Supported Genome Assemblies for Data Alignments ¹

Mapping lifts of the QTL/association data from the map version they were curated to the target maps are based on the latest EVA dbSNP "RS Releases" or by our in-house mapping lift procedures (when/where dbSNP data is not available).

ARS_UCD1.2 { Reference }	Assembly for Cattle [taurus; Breed=Hereford].
	Official assembly name: ARS-UCD1.2 Taxonomy ID=9913	Genbank accession: GCA_002263795.2 RefSeq accession: GCF_002263795.1
This is a de novo assembly of Bos taurus using long reads for assembly and short reads for scaffolding and polishing. The assembly was scaffolded using a combination of in vitro chromosome conformation capture sequencing, optical maps, and a recombination map. Subsequent scaffolding was confirmed using genetic linkage maps and a Radiation Hybrid map. This material is based on work supported by the National Institute of Food and Agriculture, U.S. Department of Agriculture, National Research Support Project NRSP8 (Cattle Genome Coordination). [Bos taurus isolate:L1 Dominette 01449 registration number 42190680 | breed:Hereford (cattle)]. Available from NCBI.
SNP map last updated: Jul 02, 2024 from dbSNP@eva
Reference 2 Rosen Benjamin D, Bickhart Derek M, Schnabel Robert D, Koren Sergey, Elsik Christine G, Tseng Elizabeth, Rowan Troy N, et al. (2020). De novo assembly of the cattle reference genome with single-molecule sequencing. GigaScience, 9(3).

ARS_UCD2.0	Assembly for cattle [Bos; Breed=Hereford].
	Official assembly name: ARS-UCD2.0 Taxonomy ID=9913	Genbank accession: GCA_002263795.4 RefSeq accession: GCF_002263795.3
The ARS-UCD2.0 was made available at NCBI in July 2023. It has a genome size of 2.8 Gb, containing 31 chromosomes, 1,957 scaffolds, 2,343 contigs. In May 2022, 254 sequences from previous assembly were suppressed because they were found to be contaminants. The completed annotation included 37,073 genes.. Available from NCBI.
SNP map last updated: Aug 03, 2024 from QTLdb SNP liftover from ARS_UCD1.2

Btau4.6	Assembly for Cattle [taurus; Breed=Hereford].
	Official assembly name: Btau_4.6.1 Taxonomy ID=9913	Genbank accession: GCA_000000095.4 RefSeq accession: GCF_000003205.5
The Bos taurus/cattle genome assembly produced by the Human Genome Sequencing Center at Baylor College of Medicine. The genome was derived from a female and a male of the Hereford breed. The sequencing strategy produced a 7-fold mixed assembly that combines whole-genome shotgun (WGS) sequence and BAC sequence. Available from NCBI.
SNP map last updated: Aug 02, 2024 from dbSNP@eva
Reference 2 Elsik Christine G, Tellam Ross L, Worley Kim C, Gibbs Richard A, Muzny Donna M, Weinstock George M, Adelson David L, Ei et al. (2009). The genome sequence of taurine cattle: a window to ruminant biology and evolution. Science (New York, N.Y.), 324 (5926): 522-8.

Btau5.0	Assembly for Cattle [taurus; Breed=Hereford].
	Official assembly name: Btau_5.0.1 Taxonomy ID=9913	Genbank accession: GCA_000003205.6 RefSeq accession: GCF_000003205.7
This version of the genome has 7x coverage and covers 95% of the genome. It was assembled from the pooled reads of BACs and whole genome shotgun sequences so is from two cattle (L1 Domino 99375 and L1 Dominette 01449). Some of the BACs were sequenced individually and some were sequenced using a pooling method.. Available from NCBI.
SNP map last updated: Aug 02, 2024 from dbSNP@eva
Reference 2 Elsik Christine G, Tellam Ross L, Worley Kim C, Gibbs Richard A, Muzny Donna M, Weinstock George M, Adelson David L, Ei et al. (2009). The genome sequence of taurine cattle: a window to ruminant biology and evolution. Science (New York, N.Y.), 324 (5926): 522-8.

