1_v2 African Caribbean In Barbados GCA_018467165.1 UCSC Genomics Institute GTF, GFF3 FASTA FASTA ClinVar VCF Gnomad VCF FTP dumps rapid.ensembl.org
HG01258.pri.mat.f1_v2 Colombian In Medellin, Colombia GCA_018469405.1 UCSC Genomics Institute GTF, GFF3 FASTA FASTA ClinVar VCF Gnomad VCF FTP dumps rapid.ensembl.org
HG03516.alt.pat.f1_v2 Esan In Nigeria GCA_018469415.1 UCSC Genomics Institute GTF, GFF3 FASTA FASTA ClinVar VCF Gnomad VCF FTP dumps rapid.ensembl.org
HG03516.pri.mat.f1_v2 Esan In Nigeria GCA_018469425.1 UCSC Genomics Institute GTF, GFF3 FASTA FASTA ClinVar VCF Gnomad VCF FTP dumps rapid.ensembl.org
HG01123.pri.mat.f1_v2.1 Colombian In Medellin, Colombia GCA_018469665.1 UCSC Genomics Institute GTF, GFF3 FASTA FASTA ClinVar VCF Gnomad VCF FTP dumps rapid.ensembl.org
HG01258.alt.pat.f1_v2 Colombian In Medellin, Colombia GCA_018469675.1 UCSC Genomics Institute GTF, GFF3 FASTA FASTA ClinVar VCF Gnomad VCF FTP dumps rapid.ensembl.org
HG01361.pri.mat.f1_v2 Colombian In Medellin, Colombia GCA_018469685.1 UCSC Genomics Institute GTF, GFF3 FASTA FASTA ClinVar VCF Gnomad VCF FTP dumps rapid.ensembl.org
HG01123.alt.pat.f1_v2.1 Colombian In Medellin, Colombia GCA_018469695.1 UCSC Genomics Institute GTF, GFF3 FASTA FASTA ClinVar VCF Gnomad VCF FTP dumps rapid.ensembl.org
HG01361.alt.pat.f1_v2 Colombian In Medellin, Colombia GCA_018469705.1 UCSC Genomics Institute GTF, GFF3 FASTA FASTA ClinVar VCF Gnomad VCF FTP dumps rapid.ensembl.org
HG01358.pri.mat.f1_v2.1 Colombian In Medellin, Colombia GCA_018469865.1 UCSC Genomics Institute GTF, GFF3 FASTA FASTA ClinVar VCF Gnomad VCF FTP dumps rapid.ensembl.org
HG02622.pri.mat.f1_v2 Gambian In Western Division, The Gambia GCA_018469875.1 UCSC Genomics Institute GTF, GFF3 FASTA FASTA ClinVar VCF Gnomad VCF FTP dumps rapid.ensembl.org
HG02622.alt.pat.f1_v2 Gambian In Western Division, The Gambia GCA_018469925.1 UCSC Genomics Institute GTF, GFF3 FASTA FASTA ClinVar VCF Gnomad VCF FTP dumps rapid.ensembl.org
HG02717.pri.mat.f1_v2 Gambian In Western Division, The Gambia GCA_018469935.1 UCSC Genomics Institute GTF, GFF3 FASTA FASTA ClinVar VCF Gnomad VCF FTP dumps rapid.ensembl.org
HG02630.alt.pat.f1_v2 Gambian In Western Division, The Gambia GCA_018469945.1 UCSC Genomics Institute GTF, GFF3 FASTA FASTA ClinVar VCF Gnomad VCF FTP dumps rapid.ensembl.org
HG02630.pri.mat.f1_v2 Gambian In Western Division, The Gambia GCA_018469955.1 UCSC Genomics Institute GTF, GFF3 FASTA FASTA ClinVar VCF Gnomad VCF FTP dumps rapid.ensembl.org
HG01358.alt.pat.f1_v2.1 Colombian In Medellin, Colombia GCA_018469965.1 UCSC Genomics Institute GTF, GFF3 FASTA FASTA ClinVar VCF Gnomad VCF FTP dumps rapid.ensembl.org
HG02717.alt.pat.f1_v2 Gambian In Western Division, The Gambia GCA_018470425.1 UCSC Genomics Institute GTF, GFF3 FASTA FASTA ClinVar VCF Gnomad VCF FTP dumps rapid.ensembl.org
