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» Oar3.1 MSDPv2.4 .bam by mixed groups
| Oar3.1 MSDPv2.4 .bam by mixed groups |
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1 - MSDPv2.4
2 - Oar3.1 MSDPv2.4 .bam by mixed groups 3 - Oar3.1 MSDPv2.4 .bam by breed |
15x WGS of MSDPv2.4 by mixed groups of 8
- To view DNA sequence data for an animal or a group of 8:
- Download and install a desktop version of IGV 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 may 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)
| Breed | USMARC animal ID | Public links | Read coverageb | GB >Q20c |
||
| Group #1, 8 genomes URL | 13.5 | 358.85 | ||||
| Dorper | 199911904 | URL | 12.4 | 41.2 | ||
| Dorset | 199912068 | URL | 12.8 | 42.8 | ||
| Finn | 199916204 | URL | 13.4 | 44.5 | ||
| Katahdin | 200008100 | URL | 19.5 | 65.1 | ||
| Rambouillet | 199735001 | URL | 12.8 | 42.7 | ||
| Romanov | 199914218 | URL | 12.1 | 40.3 | ||
| Suffolk | 199910003 |
|
12.0 | 40.1 | ||
| Texel | 199906022 | URL | 12.7 | 42.2 | ||
| Group #2, 8 genomes URL | 15.0 | 399.6 | ||||
| Dorper | 200011945 | URL | 19.6 | 65.3 | ||
| Dorset | 199912079 | URL | 12.2 | 40.7 | ||
| Finn | 200016002 | URL | 15.2 | 50.5 | ||
| Katahdin | 200008764 | URL | 13.5 | 44.9 | ||
| Rambouillet | 199935902 | URL | 12.2 | 40.5 | ||
| Romanov | 199914942 | URL | 16.0 | 53.3 | ||
| Suffolk | 200117163 | URL | 16.8 | 56.1 | ||
| Texel | 200006024 | URL | 14.5 | 48.3 | ||
| Group #3, 8 genomes URL | 16.4 | 437.8 | ||||
| Dorper | 200111910 | URL | 13.4 | 44.6 | ||
| Dorset | 200012903 | URL | 15.7 | 52.2 | ||
| Finn | 200016018 | URL | 16.6 | 55.2 | ||
| Katahdin | 200008947 | URL | 17.0 | 56.5 | ||
| Rambouillet | 199935923 | URL | 18.7 | 62.3 | ||
| Romanov | 200014943 | URL | 12.8 | 42.6 | ||
| Suffolk | 200117463 | URL | 20.4 | 68.0 | ||
| Texel | 200006910 | URL | 16.9 | 56.5 | ||
| Group #4, 8 genomes URL | 15.9 | 424.0 | ||||
| Dorper | 200111912 | URL | 14.7 | 48.9 | ||
| Dorset | 200112907 | URL | 16.4 | 54.6 | ||
| Finn | 200016129 | URL | 12.3 | 40.9 | ||
| Katahdin | 200108933 | URL | 19.1 | 63.5 | ||
| Rambouillet | 200035920 | URL | 19.3 | 64.2 | ||
| Romanov | 200117137 | URL | 12.9 | 43.1 | ||
| Suffolk | 200210060 | URL | 17.3 | 57.7 | ||
| Texel | 200106931 | URL | 15.3 | 51.1 | ||
| Group #5, 8 genomes URL | 14.2 | 378.1 | ||||
| Dorper | 200111916 | URL | 14.0 | 46.7 | ||
| Dorset | 200117009 | URL | 17.3 | 57.6 | ||
| Finn | 200016922 | URL | 12.4 | 41.2 | ||
| Katahdin | 200108934 | URL | 13.3 | 44.3 | ||
| Rambouillet | 200035921 | URL | 12.8 | 42.8 | ||
| Romanov | 200117140 | URL | 13.8 | 46.0 | ||
| Suffolk | 200210099 | URL | 14.9 | 49.5 | ||
| Texel | 200106932 | URL | 15.0 | 49.9 | ||
| Group #6, 8 genomes URL | 17.8 | 474.6 | ||||
| Dorper | 200111917 | URL | 15.0 | 49.9 | ||
| Dorset | 200117016 | URL | 26.1 | 86.9 | ||
| Finn | 200016940 | URL | 20.5 | 68.5 | ||
| Katahdin | 200108935 | URL | 12.8 | 42.6 | ||
| Rambouillet | 200035922 | URL | 16.1 | 53.7 | ||
| Romanov | 200117160 | URL | 14.4 | 47.9 | ||
| Suffolk | 200210903 | URL | 22.2 | 74.0 | ||
| Texel | 200118018 | URL | 15.3 | 51.1 | ||
| Group #7, 8 genomes URL | 14.6 | 389.9 | ||||
| Dorper, white | 200011259 | URL | 13.4 | 44.6 | ||
| Dorset | 200117080 | URL | 15.6 | 51.9 | ||
| Finn | 200116921 | URL | 12.4 | 41.3 | ||
| Katahdin | 200108936 | URL | 12.1 | 40.4 | ||
| Rambouillet | 200035924 | URL | 13.7 | 45.6 | ||
| Romanov | 200117201 | URL | 14.5 | 48.3 | ||
