3bcdba0cb7f7281dc131c2c59684980741a841e6 mspeir Tue Dec 23 15:34:36 2025 -0800 Adding better description of species coloring in conservation tracks, refs #27217 diff --git src/hg/makeDb/trackDb/human/hg38/cons241way.html src/hg/makeDb/trackDb/human/hg38/cons241way.html index bef6c990fa2..09f145098b9 100644 --- src/hg/makeDb/trackDb/human/hg38/cons241way.html +++ src/hg/makeDb/trackDb/human/hg38/cons241way.html @@ -1,2481 +1,2483 @@ <p> Downloads for data in this track are available: <ul> <li> <a href="http://hgdownload.soe.ucsc.edu/goldenPath/hg38/cactus241way/">Cactus alignments</a> (MAF format), and phylogenetic trees, and PhyloP conservation (WIG and bigWig format) </ul> <h2>Description</h2> <p><b>Warning:</b> Unlike other alignment tracks on the genome browser, this one does not show insertions in the query genomes. Also, all other alignment tracks show one query genome sequence for target target genome sequence, but in this track, each target genome sequence can be aligned to multiple query genome sequences. Only the first sequence is shown on the genome browser itself, the others are shown on the details page, when one clicks on the alignment. If you are interested in this track and want these shortcomings to be fixed, please contact us. </p> <p> This track shows multiple alignments of 241 vertebrate species and measurements of evolutionary conservation from the <a href="https://zoonomiaproject.org/the-project/">Zoonomia Project</a>. </p> <p> The multiple alignments were generated using the <a href="https://github.com/ComparativeGenomicsToolkit/cactus/" target=_blank>Cactus</a> comparative genomics alignment system. Cactus produces reference-free, whole-genome multiple alignments. <p> <p> The base-wise conservation scores are computed using <em>phyloP</em> from the <a href="http://compgen.cshl.edu/phast/" target="_BLANK"> PHAST package</a>, for all species. This version was prepared by Michael Dong (Uppsala U) with an improved neutral model incorporating better versions of ancestral repeats. </p> <p> For genome assemblies not available in the genome browser, there are alternative assembly hub genome browsers. Missing sequence in any assembly is highlighted in the track display by regions of yellow when zoomed out and by Ns when displayed at base level (see <em>Gap Annotation</em>, below).</p> <p> <blockquote> <table border=1 class='stdTbl'> <tr><th>count</th> <th>common<br>name</th> <th>CLADE</th> <th>group</th> <th>scientific<br>name</th> <th>sequencing<br>source</th> <th>NCBI<br>assembly</th> <th>species<br>status</th> </tr> <tr><th>1</th> <th>Cape golden mole</th> <th>AFROSORICIDA</th> <th>Chrysochloridae</th> <th>Chrysochloris asiatica</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004027935.1/ target=_blank>GCA_004027935.1</a></th> <th>LC</th> </tr> <tr><th>2</th> <th>Small madagascar hedgehog</th> <th>AFROSORICIDA</th> <th>Tenrecidae</th> <th>Echinops telfairi</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCF_000313985.1/ target=_blank>GCF_000313985.1</a></th> <th>LC</th> </tr> <tr><th>3</th> <th>Talazac's shrew tenrec</th> <th>AFROSORICIDA</th> <th>Tenrecidae</th> <th>Microgale talazaci</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004026705.1/ target=_blank>GCA_004026705.1</a></th> <th>LC</th> </tr> <tr><th>4</th> <th>Cheetah</th> <th>CARNIVORA</th> <th>Felidae</th> <th>Acinonyx jubatus</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCF_001443585.1/ target=_blank>GCF_001443585.1</a></th> <th>CR</th> </tr> <tr><th>5</th> <th>Giant panda</th> <th>CARNIVORA</th> <th>Ursidae</th> <th>Ailuropoda melanoleuca</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_002007445.1/ target=_blank>GCA_002007445.1</a></th> <th>VU</th> </tr> <tr><th>6</th> <th>Lesser panda</th> <th>CARNIVORA</th> <th>Ailuridae</th> <th>Ailurus fulgens</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_002007465.1/ target=_blank>GCA_002007465.1</a></th> <th>EN</th> </tr> <tr><th>7</th> <th>Domestic dog</th> <th>CARNIVORA</th> <th>Canidae</th> <th>Canis lupus