UMD3.1	Assembly for Cattle [taurus; Breed=Hereford].
	Official assembly name: Bos_taurus_UMD_3.1.1 Taxonomy ID=9913	Genbank accession: GCA_000001245.5 RefSeq accession: GCF_000003055.6
The Bos taurus/cattle genome build were assembled by the Center for Bioinformatics and Computational Biology at University of Maryland (CBCB) using the Celera Assembler. This assembly used sequences from a mixture of hierarchical and whole-genome shotgun sequencing methods. The UMD3.1 has been made available to the public in December 2009. All contigs and chromosomes are unchanged.. Available from Ensembl, NCBI, UMD.
SNP map last updated: Aug 02, 2024 from dbSNP@eva
Reference 2 Zimin Aleksey V, Delcher Arthur L, Florea Liliana, Kelley David R, Schatz Michael C, Puiu Daniela, Hanrahan Finnian, Pe et al. (2009). A whole-genome assembly of the domestic cow, Bos taurus. Genome biology, 10 (4): R42.

GG4.0	Assembly for Chicken [gallus; Breed=Red Jungle fowl,].
	Official assembly name: Gallus_gallus-4.0 Taxonomy ID=9031	Genbank accession: GCA_000002315.2 RefSeq accession: GCF_000002315.3
The Gallus gallus/chicken genome assembly, includes improvements made by the Salzberg group at the U. of Maryland Center for Bioinformatics and Computational Biology and the near-finished Z sequence of Bellott et al. (Nature 466:612-616, 2010) as well as NGS sequence reads from the Washington University Genome Center.. Available from Ensembl, NCBI, dbSNP.
SNP map last updated: Aug 02, 2024 from dbSNP@eva
Reference 2 International Chicken Genome Sequencing Consortium. (2004). Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature, 432 (7018): 695-716.

GG5.0	Assembly for Chicken [Gallus gallus; Breed=Red Jungle fowl].
	Official assembly name: Gallus_gallus-5.0 Taxonomy ID=9031	Genbank accession: GCA_000002315.3 RefSeq accession: GCF_000002315.4
This new draft assembly (GG_5.0) was generated as part of the USDA-approved sequence assembly improvement plan for the existing draft assembly (GG_4.0). At the McDonnell Genome Institute at Washington University, the previous red jungle fowl (used to create GG_4.0) and a female chicken "RJF #256" from an inbred line (UCD 001) were sequenced on the Pacific Biosciences RSII to roughly 70x genome coverage and assembled with the MHAP/PbCR algorithm, with varied sequencing technology, including Sanger, Illumina and 454.. Available from NCBI, Ensembl.
SNP map last updated: Aug 02, 2024 from dbSNP@eva
Reference 2 Warren Wesley C, Hillier LaDeana W, Tomlinson Chad, Minx Patrick, Kremitzki Milinn, Graves Tina, Markovic Chris, Bouk N et al. (2017). A New Chicken Genome Assembly Provides Insight into Avian Genome Structure. G3 (Genes | Genomics | Genetics), 7(1): 109-117.

GRCg6a	Assembly for Chicken [ Gallus gallus; Breed=Red jungle fowl].
	Official assembly name: Gallus_gallus-GRCg6a Taxonomy ID=9031	Genbank accession: GCA_000002315.5 RefSeq accession: GCF_000002315.5
The current red jungle fowl (Gallus gallus) genome assembly, GRCg6a, was sequenced and assembled with single molecule real time (SMRT) sequencing technology to a depth of approximately 80x. The same DNA reference source, a female known as "RJF #256" from an inbred line (UCD 001), was sequenced on the Pacific Biosciences RSII instrument and all reads were assembled with the FALCON assembler. The creation of the improved chromosomal sequences proceeded in a way similar to that described for the Gallus_gallus-5.0 release. GRCg6a differs from the earlier GRCg6 version only in the elimination of four redundant unlocalized scaffolds. Available from NCBI, Ensembl.
SNP map last updated: Aug 02, 2024 from dbSNP@eva
Reference 2 Bellott Daniel W, Skaletsky Helen, Cho Ting-Jan, Brown Laura, Locke Devin, Chen Nancy, Galkina Svetlana, Pyntikova Taty et al. (2017). Avian W and mammalian Y chromosomes convergently retained dosage-sensitive regulators. Nature genetics, 49(3): 387-394.