| Suffolk | 200210904 | URL | 13.9 | 46.2 | ||
| Texel | 200206039 | URL | 21.5 | 71.6 | ||
| Group #8, 8 genomes URL | 15.3 | 409.2 | ||||
| Dorper, white | 200011900 | URL | 16.4 | 54.6 | ||
| Dorset | 200212081 | URL | 14.9 | 49.5 | ||
| Finn | 200116926 | URL | 14.5 | 48.4 | ||
| Katahdin | 200108938 | URL | 13.3 | 44.3 | ||
| Rambouillet | 200135902 | URL | 22.8 | 76.1 | ||
| Romanov | 200117419 | URL | 12.6 | 41.9 | ||
| Suffolk | 200210915 | URL | 13.3 | 44.3 | ||
| Texel | 200206902 | URL | 15.0 | 50.2 | ||
| Group #9, 8 genomes URL | 15.6 | 415.0 | ||||
| Dorper, white | 200111923 | URL | 12.9 | 43.0 | ||
| Dorset | 200212908 | URL | 12.7 | 42.4 | ||
| Finn | 200117718 | URL | 16.3 | 54.3 | ||
| Navajo-Churro | 199950927 | URL | 15.8 | 52.8 | ||
| Rambouillet | 200235900 | URL | 12.0 | 40.0 | ||
| Romanov | 200117552 | URL | 29.3 | 97.7 | ||
| Suffolk | 200310906 | URL | 13.1 | 43.5 | ||
| Texel | 200206903 | URL | 12.4 | 41.3 | ||
| Group #10, 8 genomes URL | 14.0 | 374.3 | ||||
| Dorper, white | 200111924 | URL | 12.7 | 42.3 | ||
| Dorset | 200212909 | URL | 13.3 | 44.4 | ||
| Finn | 200316905 | URL | 12.5 | 41.7 | ||
| Rambouillet | 200235901 | URL | 17.5 | 58.2 | ||
| Romanov | 200314904 | URL | 13.3 | 44.4 | ||
| USMARC Composite | 200103335 | URL | 12.2 | 40.6 | ||
| USMARC Composite | 200103367 | URL | 13.9 | 46.2 | ||
| USMARC Composite | 200103459 | URL | 17.0 | 56.5 | ||
| Group #11, 8 genomes URL | 14.5 | 385.5 | ||||
| Dorset | 200212919 | URL | 19.0 | 63.5 | ||
| Texel | 200206906 | URL | 12.3 | 41.1 | ||
| USMARC Composite | 200203048 | URL | 16.4 | 54.7 | ||
| USMARC Composite | 200203128 | URL | 12.4 | 41.2 | ||
| USMARC Composite | 200203170 | URL | 13.0 | 43.5 | ||
| USMARC Composite | 200203179 | URL | 15.0 | 49.9 | ||
| USMARC Composite | 200203278 | URL | 12.9 | 43.0 | ||
| USMARC Composite | 200203310 | URL | 14.6 | 48.6 | ||
| Group #12, 8 genomes URL | 14.6 | 388.8 | ||||
| USMARC Composite | 200303158 | URL | 14.9 | 49.6 | ||
| USMARC Composite | 200303163 | URL | 15.5 | 51.6 | ||
| USMARC Composite | 200303183 | URL | 13.4 | 44.8 | ||
| USMARC Composite | 200303220 | URL | 14.7 | 49.0 | ||
| USMARC Composite | 200303274 | URL | 13.5 | 44.9 | ||
| USMARC Composite | 200303289 | URL | 14.5 | 48.4 | ||
| USMARC Composite | 200303326 | URL | 17.6 | 58.6 | ||
| USMARC Composite | 200203286 | URL | 12.6 | 41.8 | ||
| Total | 1450.7 | 4835.7 | ||||
| Average | 15.1 | 50.4 | ||||
| aGroups 1 through 12 contain purebred and USMARC Composite rams sampled ca 2008. The USMARC composite population (MARCIII) consists of: 1/2 Columbia, 1/4 Hampshire, and 1/4 Suffolk. | ||||||
| Heaton et al. BMC Vet. Res. 2010 | ||||||
| bThis estimate is based 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 | ||||||
| A poster describing the results was presented at the International meeting for Plant and Animal Genomes, San Diego CA, January 2017: | ||||||
| Using an Online Genome Resource to Identify Myostatin Variation in U.S. Sheep | ||||||
| For questions or comments about access to the data, please contact corresponding authors Mike Heaton or Ted Kalbfleisch at mike.heaton@ars.usda.gov or ted.kalbfleisch@louisville.edu, respectively. | ||||||
| cTotal 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). | ||||||
| dNot applicable | ||||||
| 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. | ||||||
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