familiaris</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCF_000002285.3/ target=_blank>GCF_000002285.3</a></th> <th>LC</th> </tr> <tr><th>8</th> <th>Domestic dog (village dog)</th> <th>CARNIVORA</th> <th>Canidae</th> <th>Canis lupus familiaris</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004027395.1/ target=_blank>GCA_004027395.1</a></th> <th>LC</th> </tr> <tr><th>9</th> <th>Fossa</th> <th>CARNIVORA</th> <th>Eupleridae</th> <th>Cryptoprocta ferox</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004023885.1/ target=_blank>GCA_004023885.1</a></th> <th>VU</th> </tr> <tr><th>10</th> <th>Sea otter</th> <th>CARNIVORA</th> <th>Mustelidae</th> <th>Enhydra lutris</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCF_002288905.1/ target=_blank>GCF_002288905.1</a></th> <th>EN</th> </tr> <tr><th>11</th> <th>Domestic cat</th> <th>CARNIVORA</th> <th>Felidae</th> <th>Felis catus</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCF_000181335.2/ target=_blank>GCF_000181335.2</a></th> <th>LC</th> </tr> <tr><th>12</th> <th>Black-footed cat</th> <th>CARNIVORA</th> <th>Felidae</th> <th>Felis nigripes</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004023925.1/ target=_blank>GCA_004023925.1</a></th> <th>VU</th> </tr> <tr><th>13</th> <th>Dwarf mongoose</th> <th>CARNIVORA</th> <th>Herpestidae</th> <th>Helogale parvula</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004023845.1/ target=_blank>GCA_004023845.1</a></th> <th>LC</th> </tr> <tr><th>14</th> <th>Striped hyena</th> <th>CARNIVORA</th> <th>Hyaenidae</th> <th>Hyaena hyaena</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004023945.1/ target=_blank>GCA_004023945.1</a></th> <th>NT</th> </tr> <tr><th>15</th> <th>Weddell seal</th> <th>CARNIVORA</th> <th>Phocidae</th> <th>Leptonychotes weddellii</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCF_000349705.1/ target=_blank>GCF_000349705.1</a></th> <th>LC</th> </tr> <tr><th>16</th> <th>African hunting dog</th> <th>CARNIVORA</th> <th>Canidae</th> <th>Lycaon pictus</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_001887905.1/ target=_blank>GCA_001887905.1</a></th> <th>EN</th> </tr> <tr><th>17</th> <th>Honey badger</th> <th>CARNIVORA</th> <th>Mustelidae</th> <th>Mellivora capensis</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004024625.1/ target=_blank>GCA_004024625.1</a></th> <th>LC</th> </tr> <tr><th>18</th> <th>Northern elephant seal</th> <th>CARNIVORA</th> <th>Phocidae</th> <th>Mirounga angustirostris</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004023865.1/ target=_blank>GCA_004023865.1</a></th> <th>LC</th> </tr> <tr><th>19</th> <th>South African banded mongoose</th> <th>CARNIVORA</th> <th>Herpestidae</th> <th>Mungos mungo</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004023785.1/ target=_blank>GCA_004023785.1</a></th> <th>LC</th> </tr> <tr><th>20</th> <th>Domestic ferret</th> <th>CARNIVORA</th> <th>Mustelidae</th> <th>Mustela putorius</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCF_000239315.1/ target=_blank>GCF_000239315.1</a></th> <th>LC</th> </tr> <tr><th>21</th> <th>Hawaiian monk seal</th> <th>CARNIVORA</th> <th>Phocidae</th> <th>Neomonachus schauinslandi</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_002201575.1/ target=_blank>GCA_002201575.1</a></th> <th>EN</th> </tr> <tr><th>22</th> <th>Pacific walrus</th> <th>CARNIVORA</th> <th>Odobenidae</th> <th>Odobenus rosmarus</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCF_000321225.1/ target=_blank>GCF_000321225.1</a></th> <th>DD</th> </tr> <tr><th>23</th> <th>Jaguar</th> <th>CARNIVORA</th> <th>Felidae</th> <th>Panthera onca</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004023805.1/ target=_blank>GCA_004023805.1</a></th> <th>NT</th> </tr> <tr><th>24</th> <th>Leopard</th> <th>CARNIVORA</th> <th>Felidae</th> <th>Panthera pardus</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_001857705.1/ target=_blank>GCA_001857705.1</a></th> <th>VU</th> </tr> <tr><th>25</th> <th>Amur tiger</th> <th>CARNIVORA</th> <th>Felidae</th> <th>Panthera