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MSTBGCv30
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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

 

 

 

    Diplotype
Breeda USMARC ID PRNPb TMEM154c CLPGd ID SNPse Public links Read coveragef GB
>Q20g
Navajo-cross 200665234 ARQ_ARK RALTEKTNIEI_RALTEKTNIEI (1_1) A_A RYRRGWGRYA URL 20.2 60.7
Composite 200423529 ARQ_VRQ RALTEKTNIEI_RALTEKTNIEI (1_1) G_G RTRRGAKGYR URL 16.4 49.3
Composite 200423666 ARR_ARR RALTEKTNIEI_AALTEEMNIEI (1_4) G_G RCRARWGACR URL 15.4 46.2
Composite 200423510 ARQ_ARQ RALTEKTNIEI_RALTEKTNIEI (1_1) G_G RCGRATGAYR URL 14.5 43.6
Rambouillet 199735002  ARR_AHQ RALTEKTNIEI_RALTEKTNIEI (1_1) A_A ACGGRWGACR URL 17.2 51.5
Texel-cross 200450394 ARR_ARH RALTEKTNIEI_RALTEETIEI (1_2) A_A RTRGRWGGYA URL 14.4 43.3
Composite 200423500 ARR_VRQ       URL 23.1 69.4
Navajo-cross 200665217 ARR_ARK RALTEKTNIEI_RALTEETIEI (1_2) A_A GYAAGWKGTA URL 14.0 42.1
Texel-cross 200450134 ARQ_ARH RALTEKTNIEI_RALTEETNIEI (1_3)
 A_A RYRAGTKAYA URL 13.9 41.7
Rambouillet 199935904 AHQ_AHQ RALTEKTNIEI_RALTEKTNIEI (1_1)
 A_A ACAGGAKRCR URL 15.9 47.8
Texel-cross 200450114 AHQ_ARH RALTEKTNIEI_RALTEETIEI (1_2)
 A_A RTRGRWGRYA URL 24.0 72.1
 Rambouillet-Romanov 200177091 AHQ_VRQ       URL 13.6 40.9
 Navajo-cross  200665201 AHQ_ARK       URL  31.2 93.7
Texel 200006024 ARH_ARH       URL 25.2 75.7
Texel-cross 200450173 ARH_VRQ       URL 23.0 68.9
Navajo-cross 200665213 ARH_ARK RALTEKTNIEI_RALTEETNIEI (1_3) A_A AYRAGAGGTA URL 19.6 58.7
Composite 200123331 VRQ_VRQ RALTEKTNIEI_RALTEKTNIEI (1_1) G_G RCRRRWGGCG URL 17.6 52.7
Navajo-cross 200665222 VRQ_ARK       URL  23.0 69.0
Barbados Black Belly 200665931 ARK_ARK RALTEKTNIEI_RALTEKTNIEI (1_1) A_A AYGGRAGRTG URL 15.8 47.4
Navajo-cross 200603590 ARQ_ARQ RALTEKTNIEI_RALTEETIEI (1_2) A_A GTGGAWKAYR URL 21.8 65.3
Composite 200277004 ARQ_ARQ       URL 14.4 43.1
 Texel 200206039 ARQ_AHQ       URL 56.7 170.0
Composite 200323140 ARR_ARQ       URL 18.2 54.7
Composite 200865003 ARQ_ARQ       URL 18.3 55.0
Composite 200117482 ARR_ARQ       URL na  0.0
Composite 200210034 ARQ_ARQ       URL na  9.2
Composite 200310125 ARQ_ARQ       URL na 25.4
Composite 200941201 ARQ_ARQ       URL 15.2 45.7
 * 200703279           na 0.0
 * 201041124           na 35.0
                 
             Total 378.2  834.8
             Ave. 19.9 52.2
                 
aThis group of animals was initially assembled for genotyping controls for scrapie genetic (PRNP) testing. Heaton et al. BMC Vet. Res. 2010
bAmino 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. 2002
eThese 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.