HG02572.alt.pat.f1_v2 Gambian In Western Division, The Gambia GCA_018470435.1 UCSC Genomics Institute GTF, GFF3 FASTA FASTA ClinVar VCF Gnomad VCF FTP dumps rapid.ensembl.org
HG02572.pri.mat.f1_v2 Gambian In Western Division, The Gambia GCA_018470445.1 UCSC Genomics Institute GTF, GFF3 FASTA FASTA ClinVar VCF Gnomad VCF FTP dumps rapid.ensembl.org
HG02886.pri.mat.f1_v2 Gambian In Western Division, The Gambia GCA_018470455.1 UCSC Genomics Institute GTF, GFF3 FASTA FASTA ClinVar VCF Gnomad VCF FTP dumps rapid.ensembl.org
HG02886.alt.pat.f1_v2 Gambian In Western Division, The Gambia GCA_018470465.1 UCSC Genomics Institute GTF, GFF3 FASTA FASTA ClinVar VCF Gnomad VCF FTP dumps rapid.ensembl.org
HG01175.alt.pat.f1_v2 Puerto Rican In Puerto Rico GCA_018471065.1 UCSC Genomics Institute GTF, GFF3 FASTA FASTA ClinVar VCF Gnomad VCF FTP dumps rapid.ensembl.org
HG01106.alt.pat.f1_v2 Puerto Rican In Puerto Rico GCA_018471075.1 UCSC Genomics Institute GTF, GFF3 FASTA FASTA ClinVar VCF Gnomad VCF FTP dumps rapid.ensembl.org
HG01175.pri.mat.f1_v2 Puerto Rican In Puerto Rico GCA_018471085.1 UCSC Genomics Institute GTF, GFF3 FASTA FASTA ClinVar VCF Gnomad VCF FTP dumps rapid.ensembl.org
HG00741.pri.mat.f1_v2 Puerto Rican In Puerto Rico GCA_018471095.1 UCSC Genomics Institute GTF, GFF3 FASTA FASTA ClinVar VCF Gnomad VCF FTP dumps rapid.ensembl.org
HG00741.alt.pat.f1_v2 Puerto Rican In Puerto Rico GCA_018471105.1 UCSC Genomics Institute GTF, GFF3 FASTA FASTA ClinVar VCF Gnomad VCF FTP dumps rapid.ensembl.org
HG01106.pri.mat.f1_v2 Puerto Rican In Puerto Rico GCA_018471345.1 UCSC Genomics Institute GTF, GFF3 FASTA FASTA ClinVar VCF Gnomad VCF FTP dumps rapid.ensembl.org
HG00438.pri.mat.f1_v2 Han Chinese South GCA_018471515.1 UCSC Genomics Institute GTF, GFF3 FASTA FASTA ClinVar VCF Gnomad VCF FTP dumps rapid.ensembl.org
HG02148.alt.pat.f1_v2 Peruvian In Lima, Peru GCA_018471525.1 UCSC Genomics Institute GTF, GFF3 FASTA FASTA ClinVar VCF Gnomad VCF FTP dumps rapid.ensembl.org
HG02148.pri.mat.f1_v2 Peruvian In Lima, Peru GCA_018471535.1 UCSC Genomics Institute GTF, GFF3 FASTA FASTA ClinVar VCF Gnomad VCF FTP dumps rapid.ensembl.org
HG01952.pri.mat.f1_v2 Peruvian In Lima, Peru GCA_018471545.1 UCSC Genomics Institute GTF, GFF3 FASTA FASTA ClinVar VCF Gnomad VCF FTP dumps rapid.ensembl.org
HG01952.alt.pat.f1_v2 Peruvian In Lima, Peru GCA_018471555.1 UCSC Genomics Institute GTF, GFF3 FASTA FASTA ClinVar VCF Gnomad VCF FTP dumps rapid.ensembl.org
HG00673.pri.mat.f1_v2 Han Chinese South GCA_018472565.1 UCSC Genomics Institute GTF, GFF3 FASTA FASTA ClinVar VCF Gnomad VCF FTP dumps rapid.ensembl.org
HG00621.alt.pat.f1_v2 Han Chinese South GCA_018472575.1 UCSC Genomics Institute GTF, GFF3 FASTA FASTA ClinVar VCF Gnomad VCF FTP dumps rapid.ensembl.org