tigris</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCF_000464555.1/ target=_blank>GCF_000464555.1</a></th> <th>EN</th> </tr> <tr><th>26</th> <th>Asian palm civet</th> <th>CARNIVORA</th> <th>Viverridae</th> <th>Paradoxurus hermaphroditus</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004024585.1/ target=_blank>GCA_004024585.1</a></th> <th>LC</th> </tr> <tr><th>27</th> <th>Giant otter</th> <th>CARNIVORA</th> <th>Mustelidae</th> <th>Pteronura brasiliensis</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004024605.1/ target=_blank>GCA_004024605.1</a></th> <th>EN</th> </tr> <tr><th>28</th> <th>Puma</th> <th>CARNIVORA</th> <th>Felidae</th> <th>Puma concolor</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCF_003327715.1/ target=_blank>GCF_003327715.1</a></th> <th>LC</th> </tr> <tr><th>29</th> <th>Western spotted skunk</th> <th>CARNIVORA</th> <th>Mephitidae</th> <th>Spilogale gracilis</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004023965.1/ target=_blank>GCA_004023965.1</a></th> <th>LC</th> </tr> <tr><th>30</th> <th>Meerkat</th> <th>CARNIVORA</th> <th>Herpestidae</th> <th>Suricata suricatta</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004023905.1/ target=_blank>GCA_004023905.1</a></th> <th>LC</th> </tr> <tr><th>31</th> <th>Polar bear</th> <th>CARNIVORA</th> <th>Ursidae</th> <th>Ursus maritimus</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCF_000687225.1/ target=_blank>GCF_000687225.1</a></th> <th>VU</th> </tr> <tr><th>32</th> <th>Arctic fox</th> <th>CARNIVORA</th> <th>Canidae</th> <th>Vulpes lagopus</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004023825.1/ target=_blank>GCA_004023825.1</a></th> <th>LC</th> </tr> <tr><th>33</th> <th>California sea lion</th> <th>CARNIVORA</th> <th>Otariidae</th> <th>Zalophus californianus</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004024565.1/ target=_blank>GCA_004024565.1</a></th> <th>LC</th> </tr> <tr><th>34</th> <th>Aoudad</th> <th>CETARTIODACTYLA</th> <th>Bovidae</th> <th>Ammotragus lervia</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_002201775.1/ target=_blank>GCA_002201775.1</a></th> <th>VU</th> </tr> <tr><th>35</th> <th>Pronghorn</th> <th>CETARTIODACTYLA</th> <th>Antilocapridae</th> <th>Antilocapra americana</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004027515.1/ target=_blank>GCA_004027515.1</a></th> <th>LC</th> </tr> <tr><th>36</th> <th>Minke whale</th> <th>CETARTIODACTYLA</th> <th>Balaenopteridae</th> <th>Balaenoptera acutorostrata</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCF_000493695.1/ target=_blank>GCF_000493695.1</a></th> <th>LC</th> </tr> <tr><th>37</th> <th>Antarctic minke whale</th> <th>CETARTIODACTYLA</th> <th>Balaenopteridae</th> <th>Balaenoptera bonaerensis</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_000978805.1/ target=_blank>GCA_000978805.1</a></th> <th>DD</th> </tr> <tr><th>38</th> <th>Hirola</th> <th>CETARTIODACTYLA</th> <th>Bovidae</th> <th>Beatragus hunteri</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004027495.1/ target=_blank>GCA_004027495.1</a></th> <th>CR</th> </tr> <tr><th>39</th> <th>American bison</th> <th>CETARTIODACTYLA</th> <th>Bovidae</th> <th>Bison bison</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCF_000754665.1/ target=_blank>GCF_000754665.1</a></th> <th>NT</th> </tr> <tr><th>40</th> <th>Zebu cattle</th> <th>CETARTIODACTYLA</th> <th>Bovidae</th> <th>Bos indicus</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_000247795.2/ target=_blank>GCA_000247795.2</a></th> <th>LC</th> </tr> <tr><th>41</th> <th>Wild yak</th> <th>CETARTIODACTYLA</th> <th>Bovidae</th> <th>Bos mutus</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCF_000298355.1/ target=_blank>GCF_000298355.1</a></th> <th>VU</th> </tr> <tr><th>42</th> <th>Cattle</th> <th>CETARTIODACTYLA</th> <th>Bovidae</th> <th>Bos taurus</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCF_000003205.7/ target=_blank>GCF_000003205.7</a></th> <th>LC</th> </tr> <tr><th>43</th> <th>Water buffalo</th> <th>CETARTIODACTYLA</th> <th>Bovidae</th> <th>Bubalus