Frequently Asked Questions: Assembly Releases and Versions

Topics

• List of UCSC genome releases
• Initial assembly release dates
• Patch sequences for human and mouse
• UCSC assemblies
• Comparison of UCSC and NCBI human assemblies
• Looking for a genome assembly not shown in the tree?
• Differences between UCSC and NCBI mouse assemblies
• Accessing older assembly versions
• Frequency of GenBank data updates
• Coordinate changes between assemblies
• Converting positions between assembly versions
• Converting SNPs between assembly versions
• How can I convert SNP annotation coordinates between assembly versions?
• How can I convert a large set of SNP annotations?
• How can I extract a list of rsIDs using chrom:start-end or vise versa?
• Missing annotation tracks
• What next with the human genome?
• Mouse strain used for mouse genome sequence

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List of UCSC genome releases

How do UCSC's release numbers correspond to those of other organizations, such as NCBI?

The first release of an assembly is given a name using the first three characters of the organism's genus and species classification in the format gggSss#, with subsequent assemblies incrementing the number. Assemblies predating the 2003 introduction of the six-letter naming system were given two-letter names in a similar gs# format and human assemblies are named hg# for human genome.

SPECIES	UCSC VERSION	RELEASE DATE	RELEASE NAME	STATUS
MAMMALS
Human	hs1	Jan. 2022	T2T Consortium CHM13v2.0	Available
	hg38	Dec. 2013	Genome Reference Consortium GRCh38	Available
	hg19	Feb. 2009	Genome Reference Consortium GRCh37	Available
	hg18	Mar. 2006	NCBI Build 36.1	Available
	hg17	May 2004	NCBI Build 35	Available
	hg16	Jul. 2003	NCBI Build 34	Available
	hg15	Apr. 2003	NCBI Build 33	Archived
	hg13	Nov. 2002	NCBI Build 31	Archived
	hg12	Jun. 2002	NCBI Build 30	Archived
	hg11	Apr. 2002	NCBI Build 29	Archived (data only)
	hg10	Dec. 2001	NCBI Build 28	Archived (data only)
	hg8	Aug. 2001	UCSC-assembled	Archived (data only)
	hg7	Apr. 2001	UCSC-assembled	Archived (data only)
	hg6	Dec. 2000	UCSC-assembled	Archived (data only)
	hg5	Oct. 2000	UCSC-assembled	Archived (data only)
	hg4	Sep. 2000	UCSC-assembled	Archived (data only)
	hg3	Jul. 2000	UCSC-assembled	Archived (data only)
	hg2	Jun. 2000	UCSC-assembled	Archived (data only)
	hg1	May 2000	UCSC-assembled	Archived (data only)
Alpaca	vicPac2	Mar. 2013	Broad Institute Vicugna_pacos-2.0.1	Available
	vicPac1	Jul. 2008	Broad Institute VicPac1.0	Available
Armadillo	dasNov3	Dec. 2011	Broad Institute DasNov3	Available
Baboon	papAnu4	Apr. 2017	Human Genome Sequencing Center	Available
	papAnu2	Mar. 2012	Baylor College of Medicine Panu_2.0	Available
	papHam1	Nov. 2008	Baylor College of Medicine HGSC Pham_1.0	Available
Bison	bisBis1	Oct. 2014	Univ. of Maryland Bison_UMD1.0	Available
Bonobo	panPan3	May 2020	University of Washington	Available
	panPan2	Dec. 2015	Max-Planck Institute for Evolutionary Anthropology panpan1.1	Available
	panPan1	May 2012	Max-Planck Institute panpan1	Available
Brown kiwi	aptMan1	Jun. 2015	Max-Planck Institute for Evolutionary Anthropology AptMant0	Available
Bushbaby	otoGar3	Mar. 2011	Broad Institute OtoGar3	Available
