Genotype Imputation

Michigan Imputation Server

The Michigan Imputation Server is a free next-generation genotype imputation platform. You can learn more about the Michigan Imputation Server by visiting their Getting Started documentation. The 1000 Genomes Phase 3 (Version 5) Reference Panel is available on the Michigan Imputation Server.

TOPMed Imputation Server

The TOPMed Imputation Server is another free next-generation genotype imputation platform developed by the University of Michigan and powered by data from the TOPMed Program investigators. You can learn more about the TOPMed Imputation Server by visiting their Getting Started documentation. The TOPMed Version 3 Reference Panel was released in December 2023.

Reference Panels

Reference Panel	Genome Assembly	No. of Samples	Sites (chr1-22)	Chr.	Imputation Server
1000 Genomes Phase 3 (Version 5)	GRCh37/hg19	2,504	49,143,605	1-22, X	Michigan Imputation Server
TOPMed (Version 3)	GRCh38/hg38	133,597	445,600,184	1-22, X	TOPMed Imputation Server

Genome Assemblies

The Genome Reference Consortium (GRC) is the main source of human genome assembly data. The most recent human genome assembly version is GRCh38, released in 2013. The “h” in “GRCh” stands for “human.” The GRC also maintains genome assembly data for rat (r), mouse (m), zebrafish (z), and chicken (g for gallus). Major updates, called “versions”, are released every few years. Minor updates are called “patches” and are released more frequently.

GRCh38 is referred to as “hg38” in the University of California Santa Cruz (UCSC) Genome Browser. The “hg” stands for “human genome.” Before the GRCh38 genome assembly, the version numbers of the GRC and UCSC Genome Browser genome assemblies did not match. For example, when the GRCh37 genome assembly was released in 2009, the UCSC Genome Browser version was “hg19.” Therefore, to minimize confusion, starting with the GRCh38 genome assembly, the UCSC Genome Browser version number was matched as “hg38.”

GRC Version	UCSC Version	Year Released	Genome Coverage	Alternate Haplotypes
GRCh37	hg19	2009	~92.5%	3 regions with 9 alternate loci
GRCh38	hg38	2013	95%	178 regions with 261 alternate loci