GRCg7b { Reference }	Assembly for Chicken [Gallus gallus; Breed=White leghorn layer cross with Broiler].
	Official assembly name: Gallus_gallus-GRCg7b Taxonomy ID=9031	Genbank accession: GCA_016699485.1 RefSeq accession: GCF_016699485.2
Gallus gallus isolate:bGalGal1 RefSeq Genome sequencing and assembly. Available from NCBI.
SNP map last updated: Aug 02, 2024 from dbSNP@eva
Reference 2 Warren,W., Formenti,G., Fedrigo,O., Haase,B., Mountcastle,J., Balacco,J., Tracey,A., Schneider,V., Okimoto,R., Cheng,H. et al. (2021). Gallus gallus (Chicken) genome, bGalGal1, GRCg7b, maternal haplotype autosomes + Z & W (Direct Submission), .

CHIR1.0	Assembly for Goat [Hircus; Breed=Yunnan black goat].
	Official assembly name: CHIR_1.0 Taxonomy ID=9925	Genbank accession: GCA_000317765.1 RefSeq accession: GCF_000317765.1
by International Goat Genome Consortium. Available from NCBI, EVA.
SNP map last updated: Aug 02, 2024 from dbSNP@eva

CHIR_ARS1 { Reference }	Assembly for Goat [Capra hircus; Breed=San Clemente].
	Official assembly name: CHIR_ARS1 Taxonomy ID=9925	Genbank accession: GCA_001704415.1 RefSeq accession: GCF_001704415.1
Goat assembly by USDA ARS submitted on 2016/08/24. The assembly was made using Celera Assembler v. 8.2 on 50x coverage of PacBio sequences of a male San Clemente goat. CH == capra_hircus. Available from NCBI, Ensembl, Ensembl.
SNP map last updated: Aug 02, 2024 from dbSNP@eva
Reference 2 Bickhart Derek M, Rosen Benjamin D, Koren Sergey, Sayre Brian L, Hastie Alex R, Chan Saki, Lee Joyce, Lam Ernest T, Lia et al. (2017). Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome. Nature genetics, 49(4): 643-650.

EC2.0	Assembly for Horse [Equus caballus; Breed=].
	Official assembly name: EquCab2.0 Taxonomy ID=9796	Genbank accession: GCA_000000165.1 RefSeq accession: GCF_000002305.2
A high-quality draft sequence of the genome of the horse (Equus caballus; 2009). Genomic DNA sequence released by the Broad Institute of MIT and Harvard as EquCab2.0 in September 2007 and used as the reference assembly for chromosome 1-31 and X (no sequence data was available for chromosome Y). The NCBI reference sequence for the mitochondrial genome was also included in the reference assembly.. Available from Ensembl, NCBI.
SNP map last updated: Aug 02, 2024 from dbSNP@eva
Reference 2 Wade C M, Giulotto E, Sigurdsson S, Zoli M, Gnerre S, Imsland F, Lear T L, Adelson D L, Bailey E, Bellone R R, Blöcker et al. (2009). Genome sequence, comparative analysis, and population genetics of the domestic horse. Science (New York, N.Y.), 326 (5954): 865-7.

EC3.0 { Reference }	Assembly for Horse [Equus caballus; Breed=].
	Official assembly name: EquCab3.0 Taxonomy ID=9796	Genbank accession: GCA_002863925.1 RefSeq accession: GCF_002863925.1
Assembly method: Celera Assembler v. 2017; HiRise v. 2017; Expected final version: yes; Reference guided assembly: de-novo; Genome coverage: 88.0x; Sequencing technology: Sanger; Illumina HiSeq; PacBio. Available from NCBI.
SNP map last updated: Aug 02, 2024 from dbSNP@eva
Reference 2 Wade C M, Giulotto E, Sigurdsson S, Zoli M, Gnerre S, Imsland F, Lear T L, Adelson D L, Bailey E, Bellone R R, Blöcker et al. (2009). Genome sequence, comparative analysis, and population genetics of the domestic horse. Science (New York, N.Y.), 326 (5954): 865-7.