Cat	felCat9	Nov. 2017	Genome Sequencing Center (GSC) at Washington University (WashU) School of Medicine Felis_catus_9.0	Available
	felCat8	Nov. 2014	ICGSC Felis_catus_8.0	Available
	felCat5	Sep. 2011	ICGSC Felis_catus-6.2	Available
	felCat4	Dec. 2008	NHGRI catChrV17e	Available
	felCat3	Mar. 2006	Broad Institute Release 3	Available
Chimp	panTro6	Jan. 2018	Clint_PTRv2	Available
	panTro5	May 2016	CGSC Build 3.0	Available
	panTro4	Feb. 2011	CGSC Build 2.1.4	Available
	panTro3	Oct. 2010	CGSC Build 2.1.3	Available
	panTro2	Mar. 2006	CGSC Build 2.1	Available
	panTro1	Nov. 2003	CGSC Build 1.1	Available
Chinese hamster	criGri1	Jul. 2013	Beijing Genomics Institution-Shenzhen C_griseus_v1.0	Available
Chinese hamster ovary cell line	criGriChoV2	Jun. 2017	Eagle Genomics Ltd CHOK1S_HZDv1	Available
	criGriChoV1	Aug. 2011	Beijing Genomics Institute CriGri_1.0	Available
Chinese pangolin	manPen1	Aug. 2014	Washington University (WashU) M_pentadactyla-1.1.1	Available
Cow	bosTau9	Apr. 2018	USDA ARS	Available
	bosTau8	Jun. 2014	University of Maryland v3.1.1	Available
	bosTau7	Oct. 2011	Baylor College of Medicine HGSC Btau_4.6.1	Available
	bosTau6	Nov. 2009	University of Maryland v3.1	Available
	bosTau4	Oct. 2007	Baylor College of Medicine HGSC Btau_4.0	Available
	bosTau3	Aug. 2006	Baylor College of Medicine HGSC Btau_3.1	Available
	bosTau2	Mar. 2005	Baylor College of Medicine HGSC Btau_2.0	Available
	bosTau1	Sep. 2004	Baylor College of Medicine HGSC Btau_1.0	Archived
Crab-eating macaque	macFas5	Jun. 2013	Washington University Macaca_fascicularis_5.0	Available
Dog	canFam6	Oct. 2020	Dog Genome Sequencing Consortium Dog10K_Boxer_Tasha	Available
	canFam5	May 2019	University of Michigan	Available
	canFam4	Mar. 2020	Uppsala University	Available
	canFam3	Sep. 2011	Broad Institute v3.1	Available
	canFam2	May 2005	Broad Institute v2.0	Available
	canFam1	Jul. 2004	Broad Institute v1.0	Available
Dolphin	turTru2	Oct. 2011	Baylor College of Medicine Ttru_1.4	Available
Elephant	loxAfr3	Jul. 2009	Broad Institute LoxAfr3	Available
Ferret	musFur1	Apr. 2011	Ferret Genome Sequencing Consortium MusPutFur1.0	Available
Garter snake	thaSir1	Jun. 2015	Washington University Thamnophis_sirtalis-6.0	Available
Gibbon	nomLeu3	Oct. 2012	Gibbon Genome Sequencing Consortium Nleu3.0	Available
	nomLeu2	Jun. 2011	Gibbon Genome Sequencing Consortium Nleu1.1	Available
	nomLeu1	Jan. 2010	Gibbon Genome Sequencing Consortium Nleu1.0	Available
Golden eagle	aquChr2	Oct. 2014	University of Washington aquChr2-1.0.2	Available
Golden snub-nosed monkey	rhiRox1	Oct. 2014	Novogene Rrox_v1	Available
Gorilla	gorGor6	Aug. 2019	University of Washington	Available
	gorGor5	Mar. 2016	University of Washington GSMRT3	Available
	gorGor4	Dec. 2014	Wellcome Trust Sanger Institute gorGor4	Available
	gorGor3	May 2011	Wellcome Trust Sanger Institute gorGor3.1	Available
Green Monkey	chlSab2	Mar. 2014	Vervet Genomics Consortium 1.1	Available
Guinea pig	cavPor3	Feb. 2008	Broad Institute cavPor3	Available
Hawaiian monk seal	neoSch1	Jun. 2017	Johns Hopkins University ASM220157v1	Available
Hedgehog	eriEur2	May 2012	Broad Institute EriEur2.0	Available
	eriEur1	Jun. 2006	Broad Institute Draft_v1	Available
Horse	equCab3	Jan. 2018	University of Louisville	Available
	equCab2	Sep. 2007	Broad Institute EquCab2	Available