HG00673.alt.pat.f1_v2 Han Chinese South GCA_018472585.1 UCSC Genomics Institute GTF, GFF3 FASTA FASTA ClinVar VCF Gnomad VCF FTP dumps rapid.ensembl.org
HG00438.alt.pat.f1_v2 Han Chinese South GCA_018472595.1 UCSC Genomics Institute GTF, GFF3 FASTA FASTA ClinVar VCF Gnomad VCF FTP dumps rapid.ensembl.org
HG00621.pri.mat.f1_v2 Han Chinese South GCA_018472605.1 UCSC Genomics Institute GTF, GFF3 FASTA FASTA ClinVar VCF Gnomad VCF FTP dumps rapid.ensembl.org
HG01071.pri.mat.f1_v2 Puerto Rican In Puerto Rico GCA_018472685.1 UCSC Genomics Institute GTF, GFF3 FASTA FASTA ClinVar VCF Gnomad VCF FTP dumps rapid.ensembl.org
HG01928.pri.mat.f1_v2 Peruvian In Lima, Peru GCA_018472695.1 UCSC Genomics Institute GTF, GFF3 FASTA FASTA ClinVar VCF Gnomad VCF FTP dumps rapid.ensembl.org
HG01928.alt.pat.f1_v2 Peruvian In Lima, Peru GCA_018472705.1 UCSC Genomics Institute GTF, GFF3 FASTA FASTA ClinVar VCF Gnomad VCF FTP dumps rapid.ensembl.org
HG00735.alt.pat.f1_v2 Puerto Rican In Puerto Rico GCA_018472715.1 UCSC Genomics Institute GTF, GFF3 FASTA FASTA ClinVar VCF Gnomad VCF FTP dumps rapid.ensembl.org
HG01071.alt.pat.f1_v2 Puerto Rican In Puerto Rico GCA_018472725.1 UCSC Genomics Institute GTF, GFF3 FASTA FASTA ClinVar VCF Gnomad VCF FTP dumps rapid.ensembl.org
HG00735.pri.mat.f1_v2 Puerto Rican In Puerto Rico GCA_018472765.1 UCSC Genomics Institute GTF, GFF3 FASTA FASTA ClinVar VCF Gnomad VCF FTP dumps rapid.ensembl.org
HG03579.pri.mat.f1_v2 Mende In Sierra Leone GCA_018472825.1 UCSC Genomics Institute GTF, GFF3 FASTA FASTA ClinVar VCF Gnomad VCF FTP dumps rapid.ensembl.org
HG03579.alt.pat.f1_v2 Mende In Sierra Leone GCA_018472835.1 UCSC Genomics Institute GTF, GFF3 FASTA FASTA ClinVar VCF Gnomad VCF FTP dumps rapid.ensembl.org
HG01978.alt.pat.f1_v2 Peruvian In Lima, Peru GCA_018472845.1 UCSC Genomics Institute GTF, GFF3 FASTA FASTA ClinVar VCF Gnomad VCF FTP dumps rapid.ensembl.org
HG03453.pri.mat.f1_v2 Mende In Sierra Leone GCA_018472855.1 UCSC Genomics Institute GTF, GFF3 FASTA FASTA ClinVar VCF Gnomad VCF FTP dumps rapid.ensembl.org
HG01978.pri.mat.f1_v2 Peruvian In Lima, Peru GCA_018472865.1 UCSC Genomics Institute GTF, GFF3 FASTA FASTA ClinVar VCF Gnomad VCF FTP dumps rapid.ensembl.org
HG03540.pri.mat.f1_v2 Gambian In Western Division, The Gambia GCA_018473295.1 UCSC Genomics Institute GTF, GFF3 FASTA FASTA ClinVar VCF Gnomad VCF FTP dumps rapid.ensembl.org
HG03453.alt.pat.f1_v2 Mende In Sierra Leone GCA_018473305.1 UCSC Genomics Institute GTF, GFF3 FASTA FASTA ClinVar VCF Gnomad VCF FTP dumps rapid.ensembl.org
HG03540.alt.pat.f1_v2 Gambian In Western Division, The Gambia GCA_018473315.1 UCSC Genomics Institute GTF, GFF3 FASTA FASTA ClinVar VCF Gnomad VCF FTP dumps rapid.ensembl.org
HG03486.alt.pat.f1_v2 Mende Of Sierra Leone GCA_018503245.1 UCSC Genomics Institute GTF, GFF3 FASTA FASTA ClinVar VCF Gnomad VCF FTP dumps rapid.ensembl.org
