Table 2.  WGS IGV links for Cetartiodactyla species mapped to sheepa

Mapped to ovine Oar3.1

Estimatedc read coverage

Taxa

Common name

Species

Public linksb

.bam file

GB >Q20d

Breed/type

Tissue source/location

Data source

Source ID

Sex

USMARC animal ID

Bighorn sheep (BS)

Ovis canadensis

In progress

In progress

In progress

In progress

Wild

Montanae

USMARC

MP2001

U

200115009

Bighorn sheep

Ovis canadensis

In progress

In progress

In progress

In progress

Wild

Wyominge

USMARC

MP2001

M

200115011

BS, 2 genomes

Goat (GO)

Capra hircus

In progress

In progress

In progress

In progress

Spanish

NAPGf

USMARC

339

M

201216007

Goat

Capra hircus

In progress

40

-g

Yunnan black

Chinah

GenBank

-

F

Yunnan black

GO, 2 genomes

BS and GO, 4 genomes

Mountain goat (MG)

Oreamnos americanus

In progress

In progress

In progress

In progress

Wild

Coloradoe

USMARC

MP2011

F

201117010

Mountain goat

Oreamnos americanus

In progress

In progress

In progress

In progress

Wild

British Columbiae

USMARC

MP2011

U

201117012

MG, 2 genomes

BS, GO, and MG, 6 genomes

Muskox (MO)

Ovibos moschatus

In progress

In progress

In progress

In progress

Wild

U. Alaska Fairbanksi

USMARC

AF1191, UA30652

U

200314001

Muskox

Ovibos moschatus

In progress

In progress

In progress

In progress

Wild

U. Alaska Fairbanks

USMARC

AF1192, UA30653

U

200314002

MO, 2 genomes

BS, GO, MG, MO, 6 genomes

Cattle (CA)

Bos taurus

In progress

In progress

12.7

51.4

Angus

USMARC

USMARC

-

M

19879801

Cattle

Bos taurus

In progress

In progress

12.1

49.2

Brahman

USMARC

USMARC

-

M

19999819

CA, 2 genomes

BS, GO, MG, MO, CA, 8 genomes

Moose

Alces americanus

View in IGV

7762134017

16

64.1

Wild

Paxson, AKe

USMARC

HM2013

M

201524011

Moose

Alces americanus

View in IGV

7762134056

16

66.8

Wild

Elk River, IDj

USMARC

Clearwater06

M

Clearwater06

Moose

Alces americanus

View in IGV

7762134030

11

45.7

Wild

Grn. Riv. Lakes, WYe

USMARC

JC2001

F

200124009

Moose

Alces americanus

View in IGV

7762134043

19

77.3

Wild

Lowell, VTk

USMARC

R199

M

R199

Moose (MO), 4 genomes

View in IGV

63

Minke whale (MI)

Balaenoptera acutorostrata

30

-

Wild

Koreal

GenBank

-

M

Whale

Ovis

Caprinae

Bovidae

Pecora

Cetartiodactyla

aThese hyperlinks to USMARC whole genome sequence (WGS) data are from an ARS Specific Cooperative Agreement with Intrepid Bioinformatics in collaboration with the University of Louisville.

bFor questions or comments about progress and access to the data, please contact Mike Heaton or Ted Kalbfleisch at mike.heaton@ars.usda.gov or ted.kalbfleisch@louisville.edu, respectively.

cThe hypothetical estimated read coverage if the reads were mapped to a reference genome of the same species.

dTotal 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).

eUSMARC sample obtained voluntarily from U.S citizens after being lawfully taken during a State-approved legal hunt.

fProvided and curated by Dr. Havery Blackburn, National Animal Germplasm Program (NAGP), USDA, ARS, Fort Collins, CO.

gNot available or not applicable.

hYunnan black domestic goat.

Dong et al. 2013, Nature Biotechnology 31:135–141

iProvided by Dr. Jennifer I. Schmidt from the University of Alaska-Fairbanks Museum.

jProvided and curated by Dr. Brenda Murdoch, Animal and Veterinary Science, University of Idaho.

kProvided and curated by Dr. Stephanie McKay, Department of Animal & Veterinary Sciences, University of Vermont.

lEast coast of Korea.

Yim et al.  2014, Nature Genetics 46:88–92

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.

Updated 10/6/2015, Mike Heaton