	equCab1	Jan. 2007	Broad Institute EquCab1	Available
Kangaroo rat	dipOrd1	Jul. 2008	Baylor/Broad Institute DipOrd1.0	Available
Little brown bat	myoLuc2	Jul. 2010	Broad Institute MyoLuc2.0	Available
Malayan flying lemur	galVar1	Jul. 2014	WashU G_variegatus-3.0.2	Available
Manatee	triMan1	Oct. 2011	Broad Institute TriManLat1.0	Available
Marmoset	calJac4	May 2020	Washington University Callithrix_jacchus_cj1700_1.1	Available
Marmoset	calJac3	Mar. 2009	WUSTL Callithrix_jacchus-v3.2	Available
	calJac1	Jun. 2007	WUSTL Callithrix_jacchus-v2.0.2	Available
Megabat	pteVam1	Jul. 2008	Broad Institute Ptevap1.0	Available
Minke whale	balAcu1	Oct. 2013	KORDI BalAcu1.0	Available
Mouse	mm39	Jun. 2020	Genome Reference Consortium Mouse Build 39	Available
	mm10	Dec. 2011	Genome Reference Consortium GRCm38	Available
	mm9	Jul. 2007	NCBI Build 37	Available
	mm8	Feb. 2006	NCBI Build 36	Available
	mm7	Aug. 2005	NCBI Build 35	Available
	mm6	Mar. 2005	NCBI Build 34	Archived
	mm5	May 2004	NCBI Build 33	Archived
	mm4	Oct. 2003	NCBI Build 32	Archived
	mm3	Feb. 2003	NCBI Build 30	Archived
	mm2	Feb. 2002	MGSCv3	Archived
	mm1	Nov. 2001	MGSCv2	Archived (data only)
Mouse lemur	micMur2	May 2015	Baylor/Broad Institute Mmur_2.0	Available
	micMur1	Jul. 2007	Broad Institute MicMur1.0	Available
Naked mole-rat	hetGla2	Jan. 2012	Broad Institute HetGla_female_1.0	Available
	hetGla1	Jul. 2011	Beijing Genomics Institute HetGla_1.0	Available
Opossum	monDom5	Oct. 2006	Broad Institute release MonDom5	Available
	monDom4	Jan. 2006	Broad Institute release MonDom4	Available
	monDom1	Oct. 2004	Broad Institute release MonDom1	Available
Orangutan	ponAbe2	Jul. 2007	WUSTL Pongo_albelii-2.0.2	Available
	ponAbe3	Jan. 2018	Susie_PABv2/ponAbe3	Available
Panda	ailMel1	Dec. 2009	BGI-Shenzhen AilMel 1.0	Available
Pig	susScr11	Feb. 2017	Swine Genome Sequencing Consortium Sscrofa11.1	Available
	susScr3	Aug. 2011	Swine Genome Sequencing Consortium Sscrofa10.2	Available
	susScr2	Nov. 2009	Swine Genome Sequencing Consortium Sscrofa9.2	Available
Pika	ochPri3	May 2012	Broad Institute OchPri3.0	Available
	ochPri2	Jul. 2008	Broad Institute OchPri2	Available
Platypus	ornAna2	Feb. 2007	WUSTL v5.0.1	Available
	ornAna1	Mar. 2007	WUSTL v5.0.1	Available
Proboscis Monkey	nasLar1	Nov. 2014	Proboscis Monkey Functional Genome Consortium Charlie1.0	Available
Rabbit	oryCun2	Apr. 2009	Broad Institute release OryCun2	Available
Rat	rn7	Nov. 2020	Wellcome Sanger Institute mRatBN7.2	Available
	rn6	Jul. 2014	RGSC Rnor_6.0	Available
	rn5	Mar. 2012	RGSC Rnor_5.0	Available
	rn4	Nov. 2004	Baylor College of Medicine HGSC v3.4	Available
	rn3	Jun. 2003	Baylor College of Medicine HGSC v3.1	Available
	rn2	Jan. 2003	Baylor College of Medicine HGSC v2.1	Archived
	rn1	Nov. 2002	Baylor College of Medicine HGSC v1.0	Archived
Rhesus	rheMac10	Feb. 2019	The Genome Institute at Washington University School of Medicine Mmul_10	Available
	rheMac8	Nov. 2015	Baylor College of Medicine HGSC Mmul_8.0.1	Available
	rheMac3	Oct. 2010	Beijing Genomics Institute CR_1.0	Available
	rheMac2	Jan. 2006	Baylor College of Medicine HGSC v1.0 Mmul_051212	Available
	rheMac1	Jan. 2005	Baylor College of Medicine HGSC Mmul_0.1	Archived
Rock hyrax	proCap1	Jul. 2008	Baylor College of Medicine HGSC Procap1.0	Available