NA18906.pri.mat.f1_v2 Yoruban In Ibadan, Nigeria GCA_018503255.1 UCSC Genomics Institute GTF, GFF3 FASTA FASTA ClinVar VCF Gnomad VCF FTP dumps rapid.ensembl.org
NA19240.alt.pat.f1_v2 Yoruban GCA_018503265.1 UCSC Genomics Institute GTF, GFF3 FASTA FASTA FTP dumps rapid.ensembl.org
NA19240.pri.mat.f1_v2 Yoruban GCA_018503275.1 UCSC Genomics Institute GTF, GFF3 FASTA FASTA FTP dumps rapid.ensembl.org
NA18906.alt.pat.f1_v2 Yoruban In Ibadan, Nigeria GCA_018503285.1 UCSC Genomics Institute GTF, GFF3 FASTA FASTA ClinVar VCF Gnomad VCF FTP dumps rapid.ensembl.org
HG03486.pri.mat.f1_v2 Mende Of Sierra Leone GCA_018503525.1 UCSC Genomics Institute GTF, GFF3 FASTA FASTA ClinVar VCF Gnomad VCF FTP dumps rapid.ensembl.org
HG02818.alt.pat.f1_v2 Gambian In Western Division Of Gambia GCA_018503575.1 UCSC Genomics Institute GTF, GFF3 FASTA FASTA ClinVar VCF Gnomad VCF FTP dumps rapid.ensembl.org
HG02818.pri.mat.f1_v2 Gambian In Western Division Of Gambia GCA_018503585.1 UCSC Genomics Institute GTF, GFF3 FASTA FASTA ClinVar VCF Gnomad VCF FTP dumps rapid.ensembl.org
HG01243.alt.pat.f1_v2 Puerto Rican In Puerto Rico GCA_018504045.1 UCSC Genomics Institute GTF, GFF3 FASTA FASTA ClinVar VCF Gnomad VCF FTP dumps rapid.ensembl.org
HG02080.alt.pat.f1_v2 Vietnamese Kinh In Ho Chi Minh City, Vietnam GCA_018504055.1 UCSC Genomics Institute GTF, GFF3 FASTA FASTA ClinVar VCF Gnomad VCF FTP dumps rapid.ensembl.org
HG02723.pri.mat.f1_v2 Gambian In Western Division, The Gambia GCA_018504065.1 UCSC Genomics Institute GTF, GFF3 FASTA FASTA ClinVar VCF Gnomad VCF FTP dumps rapid.ensembl.org
HG02723.alt.pat.f1_v2 Gambian In Western Division, The Gambia GCA_018504075.1 UCSC Genomics Institute GTF, GFF3 FASTA FASTA ClinVar VCF Gnomad VCF FTP dumps rapid.ensembl.org
HG02080.pri.mat.f1_v2 Vietnamese Kinh In Ho Chi Minh City, Vietnam GCA_018504085.1 UCSC Genomics Institute GTF, GFF3 FASTA FASTA ClinVar VCF Gnomad VCF FTP dumps rapid.ensembl.org
HG01109.pri.mat.f1_v2 Puerto Rico GCA_018504365.1 UCSC Genomics Institute GTF, GFF3 FASTA FASTA ClinVar VCF Gnomad VCF FTP dumps rapid.ensembl.org
HG01243.pri.mat.f1_v2 Puerto Rican In Puerto Rico GCA_018504375.1 UCSC Genomics Institute GTF, GFF3 FASTA FASTA ClinVar VCF Gnomad VCF FTP dumps rapid.ensembl.org
NA20129.alt.pat.f1_v2 Southwest USA GCA_018504625.1 UCSC Genomics Institute GTF, GFF3 FASTA FASTA ClinVar VCF Gnomad VCF FTP dumps rapid.ensembl.org
NA20129.pri.mat.f1_v2 Southwest USA GCA_018504635.1 UCSC Genomics Institute GTF, GFF3 FASTA FASTA ClinVar VCF Gnomad VCF FTP dumps rapid.ensembl.org
HG01109.alt.pat.f1_v2 Puerto Rico GCA_018504645.1 UCSC Genomics Institute GTF, GFF3 FASTA FASTA ClinVar VCF Gnomad VCF FTP dumps rapid.ensembl.org
NA21309.pri.mat.f1_v2 Kinyawa, Kenya GCA_018504655.1 UCSC Genomics Institute GTF, GFF3 FASTA FASTA ClinVar VCF Gnomad VCF FTP dumps rapid.ensembl.org