SS10.2	Assembly for Pig [Sus scrofa; Breed=Duroc].
	Official assembly name: Sscrofa10.2 Taxonomy ID=9823	Genbank accession: GCA_000003025.4 RefSeq accession: GCF_000000215.5
The Sus scrofa/pig genome was produced in August 2011 by the Swine Genome Sequencing Consortium (SGSC). It consists of 20 chromosomes (1-18, X and Y) and 4562 unplaced scaffolds. This genome assembly has GCA_000003025.4 as its GenBank assembly accession. Available from Ensembl, NCBI.
SNP map last updated: Aug 07, 2024 from dbSNP@eva
Reference 2 Groenen Martien A M, Archibald Alan L, Uenishi Hirohide, Tuggle Christopher K, Takeuchi Yasuhiro, Rothschild Max F, Rog et al. (2012). Analyses of pig genomes provide insight into porcine demography and evolution. Nature, 491 (7424): 393-8.

SS11.1 { Reference }	Assembly for Pig [Sus scrofa; Breed=Duroc].
	Official assembly name: Sscrofa11.1 Taxonomy ID=9823	Genbank accession: GCA_000003025.6 RefSeq accession: GCF_000003025.6
The sequence data from which this assembly was constructed largely comprise 65x genome coverage in whole genome shotgun (WGS) Pacific Biosciences long reads (Pacific Biosciences RSII, with P6/C4 chemistry). Illumina HiSeq2500 WGS paired-end and mate pair reads were used for final error correction using PILON. Sanger and Oxford Nanopore sequence data from a few CHORI-242 BAC clones were used to fill gaps. All the WGS data were generated from a single Duroc female (TJ Tabasco, also known as Duroc 2-14) which was also the source of DNA for the CHORI-BAC library. Sscrofa11 replaces the previous assembly, Sscrofa10.2, which was largely established from the same Duroc 2-14 DNA source.. Available from NCBI.
SNP map last updated: Aug 06, 2024 from dbSNP@eva
Reference 2 Groenen Martien A M, Archibald Alan L, Uenishi Hirohide, Tuggle Christopher K, Takeuchi Yasuhiro, Rothschild Max F, Rog et al. (2012). Analyses of pig genomes provide insight into porcine demography and evolution. Nature, 491 (7424): 393-8.

SS_MARC1	Assembly for Pig [Sus_scrofa; Breed=Cross-bred].
	Official assembly name: USMARCv1.0 Taxonomy ID=	Genbank accession: GCA_002844635.1 RefSeq accession:
USMARCv1.0, was assembled using 65× coverage of PacBio long reads from DNA of lung tissue of a cross-bred pig (½ Landrace- ¼ Duroc- ¼ Yorkshire). Available from NCBI, Ensembl.
SNP map last updated: Aug 06, 2024 from QTLdb SNP liftover from SS11.1
Reference 2 Hannum,G.I., Koren,S., Schroeder,S.G., Chin,S.C., Nonneman,D.J., Becker,S.A., Rosen,B.D., Bickhart,D.M., Putnam,N.H., G et al. (2017). Sus scrofa breed Cross-bred isolate 201423004, whole genome shotgun sequencing project (Direct Submission), Aug 2.

OM1.0	Assembly for Rainbow trout [Oncorhynchus mykiss; Breed=Swanson isolate].
	Official assembly name: Omyk_1.0 Taxonomy ID=8022	Genbank accession: GCA_002163495.1 RefSeq accession: GCF_002163495.1
Organism name: Oncorhynchus mykiss (rainbow trout) Isolate: Swanson Sex: male BioSample: SAMN05449231 BioProject: PRJNA335610 Submitter: USDA/ARS Date: 2017/06/02 Assembly level: Chromosome Genome representation: full. Available from NCBI.
SNP map last updated: Aug 02, 2024 from dbSNP@eva

OM1.1 { Reference }	Assembly for Rainbow trout [Oncorhynchus mykiss; Breed=].
	Official assembly name: USDA_OmykA_1.1 Taxonomy ID=8022	Genbank accession: GCA_013265735.3 RefSeq accession: GCF_013265735.2
The rainbow trout genomic libraries were prepared using genomic DNA from a single homozygous doubled haploid YY male. Each library was sequenced using Pico Titer Plates on a 454 GSFlx instrument with Titanium or long read chemistry and were assembled together with Newbler. The resulting assembly was 1.9 Gb in leangth.. Available from NCBI, EVA.
SNP map last updated: Aug 02, 2024 from dbSNP@eva
Reference 2 Berthelot Camille, Brunet Fr�d�ric, Chalopin Domitille, Juanchich Am�lie, Bernard Maria, No�l Benjamin, Bento P et al. (2014). The rainbow trout genome provides novel insights into evolution after whole-genome duplication in vertebrates. Nature communications, 5: 3657.