Sheep	oviAri4	Dec. 2015	ISGC Oar_v4.0	Available
	oviAri3	Aug. 2012	ISGC Oar_v3.1	Available
	oviAri1	Feb. 2010	ISGC Ovis aries 1.0	Available
Shrew	sorAra2	Aug. 2008	Broad Institute SorAra2.0	Available
	sorAra1	Jun. 2006	Broad Institute SorAra1.0	Available
Sloth	choHof1	Jul. 2008	Broad Institute ChoHof1.0	Available
Squirrel	speTri2	Nov. 2011	Broad Institute SpeTri2.0	Available
Squirrel monkey	saiBol1	Oct. 2011	Broad Institute SaiBol1.0	Available
Tarsier	tarSyr2	Sep. 2013	WashU Tarsius_syrichta-2.0.1	Available
	tarSyr1	Aug. 2008	WUSTL/Broad Institute Tarsyr1.0	Available
Tasmanian devil	sarHar1	Feb. 2011	Wellcome Trust Sanger Institute Devil_refv7.0	Available
Tenrec	echTel2	Nov. 2012	Broad Institute EchTel2.0	Available
	echTel1	Jul. 2005	Broad Institute echTel1	Available
Tree shrew	tupBel1	Dec. 2006	Broad Institute Tupbel1.0	Available
Wallaby	macEug2	Sep. 2009	Tammar Wallaby Genome Sequencing Consortium Meug_1.1	Available
White rhinoceros	cerSim1	May 2012	Broad Institute CerSimSim1.0	Available
VERTEBRATES
African clawed frog	xenLae2	Aug. 2016	Int. Xenopus Sequencing Consortium	Available
American alligator	allMis1	Aug. 2012	Int. Crocodilian Genomes Working Group allMis0.2	Available
Atlantic cod	gadMor1	May 2010	Genofisk GadMor_May2010	Available
Budgerigar	melUnd1	Sep. 2011	WUSTL v6.3	Available
Chicken	galGal6	Mar. 2018	GRCg6 Gallus-gallus-6.0	Available
	galGal5	Dec. 2015	ICGC Gallus-gallus-5.0	Available
	galGal4	Nov. 2011	ICGC Gallus-gallus-4.0	Available
	galGal3	May 2006	WUSTL Gallus-gallus-2.1	Available
	galGal2	Feb. 2004	WUSTL Gallus-gallus-1.0	Available
Coelacanth	latCha1	Aug. 2011	Broad Institute LatCha1	Available
Elephant shark	calMil1	Dec. 2013	IMCB Callorhinchus_milli_6.1.3	Available
Fugu	fr3	Oct. 2011	JGI v5.0	Available
	fr2	Oct. 2004	JGI v4.0	Available
	fr1	Aug. 2002	JGI v3.0	Available
Lamprey	petMar3	Dec. 2017	University of Kentucky Pmar_germline 1.0	Available
	petMar2	Sep. 2010	WUGSC 7.0	Available
	petMar1	Mar. 2007	WUSTL v3.0	Available
Lizard	anoCar2	May 2010	Broad Institute AnoCar2	Available
	anoCar1	Feb. 2007	Broad Institute AnoCar1	Available
Medaka	oryLat2	Oct. 2005	NIG v1.0	Available
Medium ground finch	geoFor1	Apr. 2012	BGI GeoFor_1.0 / NCBI 13302	Available
Nile tilapia	oreNil2	Jan. 2011	Broad Institute Release OreNil1.1	Available
Painted turtle	chrPic1	Dec. 2011	IPTGSC Chrysemys_picta_bellii-3.0.1	Available
Stickleback	gasAcu1	Feb. 2006	Broad Institute Release 1.0	Available
Tetraodon	tetNig2	Mar. 2007	Genoscope v7	Available
	tetNig1	Feb. 2004	Genoscope v7	Available
Tibetan frog	nanPar1	Mar. 2015	Beijing Genomics Institute BGI_ZX_20015	Available
Turkey	melGal5	Nov. 2014	Turkey Genome Consortium v5.0	Available
	melGal1	Dec. 2009	Turkey Genome Consortium v2.01	Available
X. tropicalis	xenTro10	Nov. 2019	University of California, Berkeley UCB_Xtro_10.0	Available
	xenTro9	Jul. 2016	JGI v.9.1	Available
	xenTro7	Sep. 2012	JGI v.7.0	Available
	xenTro3	Nov. 2009	JGI v.4.2	Available
	xenTro2	Aug. 2005	JGI v.4.1	Available
	xenTro1	Oct. 2004	JGI v.3.0	Available
Zebra finch	taeGut2	Feb. 2013	WashU taeGut324	Available
	taeGut1	Jul. 2008	WUSTL v3.2.4	Available
Zebrafish	danRer11	May 2017	Genome Reference Consortium GRCz11	Available
	danRer10	Sep. 2014	Genome Reference Consortium GRCz10	Available
