U.S. flagAn official website of the United States government
                    Here's how you know **Official websites use .gov**
                            
                            A **.gov** website belongs to an official government organization in the United States.
 **Secure .gov websites use HTTPS**
                            
                            A **lock** (                            
                              A locked padlock                                                      
                            
                            ) or **https://** means you’ve safely connected to the .gov website. Share sensitive information only on official, secure websites.


Menu Agricultural Research Service
						
                    U.S. DEPARTMENT OF AGRICULTURE
 U.S. Meat Animal Research Center: Clay Center, NE
 close



    Research

                    Research Projects
                                    Publications
                                    Collaborations
                                    News
                People

                    Staff Listing
                                    Careers


        


                    WGS
                        WGS main page
                                    Cattle reference (v2.9)
                                    Cattle extended (v1.0)
                                    Sheep reference (v2.4)
                                    Sheep extended (v1.0)
                                    Sheep ISGC75
                                    Species mapped to cattle
                                    Species mapped to sheep
                                    Cell lines
                    USMARC Research Units
                        Animal Health Genomics
                                    Genetics and Animal Breeding
                                    Livestock Bio-systems
                                    Meat Safety & Quality
                                    Nutrition, Growth and PhysiologySearch small
                    Search
            
            ARS Home
                                About ARS
                                Contact Us




ARS Home Plains Area Clay Center, Nebraska U.S. Meat Animal Research Center WGS





- Main page
- Cattle reference (v2.9)
- Cattle extended (v1.0)
- Sheep reference (v2.4)
- Sheep extended (v1.0)
- Sheep international (v75)
- Sheep Tissues Bank (v30)
- Species Mapped to Cattle
- Species Mapped to Sheep
- Cell Lines

MSTBGCv30headline bar **15x WGS USMARC Sheep Tissues Bank Genotyping Controls (MSTBGCv30)** (Under Construction) Thirty reference sheep used genotyping controls.  Initially, these were used for scrapie genotype testing, but access to 15x WGS also allows these samples to be used as controls for other genes and markers.  This resource differs from other collections in that a large amount of tissues has been saved from each animal.  This collection allows USMARC to provide high-quality DNA with known genotypes for developing assays or evaluating the performance of existing assays.  Purified DNA from these animals (5 ug/each) is available to requesting institutions and companies.**** Sheep reference animals tissues bank  **To view DNA sequence data for an animal or a group:**
Download and install a desktop version ofIGV 2.14.1
Load a custom, gene-searchable, 2012 Oarv3.1 reference assembly  .json file
Genomes tab> "Load Genome from URL..." then paste in .json file URL (from above)
Note, this will be slow the first time the genome is loaded, then faster thereafter.
***Copy* an animal or group URL link address from**below (right-click)
File tab> "Load from URL..." > then paste in URL (from below)
Note, thegroup URLs are not workingand have to be rebuilt (MPH, 9-15-22)   DiplotypeBreeda
USMARC ID
PRNPb
TMEM154c
CLPGd
ID SNPse
Public links
Read coveragef
GB>Q20gNavajo-cross
200665234
ARQ_ARK
RALTEKTNIEI_RALTEKTNIEI (1_1)
A_A
RYRRGWGRYA
URL
20.2
60.7Composite
200423529
ARQ_VRQ
RALTEKTNIEI_RALTEKTNIEI (1_1)
G_G
RTRRGAKGYR
URL
16.4
49.3Composite
200423666
ARR_ARR
RALTEKTNIEI_**A**ALTEEMNIEI (1_4)
G_G
RCRARWGACR
URL
15.4
46.2Composite
200423510
ARQ_ARQ
RALTEKTNIEI_RALTEKTNIEI (1_1)
G_G
RCGRATGAYR
URL
14.5
43.6Rambouillet
199735002
ARR_AHQ
RALTEKTNIEI_RALTEKTNIEI (1_1)
A_A
ACGGRWGACR
URL
17.2
51.5Texel-cross
200450394
ARR_ARH
RALTEKTNIEI_RALTE**E**T**I**EI (1_2)
A_A
RTRGRWGGYA
URL
14.4
43.3Composite
200423500
ARR_VRQ



URL
23.1
69.4Navajo-cross
200665217
ARR_ARK
RALTEKTNIEI_RALTE**E**T**I**EI(1_2)
A_A
GYAAGWKGTA
URL
14.0
42.1Texel-cross
200450134
ARQ_ARH
RALTEKTNIEI_RALTE**E**TNIEI(1_3)
A_A
RYRAGTKAYA
URL
13.9
41.7Rambouillet
199935904
AHQ_AHQ
RALTEKTNIEI_RALTEKTNIEI(1_1)
A_A
ACAGGAKRCR
URL
15.9
47.8Texel-cross
200450114
AHQ_ARH
RALTEKTNIEI_RALTE**E**T**I**EI(1_2)
A_A
RTRGRWGRYA
URL
24.0
72.1Rambouillet-Romanov
200177091
AHQ_VRQ