OAR3.1	Assembly for Sheep [Ovis aries; Breed=Texel].
	Official assembly name: Oar_v3.1 Taxonomy ID=9940	Genbank accession: GCA_000298745.1 RefSeq accession: GCF_000298735.1
The Ovis_aries/sheep genome built was derived using next generation sequence derived from one female and one male Texel. The primary de novo assembly was performed using 75 fold Illumina GA sequence from the female, before the mate pair characteristics of the paired end reads were used to produce scaffolds spanning 2.71 Gb or approximately 91% of the sheep genome. A further 45 fold coverage of the male Texel was used for gap filling, before scaffolds are anchored onto the 27 sheep chromosomes.. Available from Ensembl, NCBI.
SNP map last updated: Aug 02, 2024 from dbSNP@eva
Reference 2 Jiang Yu, Xie Min, Chen Wenbin, Talbot Richard, Maddox Jillian F, Faraut Thomas, Wu Chunhua, Muzny Donna M, Li Yuxiang, et al. (2014). The sheep genome illuminates biology of the rumen and lipid metabolism. Science (New York, N.Y.), 344(6188): 1168-73.

OAR4.0	Assembly for Sheep [Ovis aries; Breed=Texel].
	Official assembly name: Oar_v4.0 Taxonomy ID=9940	Genbank accession: GCA_000298745.2 RefSeq accession: GCF_000298735.2
The Ovis aries genome is distributed over 26 autosomes and two sex chromosomes. The annotation produced for this release (102) was compared to the annotation in the previous release (101) for each assembly annotated in both releases. Scores for current and previous gene and transcript features were calculated based on overlap in exon sequence and matches in exon boundaries. Pairs of current and previous features were categorized based on these scores, whether they are reciprocal best matches, and changes in attributes (gene biotype, completeness, etc.).. Available from NCBI.
SNP map last updated: Aug 02, 2024 from dbSNP@eva
Reference 2 Archibald A L, Cockett N E, Dalrymple B P, Faraut T, Kijas J W, Maddox J F, McEwan J C, Hutton Oddy V, Raadsma H W, Wad et al. (2010). The sheep genome reference sequence: a work in progress. Animal genetics, 41(5): 449-53.

OAR_rambo1	Assembly for Sheep [Ovis aries; Breed=Rambouillet].
	Official assembly name: Oar_rambouillet_v1.0 Taxonomy ID=9940	Genbank accession: GCA_002742125.1 RefSeq accession: GCF_002742125.1
Rambouilletsheep (Strain: OAR_USU_Benz2616); 126x coverage, assembled with celera v. 8.2.. Available from NCBI.
SNP map last updated: Aug 05, 2024 from QTLdb SNP liftover from OAR_rambo2
Reference 2 Liu,Y., Harris,A., Meng,Q., Qin,X., English,A., Vee,V., Weissenberger,G., Chao,H., Wang,M., Perez,L., Heaton,M., Smith, et al. (2017). Ovis aries Rambouillet Genome sequencing and assembly (Direct Submission), Oct. 12.

OAR_rambo2 { Reference }	Assembly for Sheep [Aries; Breed=Rambouillet].
	Official assembly name: ARS-UI_Ramb_v2.0 Taxonomy ID=9940	Genbank accession: GCA_016772045.1 RefSeq accession: GCF_016772045.1
RefSeq category: representative genome Expected final version: yes Annotation Release 104 (AR 104) of ARS-UI_Ramb_v2.0 reflects improvements from Oar_rambouillet_v1.0. Available from NCBI.
SNP map last updated: Aug 04, 2024 from dbSNP@eva
Reference 2 Davenport,K.M., Bickhart,D.M., Smith,T.P.L., Murdoch,B.M. and Rosen,B.D (2020). Ovis aries strain OAR_USU_Benz2616 breed Rambouillet, whole genome shotgun sequencing project (Direct Submission), Nov. 16.