	danRer7	Jul. 2010	Sanger Institute Zv9	Available
	danRer6	Dec. 2008	Sanger Institute Zv8	Available
	danRer5	Jul. 2007	Sanger Institute Zv7	Available
	danRer4	Mar. 2006	Sanger Institute Zv6	Available
	danRer3	May 2005	Sanger Institute Zv5	Available
	danRer2	Jun. 2004	Sanger Institute Zv4	Archived
	danRer1	Nov. 2003	Sanger Institute Zv3	Archived
DEUTEROSTOMES
C. intestinalis	ci3	Apr. 2011	Kyoto KH	Available
C. intestinalis	ci2	Mar. 2005	JGI v2.0	Available
	ci1	Dec. 2002	JGI v1.0	Available
Lancelet	braFlo1	Mar. 2006	JGI v1.0	Available
S. purpuratus	strPur2	Sep. 2006	Baylor College of Medicine HGSC v. Spur 2.1	Available
	strPur1	Apr. 2005	Baylor College of Medicine HGSC v. Spur_0.5	Available
INSECTS
A. mellifera	apiMel2	Jan. 2005	Baylor College of Medicine HGSC v.Amel_2.0	Available
	apiMel1	Jul. 2004	Baylor College of Medicine HGSC v.Amel_1.2	Available
A. gambiae	anoGam3	Oct. 2006	International Consortium for the Sequencing of Anopheles Genome AgamP3	Available
	anoGam1	Feb. 2003	IAGP v.MOZ2	Available
D. ananassae	droAna2	Aug. 2005	Agencourt Arachne release	Available
	droAna1	Jul. 2004	TIGR Celera release	Available
D. erecta	droEre1	Aug. 2005	Agencourt Arachne release	Available
D. grimshawi	droGri1	Aug. 2005	Agencourt Arachne release	Available
D. melanogaster	dm6	Aug. 2014	BDGP Release 6 + ISO1 MT	Available
	dm3	Apr. 2006	BDGP Release 5	Available
	dm2	Apr. 2004	BDGP Release 4	Available
	dm1	Jan. 2003	BDGP Release 3	Available
D. mojavensis	droMoj2	Aug. 2005	Agencourt Arachne release	Available
	droMoj1	Aug. 2004	Agencourt Arachne release	Available
D. persimilis	droPer1	Oct. 2005	Broad Institute release	Available
D. pseudoobscura	dp3	Nov. 2004	FlyBase Release 1.0	Available
	dp2	Aug. 2003	Baylor College of Medicine HGSC Freeze 1	Available
D. sechellia	droSec1	Oct. 2005	Broad Institute Release 1.0	Available
D. simulans	droSim1	Apr. 2005	WUSTL Release 1.0	Available
D. virilis	droVir2	Aug. 2005	Agencourt Arachne release	Available
	droVir1	Jul. 2004	Agencourt Arachne release	Available
D. yakuba	droYak2	Nov. 2005	WUSTL Release 2.0	Available
	droYak1	Apr. 2004	WUSTL Release 1.0	Available
NEMATODES
C. brenneri	caePb2	Feb. 2008	WUSTL 6.0.1	Available
	caePb1	Jan. 2007	WUSTL 4.0	Available
C. briggsae	cb3	Jan. 2007	WUSTL Cb3	Available
	cb1	Jul. 2002	WormBase v. cb25.agp8	Available
C. elegans	ce11	Feb. 2013	C. elegans Sequencing Consortium WBcel235	Available
	ce10	Oct. 2010	WormBase v. WS220	Available
	ce6	May 2008	WormBase v. WS190	Available
	ce4	Jan. 2007	WormBase v. WS170	Available
	ce2	Mar. 2004	WormBase v. WS120	Available
	ce1	May 2003	WormBase v. WS100	Archived
C. japonica	caeJap1	Mar. 2008	WUSTL 3.0.2	Available
C. remanei	caeRem3	May 2007	WUSTL 15.0.1	Available
	caeRem2	Mar. 2006	WUSTL 1.0	Available
P. pacificus	priPac1	Feb. 2007	WUSTL 5.0	Available
OTHER
Sea Hare	aplCal1	Sep. 2008	Broad Release Aplcal2.0	Available
Yeast	sacCer3	April 2011	SGD April 2011 sequence	Available
	sacCer2	June 2008	SGD June 2008 sequence	Available
	sacCer1	Oct. 2003	SGD 1 Oct 2003 sequence	Available
VIRUSES
Ebola Virus	eboVir3	June 2014	Sierra Leone 2014 (G3683/KM034562.1)	Available
Monkeypox Virus	mpxvRivers	May 2022	MPXV-M5312_HM12_Rivers (MT903340.1/GCF_014621545.1)	Available
SARS-CoV-2	wuhCor1	Jan. 2020	SARS-CoV-2 ASM985889v3	Available