NA21309.alt.pat.f1_v2 Kinyawa, Kenya GCA_018504665.1 UCSC Genomics Institute GTF, GFF3 FASTA FASTA ClinVar VCF Gnomad VCF FTP dumps rapid.ensembl.org
HG02109.pri.mat.f1_v2 African Ancestry From Barbados In The Caribbean GCA_018505825.1 UCSC Genomics Institute GTF, GFF3 FASTA FASTA ClinVar VCF Gnomad VCF FTP dumps rapid.ensembl.org
HG03492.alt.pat.f1_v2 Punjabi In Lahore, Pakistan GCA_018505835.1 UCSC Genomics Institute GTF, GFF3 FASTA FASTA ClinVar VCF Gnomad VCF FTP dumps rapid.ensembl.org
HG03492.pri.mat.f1_v2 Punjabi In Lahore, Pakistan GCA_018505845.1 UCSC Genomics Institute GTF, GFF3 FASTA FASTA ClinVar VCF Gnomad VCF FTP dumps rapid.ensembl.org
HG02055.alt.pat.f1_v2 Barbados GCA_018505855.1 UCSC Genomics Institute GTF, GFF3 FASTA FASTA ClinVar VCF Gnomad VCF FTP dumps rapid.ensembl.org
HG02109.alt.pat.f1_v2 African Ancestry From Barbados In The Caribbean GCA_018505865.1 UCSC Genomics Institute GTF, GFF3 FASTA FASTA ClinVar VCF Gnomad VCF FTP dumps rapid.ensembl.org
HG02055.pri.mat.f1_v2 Barbados GCA_018506125.1 UCSC Genomics Institute GTF, GFF3 FASTA FASTA ClinVar VCF Gnomad VCF FTP dumps rapid.ensembl.org
HG03098.alt.pat.f1_v2 Mende In Sierra Leone GCA_018506155.1 UCSC Genomics Institute GTF, GFF3 FASTA FASTA ClinVar VCF Gnomad VCF FTP dumps rapid.ensembl.org
HG03098.pri.mat.f1_v2 Mende In Sierra Leone GCA_018506165.1 UCSC Genomics Institute GTF, GFF3 FASTA FASTA ClinVar VCF Gnomad VCF FTP dumps rapid.ensembl.org
HG005.alt.pat.f1_v2 Asian GCA_018506945.1 UCSC Genomics Institute GTF, GFF3 FASTA FASTA FTP dumps rapid.ensembl.org
HG00733.alt.pat.f1_v2 Puerto Rican In Puerto Rico GCA_018506955.1 UCSC Genomics Institute GTF, GFF3 FASTA FASTA ClinVar VCF Gnomad VCF FTP dumps rapid.ensembl.org
HG005.pri.mat.f1_v2 Asian GCA_018506965.1 UCSC Genomics Institute GTF, GFF3 FASTA FASTA FTP dumps rapid.ensembl.org
HG00733.pri.mat.f1_v2 Puerto Rican In Puerto Rico GCA_018506975.1 UCSC Genomics Institute GTF, GFF3 FASTA FASTA ClinVar VCF Gnomad VCF FTP dumps rapid.ensembl.org
HG02145.pri.mat.f1_v2 African Ancestry From Barbados In The Caribbean GCA_018852585.1 UCSC Genomics Institute GTF, GFF3 FASTA FASTA ClinVar VCF Gnomad VCF FTP dumps rapid.ensembl.org
HG02145.alt.pat.f1_v2 African Ancestry From Barbados In The Caribbean GCA_018852595.1 UCSC Genomics Institute GTF, GFF3 FASTA FASTA ClinVar VCF Gnomad VCF FTP dumps rapid.ensembl.org
HG002.alt.pat.f1_v2 Caucasian GCA_018852605.1 UCSC Genomics Institute GTF, GFF3 FASTA FASTA FTP dumps rapid.ensembl.org
HG002.pri.mat.f1_v2 Caucasian GCA_018852615.1 UCSC Genomics Institute GTF, GFF3 FASTA FASTA FTP dumps rapid.ensembl.org
HG002.pat.cur.20211005 Caucasian GCA_021950905.1 UCSC Genomics Institute GTF, GFF3 FASTA FASTA FTP dumps rapid.ensembl.org
HG002.mat.cur.20211005 Caucasian GCA_021951015.1 UCSC Genomics Institute GTF, GFF3 FASTA FASTA FTP dumps rapid.ensembl.org