URL
13.6
40.9Navajo-cross
200665201
AHQ_ARK



URL
31.2
93.7Texel
200006024
ARH_ARH



URL
25.2
75.7Texel-cross
200450173
ARH_VRQ



URL
23.0
68.9Navajo-cross
200665213
ARH_ARK
RALTEKTNIEI_RALTE**E**TNIEI(1_3)
A_A
AYRAGAGGTA
URL
19.6
58.7Composite
200123331
VRQ_VRQ
RALTEKTNIEI_RALTEKTNIEI (1_1)
G_G
RCRRRWGGCG
URL
17.6
52.7Navajo-cross
200665222
VRQ_ARK



URL
23.0
69.0Barbados Black Belly
200665931
ARK_ARK
RALTEKTNIEI_RALTEKTNIEI (1_1)
A_A
AYGGRAGRTG
URL
15.8
47.4Navajo-cross
200603590
ARQ_ARQ
RALTEKTNIEI_RALTE**E**T**I**EI(1_2)
A_A
GTGGAWKAYR
URL
21.8
65.3Composite
200277004
ARQ_ARQ



URL
14.4
43.1Texel
200206039
ARQ_AHQ



URL
56.7
170.0Composite
200323140
ARR_ARQ



URL
18.2
54.7Composite
200865003
ARQ_ARQ



URL
18.3
55.0Composite
200117482
ARR_ARQ



URL
na
0.0Composite
200210034
ARQ_ARQ



URL
na
9.2Composite
200310125
ARQ_ARQ



URL
na
25.4Composite
200941201
ARQ_ARQ



URL
15.2
45.7*
200703279





na
0.0*
201041124





na
35.0Total
378.2
834.8Ave.
19.9
52.2aThis group of animals was initially assembled for genotyping controls for scrapie genetic (PRNP) testing. Heaton et al. BMC Vet. Res. 2010bAmino acids at PRNP codons 136, 154, 171; corresponding SNPs on chr13 (OARv3.1) at positions: 46225660 (A136V), 46225714 (R154H), 46225765 (Q171R), 46225766 (Q171H), 46225764(Q171K).cHaplotype codes for TMEM154 at positions 4, 13, 14, 25, 31, 33, 35, 44, 70, 74, 82 and 102 described in Heaton et al. PLoSOne 2013.  The respective corresponding SNPs are on chr17 (OARv3.1) at positions: 4832850 (R4A_delta53); 4832878 (A13V); 4832881 (L14H); 4832914 (T25I); 4857232 (E31Q); 4857238 (D33N); 4857244 (E35K); 4857272 (T44M); 4857350 (N70I); 4857361 (I74F); 4857382-91 (E82Y_delta82); 4857446(I102T).dCallipyge SNP is at position chr18:64,391,549 genotypes: "A" nucleotide = normal (N), "G" nucleotide = Callipyge (C); "A_A" = NN, "A_G" = NC, "G_G" = CC,  described in Freking et al. Genome Res. 2002eThese are sheep parentage SNP genotypes (OARv3.1) at positions chr7:74,851,595; chr20:31,388,950; chr1:187,088,011; chr4:58,900,947; chr1:18,803,224;  chr1:189088599; chr11:32492623; chr2:23366203; chr18:54520252; chr4:23958565; Heaton et al. PLosOne2014.  These markers can serve as a "barcode" to confirm sample identity.fThis estimate is based on results in cattle where the genome coverage for an animal was ~(0.3)(Q20 GB) produced from a NextSeq500 machine.  Heaton et al. F1000Research 2016.gTotal gigabases of genomic sequence with a quality score greater than or equal to 20.   Tru-Seq paired-end libraries were sequenced with NextSeq500 high-output kits (300 cycles, Illumina Inc. San Diego CA).hIn progress.For questions or comments about access to the data, please contact the corresponding author Mike Heaton (mike.heaton@ars.usda.gov).Mention of trade names or commercial products in this public information release is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the USDA.


Return to top


Connect with ARS Sign up


ARS Home
                            USDA.gov
                            Plain Writing
                            Policies & Links
                            Civil Rights Statements
                            FOIA
                            Accessibility Statement
                            Privacy Policy
                            Non-Discrimination Statement
                            Quality of Information
                            USA.gov
                            WhiteHouse.gov