Initial assembly release dates

When will the next assembly be out?

UCSC does not produce its own genome assemblies, but instead obtains them from standard sources. Because of this, you can expect us to release a new version of a genome soon after the assembling organization has released the version. A new assembly release initially consists of the genome sequence and a small set of aligned annotation tracks. Additional annotation tracks are added as they are obtained or generated. Bulk downloads of the data are typically available in the first week after the assembly is released in the browser.

Patch sequences for genome assemblies

Why am I seeing chr_alt or chr_fix chromosomes on the Genome Browser?

Since the intial Genome Reference Consortium (GRC) release of the human and mouse genome assemblies, there have been updates to these assemblies known as "patches". Patches are accessioned scaffold sequences that add information to the assembly without disrupting the chromosome coordinates. Patches are given chromosome context by aligning the sequence to the current assembly. Together the scaffod sequence and the alignment define the patch to the genome assembly. The GRC patch releases do not change any previously existing sequences; they simply add new sequences for fix patches or alternate haplotypes that correspond to specific regions of the main chromosome sequences. For most users, the patches are unlikely to make a difference and may complicate the analysis as they can introduce duplication.

There are two kinds of GRC patch sequences, chr_alt and chr_fix sequences:

• Novel patches (alternative haplotypes) - Chromosomal regions of the genome that exhibit sufficient variability to prevent adequate representation by a single sequence. Also referred to as alternate loci. The Genome Browser labels these haplotype sequences by appending "_alt" to their names, i.e., chr5_KI270794v1_alt.
• Fix patches - Error corrections (addressed by approaches such as base changes, component replacements/updates, switch-point updates or tiling-path changes) or assembly improvements, such as the extension of sequence into gaps. The Genome Browser labels these fix sequences by appending "_fix" to their names, i.e., chr1_KN538361v1_fix.

The Patching up the Genome blog post contains more information on how patch sequences are incorporated into the UCSC Genome Browser. For more information about how patch sequences can affects BLAT and isPCR results, please refer to the following BLAT FAQ.

Data sources - UCSC assemblies

Where does UCSC obtain the assembly and annotation data displayed in the Genome Browser?

All the assembly data displayed in the UCSC Genome Browser are obtained from external sequencing centers. To determine the data source and version for a given assembly, see the assembly's description on the Genome Browser Gateway page or the List of UCSC Genome Releases.

The annotations accompanying an assembly are obtained from a variety of sources. The UCSC Genome Bioinformatics Group generates several of the tracks; the remainder are contributed by collaborators at other sites. Each track has an associated description page that credits the authors of the annotation.

For detailed information about the individuals and organizations who contributed to a specific assembly, see the Credits page.

Which UCSC assemblies are equivalent to Ensembl or NCBI assemblies?

The asmEquivalent table on the hgFixed database is available on the public MySQL server to show which assemblies versions are identical (or almost identical) to each other between UCSC, Ensembl, Genbank, and RefSeq assemblies.

mysql --user=genome --host=genome-mysql.soe.ucsc.edu -A -e 'desc asmEquivalent;' hgFixed
+----------------------+-------------------------------------------+
| Field                | Type                                      |
+----------------------+-------------------------------------------+
| source               | varchar(255)                              |
| destination          | varchar(255)                              |
| sourceAuthority      | enum('ensembl','ucsc','genbank','refseq') |
| destinationAuthority | enum('ensembl','ucsc','genbank','refseq') |
| matchCount           | bigint(20)                                |
| sourceCount          | bigint(20)                                |
| destinationCount     | bigint(20)                                |
+----------------------+-------------------------------------------+

The "Count" indications are the count of individual sequences in the assembly. When all three counts are identical, matchCount == sourceCount == destinationCount, then the match between genome assemblies is perfectly identical.

Non-perfect matches can be due to a number of factors:

1. different or not included chrMT genome sequences in an assembly
2. identical duplicated sequences present or absent from an assembly
3. some smaller contigs not included in an assembly
4. slight differences in versions of assemblies where some contain sequences not in the other assembly

Comparison of UCSC and NCBI human assemblies

How do the human assemblies displayed in the UCSC Genome Browser differ from the NCBI human assemblies?

Human assemblies displayed in the Genome Browser (hg10 and higher) are near identical to the NCBI assemblies when it comes to primary sequence. Minor differences may be present, however. Sources include:

• NCBI genomes are repeat masked with RepeatMasker, however, UCSC genomes are independently masked with both RepeatMasker (with different flags) and WindowMasker, ultimately using the program output with the highest percentage masked for the base sequence
• In genome download files, UCSC uses the 'chr1' nomenclature for sequence identifiers, whereas the primary NCBI sequence identifiers are RefSeq accessions
• The original mitochondrion (chrM) for hg19 differs from the one in NCBI (GRCh37)
• The mitochondrion released by NCBI after the hg19 browser was built has been added to the assemby as chrMT. See our documentation for details.

Looking for a genome assembly not shown in the tree?

When looking for a specific assembly, the best place to start is the Gateway page. If you begin to type the common name, species name, or NCBI RefSeq accession number in the search box on the left side of the screen, suggestions will appear if any matches are found. This search will also match any assembly hubs that are listed in UCSC's Public Hubs. Nearly every NCBI RefSeq assembly and Vertebrate Genomes Project assembly is included here within the GenArk hubs. NCBI RefSeq assemblies can be loaded with direct links such as http://genome.ucsc.edu/h/GCF_001984765.1 with the GCF accession. These assembly hubs are automatically updated, but not reviewed by UCSC. The species tree shows all genomes reviewed by UCSC.

If the assembly of interest is not found, please visit our assembly request page. Search that page for your assembly. If there is a "view" link you can launch the existing genome browser. Otherwise, click the "request" button to fill out a form to add your genome of interest. An existing GCA_ or GCF_ identifier must exist, reflecting that the assembly has been deposited into Genbank at NCBI, before we can process it. See the Assembly Submission Guidelines page at NCBI for directions on their submission process if your genome needs to be deposited. Also, review the UCSC GenArk Blog posts for examples of accessing and reviewing technical details about GenArk hubs.

Another option available to all users is to create an assembly hub. These are assemblies created and hosted by users and displayed on the Genome Browser. This requires no intervention by the UCSC Genome Browser and can be done for any assembly. See our Quick Start Guide to Assembly Hubs page for additional information and resources. If you create an assembly hub, consider sharing it with others as a Public Hub.

If you would like information about creating a track hub for an existing assembly hub, please refer to the following FAQ entry.

Differences between UCSC and NCBI mouse assemblies

Is the mouse genome assembly displayed in the UCSC Genome Browser the same as the one on the NCBI website?

The mouse genome assemblies featured in the UCSC Genome Browser are the same as those on the NCBI web site with one difference: the UCSC versions contain only the reference strain data (C57BL/6J). NCBI provides data for several additional strains in their builds.

Accessing older assembly versions

I need to access an older version of a genome assembly that's no longer listed in the Genome Browser menu. What should I do?

In addition to the assembly versions currently available in the Genome Browser, you can access the data for older assemblies of the browser through our Downloads page.

Frequency of GenBank data updates

How frequently does UCSC update its databases with new data from GenBank?

GenBank updates for mRNA, RefSeq, and EST data occur on a semi-quarterly basis, following major NCBI releases. These updates are in place for most Genome Browser assemblies. Assemblies that are not on an incremental update schedule are updated whenever we load a new assembly or make a major revision to a table.

Coordinate changes between assemblies

I noticed that the chromosomal coordinates for a particular gene that I'm looking at have changed since the last time I used your browser. What happened?

A common source of confusion for users arises from mixing up different assemblies. It is very important to be aware of which assembly you are looking at. Within the Genome Browser display, assemblies are labeled by organism and date. To look up the corresponding UCSC database name or NCBI build number, use the release table.

UCSC database labels are of the form hg#, panTro#, etc. The letters designate the organism, e.g. hg for human genome or panTro for Pan troglodytes. The number denotes the UCSC assembly version for that organism. For example, ce1 refers to the first UCSC assembly of the C. elegans genome.

The coordinates of your favorite gene in one assembly may not be the same as those in the next release of the assembly unless the gene happens to lie on a completely sequenced and unrevised chromosome. For information on integrating data from one assembly into another, see the Converting positions between assembly versions section.

Converting positions between assembly versions

I've been researching a specific area of the human genome on the current assembly, and now you've just released a new version. Is there an easy way to locate my area of interest on the new assembly?

See the section on converting coordinates for information on assembly migration tools.

Converting SNPs between assembly versions

How can I convert SNP annotation coordinates between assembly versions?

While the LiftOver tool exists to convert coordinates between assemblies, it is NOT recommended to use LiftOver to convert SNPs between two assembly versions. Using LiftOver to convert a very small region, especially a single base SNP, is not always a trivial task as the alignment may not get a high enough score to be considered a successful conversion.

The mapping from one genome assembly to the next is automatically generated from sequence alignments and is not complete nor perfect, just a best attempt. The stability of rsIDs is why we recommend mapping across assemblies using rsIDs first and then falling back to using cross-assembly mappings to look up the positions of items that didn't map. When an rsID in hg18 is not found in the hg38 dbSNP data, that rsID has been withdrawn or replaced by a different rsID. In that case, mapping the hg18 position of the disappeared rsID to hg38 and looking for a new rsID at the corresponding position may help to find the new rsID.

dbSNP started assigning rsIDs in the 1990s, before the human genome was assembled. At that point, SNPs were defined by flanking sequences with the varying base(s) in the middle -- local sequence context, with no genomic location because there was no genome. rsIDs are supposed to be stable across genome assemblies despite the changing genomic positions. Regardless of the genome assembly version, "rs429358" refers to the same polymorphic variant in the 4th exon of the ApoE gene with T as the major allele and C as the minor allele. Its genomic position in hg18 is chr19:50103781, and its genomic position in hg38 is chr19:44908684.

Instead, the recommended process to convert a SNP's coordinates between assemblies is to use a SNP track to search for each rsID on the target genome assembly. For example, after creating a list of rsIDs for your conversion, you would then search for each rsID on the target's Genome Browser using the dbSNP track for human assemblies (i.e. hg19 or hg38) or the EVA SNP track on mouse assemblies (i.e. mm10 or mm39) to perform the conversion.

To summarize the setps:

1. Create a file of all rsIDs
2. Use the Table Browser to map the file of rsIDs to the other assembly's coordinates
3. Create another file containing any rsIDs that were not mapped by the Table Browser
4. Using the file from the previous step, use the Table Browser to create a BED4 file for the rsIDs that were not mapped by the Table Browser
5. Run LiftOver on the BED4 file to get the new coordinates in the other assembly
6. Use the Data Integrator to map the LiftOver results to new rsIDs where possible
7. Combine the Table Browser rsID-mapped BED4 with the LiftOver/Data Integrator-mapped BED4. Beware duplicates that will cause downstream problems. You will need to decide whether to remove duplicates as unreliable or resolve duplicates

How can I convert a large set of SNP annotations?

For bulk conversions, the Table Browser can be used to extract the coordinates for the rsIDs on the target assembly. More information about performing batch queries on the Table Browser can be found on the following Table Browser help page. An example of using the Table Browser to convert SNP between assemblies can be found on a previously answered question available on the mailing list archive.

If you are using versions dbSNP 153 and above, the data are formatted as bigBed files instead of being stored as a MariaDb table. For very large queries, this may cause the Table Browser to timeout before the query finishes as dbSNP has grown to include over 700 million variants. If you find that your Table Browser query timesout for your list of rsIDs, you can use the bigBedNamedItems command-line tool to extract the rsID coordinates directly from the bigBed file instead of using the Table Browser.

More information and examples using the bigBedNamedItems utility can be found on the following FAQ entry. As a reminder, you can run any Kent command-line tool without arguments to get the usage statement.

How can I extract a list of rsIDs using chrom:start-end or vise versa?

Several utilities for working with bigBed-formatted binary files can be downloaded here. Run a utility with no arguments to see a brief description of the utility and its options.

• bigBedInfo provides summary statistics about a bigBed file including the number of items in the file. With the -as option, the output includes an autoSql definition of data columns, useful for interpreting the column values.
• bigBedToBed converts the binary bigBed data to tab-separated text. Output can be restricted to a particular region by using the -chrom, -start and -end options.
• bigBedNamedItems extracts rows for one or more rs# IDs.

Examples:

1. Retrieve all variants in the region chr1:200001-200400

   bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hg38/snp/dbSnp155.bb -chrom=chr1 -start=200000 -end=200400 stdout

2. Retrieve variant rs6657048

   bigBedNamedItems dbSnp155.bb rs6657048 stdout

3. Retrieve all variants with rs# IDs in file myIds.txt

   bigBedNamedItems -nameFile dbSnp155.bb myIds.txt dbSnp155.myIds.bed

Missing annotation tracks

Why is my favorite annotation track missing from your latest release?

The initial release of a new genome assembly typically contains a small subset of core annotation tracks. New tracks are added as they are generated. In many cases, our annotation tracks are contributed by scientists not affiliated with UCSC who must first obtain the sequence, repeatmasked data, etc. before they can produce their tracks. If you have need of an annotation that has not appeared on an assembly within a month or so of its release, feel free to send an inquiry to genome@soe.ucsc.edu. Messages sent to this address will be posted to the moderated genome mailing list, which is archived on a SEARCHABLE, PUBLIC Google Groups forum.

What next with the human genome?

Now that the human genome is "finished", will there be any more releases?

Rest assured that work will continue. There will be updates to the assembly over the next several years. This has been the case for all other finished (i.e. essentially complete) genome assemblies as gaps are closed. For example, the C. elegans genome has been "finished" for several years, but small bits of sequence are still being added and corrections are being made. NCBI will continue to coordinate the human genome assemblies in collaboration with the individual chromosome coordinators, and UCSC will continue to QC the assembly in conjunction with NCBI (and, to a lesser extent, Ensembl). UCSC, NCBI, Ensembl, and others will display the new releases on their sites as they become available.

Mouse strain used for mouse genome sequence

What strain of mouse was used for the Mus musculus genome?

C57BL/6J.