bubalis</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCF_000471725.1/ target=_blank>GCF_000471725.1</a></th> <th>LC</th> </tr> <tr><th>44</th> <th>Bactrian camel</th> <th>CETARTIODACTYLA</th> <th>Camelidae</th> <th>Camelus bactrianus</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCF_000767855.1/ target=_blank>GCF_000767855.1</a></th> <th>LC</th> </tr> <tr><th>45</th> <th>Arabian camel</th> <th>CETARTIODACTYLA</th> <th>Camelidae</th> <th>Camelus dromedarius</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCF_000767585.1/ target=_blank>GCF_000767585.1</a></th> <th>LC</th> </tr> <tr><th>46</th> <th>Wild bactrian camel</th> <th>CETARTIODACTYLA</th> <th>Camelidae</th> <th>Camelus ferus</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCF_000311805.1/ target=_blank>GCF_000311805.1</a></th> <th>CR</th> </tr> <tr><th>47</th> <th>Wild goat</th> <th>CETARTIODACTYLA</th> <th>Bovidae</th> <th>Capra aegagrus</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_000978405.1/ target=_blank>GCA_000978405.1</a></th> <th>VU</th> </tr> <tr><th>48</th> <th>Goat</th> <th>CETARTIODACTYLA</th> <th>Bovidae</th> <th>Capra hircus</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCF_001704415.1/ target=_blank>GCF_001704415.1</a></th> <th>LC</th> </tr> <tr><th>49</th> <th>Chacoan peccary</th> <th>CETARTIODACTYLA</th> <th>Tayassuidae</th> <th>Catagonus wagneri</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004024745.1/ target=_blank>GCA_004024745.1</a></th> <th>EN</th> </tr> <tr><th>50</th> <th>Beluga whale</th> <th>CETARTIODACTYLA</th> <th>Monodontidae</th> <th>Delphinapterus leucas</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCF_002288925.1/ target=_blank>GCF_002288925.1</a></th> <th>LC</th> </tr> <tr><th>51</th> <th>Pere david's deer</th> <th>CETARTIODACTYLA</th> <th>Cervidae</th> <th>Elaphurus davidianus</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_002443075.1/ target=_blank>GCA_002443075.1</a></th> <th>CR</th> </tr> <tr><th>52</th> <th>Grey whale</th> <th>CETARTIODACTYLA</th> <th>Eschrichtiidae</th> <th>Eschrichtius robustus</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004363415.1/ target=_blank>GCA_004363415.1</a></th> <th>LC</th> </tr> <tr><th>53</th> <th>North Pacific right whale</th> <th>CETARTIODACTYLA</th> <th>Balaenidae</th> <th>Eubalaena japonica</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004363455.1/ target=_blank>GCA_004363455.1</a></th> <th>EN</th> </tr> <tr><th>54</th> <th>Giraffe</th> <th>CETARTIODACTYLA</th> <th>Giraffidae</th> <th>Giraffa tippelskirchi</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_001651235.1/ target=_blank>GCA_001651235.1</a></th> <th>VU</th> </tr> <tr><th>55</th> <th>Nilgiri tahr</th> <th>CETARTIODACTYLA</th> <th>Bovidae</th> <th>Hemitragus hylocrius</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004026825.1/ target=_blank>GCA_004026825.1</a></th> <th>EN</th> </tr> <tr><th>56</th> <th>Hippopotamus</th> <th>CETARTIODACTYLA</th> <th>Hippopotamidae</th> <th>Hippopotamus amphibius</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004027065.1/ target=_blank>GCA_004027065.1</a></th> <th>VU</th> </tr> <tr><th>57</th> <th>Amazon river dolphin</th> <th>CETARTIODACTYLA</th> <th>Iniidae</th> <th>Inia geoffrensis</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004363515.1/ target=_blank>GCA_004363515.1</a></th> <th>DD</th> </tr> <tr><th>58</th> <th>Pygmy sperm whale</th> <th>CETARTIODACTYLA</th> <th>Physeteridae</th> <th>Kogia breviceps</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004363705.1/ target=_blank>GCA_004363705.1</a></th> <th>DD</th> </tr> <tr><th>59</th> <th>Yangtze river dolphin</th> <th>CETARTIODACTYLA</th> <th>Iniidae</th> <th>Lipotes vexillifer</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCF_000442215.1/ target=_blank>GCF_000442215.1</a></th> <th>CR</th> </tr> <tr><th>60</th> <th>Sowerby's beaked whale</th> <th>CETARTIODACTYLA</th> <th>Ziphiidae</th> <th>Mesoplodon bidens</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004027085.1/ target=_blank>GCA_004027085.1</a></th> <th>DD</th> </tr> <tr><th>61</th> <th>Narwhal</th> <th>CETARTIODACTYLA</th> <th>Monodontidae</th> <th>Monodon monoceros</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004026685.1/ target=_blank>GCA_004026685.1</a></th> <th>LC</th> </tr> <tr><th>62</th> <th>Siberian musk deer</th> <th>CETARTIODACTYLA</th> <th>Moschidae</th> <th>Moschus moschiferus</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004024705.1/ target=_blank>GCA_004024705.1</a></th> <th>VU</th> </tr> <tr><th>63</th> <th>Yangtze finless porpoise</th> <th>CETARTIODACTYLA</th> <th>Phocoenidae</th> <th>Neophocaena asiaeorientalis</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_003031525.1/ target=_blank>GCA_003031525.1</a></th> <th>EN</th> </tr> <tr><th>64</th> <th>White-tailed deer</th> <th>CETARTIODACTYLA</th> <th>Cervidae</th> <th>Odocoileus virginianus</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_002102435.1/ target=_blank>GCA_002102435.1</a></th> <th>LC</th> </tr> <tr><th>65</th> <th>Okapi</th> <th>CETARTIODACTYLA</th> <th>Giraffidae</th> <th>Okapia johnstoni</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_001660835.1/ target=_blank>GCA_001660835.1</a></th> <th>EN</th> </tr> <tr><th>66</th> <th>Killer whale</th> <th>CETARTIODACTYLA</th> <th>Delphinidae</th> <th>Orcinus orca</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCF_000331955.2/ target=_blank>GCF_000331955.2</a></th> <th>DD</th> </tr> <tr><th>67</th> <th>Sheep</th> <th>CETARTIODACTYLA</th> <th>Bovidae</th> <th>Ovis aries</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCF_000298735.2/ target=_blank>GCF_000298735.2</a></th> <th>LC</th> </tr> <tr><th>68</th> <th>Peninsular bighorn sheep</th> <th>CETARTIODACTYLA</th> <th>Bovidae</th> <th>Ovis canadensis cremnobates</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004026945.1/ target=_blank>GCA_004026945.1</a></th> <th>EN</th> </tr> <tr><th>69</th> <th>Chiru</th> <th>CETARTIODACTYLA</th> <th>Bovidae</th> <th>Pantholops hodgsonii</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCF_000400835.1/ target=_blank>GCF_000400835.1</a></th> <th>NT</th> </tr> <tr><th>70</th> <th>Harbor porpoise</th> <th>CETARTIODACTYLA</th> <th>Phocoenidae</th> <th>Phocoena phocoena</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004363495.1/ target=_blank>GCA_004363495.1</a></th> <th>LC</th> </tr> <tr><th>71</th> <th>Indus river dolphin</th> <th>CETARTIODACTYLA</th> <th>Platanistidae</th> <th>Platanista gangetica minor</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004363435.1/ target=_blank>GCA_004363435.1</a></th> <th>EN</th> </tr> <tr><th>72</th> <th>Siberian reindeer</th> <th>CETARTIODACTYLA</th> <th>Cervidae</th> <th>Rangifer tarandus</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004026565.1/ target=_blank>GCA_004026565.1</a></th> <th>VU</th> </tr> <tr><th>73</th> <th>Russian saiga</th> <th>CETARTIODACTYLA</th> <th>Bovidae</th> <th>Saiga tatarica tatarica</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004024985.1/ target=_blank>GCA_004024985.1</a></th> <th>CR</th> </tr> <tr><th>74</th> <th>Pig</th> <th>CETARTIODACTYLA</th> <th>Suidae</th> <th>Sus scrofa</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCF_000003025.5/ target=_blank>GCF_000003025.5</a></th> <th>LC</th> </tr> <tr><th>75</th> <th>Java lesser chevrotain</th> <th>CETARTIODACTYLA</th> <th>Tragulidae</th> <th>Tragulus javanicus</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004024965.1/ target=_blank>GCA_004024965.1</a></th> <th>DD</th> </tr> <tr><th>76</th> <th>Bottlenose dolphin</th> <th>CETARTIODACTYLA</th> <th>Delphinidae</th> <th>Tursiops truncatus</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_001922835.1/ target=_blank>GCA_001922835.1</a></th> <th>LC</th> </tr> <tr><th>77</th> <th>Alpaca</th> <th>CETARTIODACTYLA</th> <th>Camelidae</th> <th>Vicugna pacos</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_000767525.1/ target=_blank>GCA_000767525.1</a></th> <th>LC</th> </tr> <tr><th>78</th> <th>Cuvier's beaked whale</th> <th>CETARTIODACTYLA</th> <th>Ziphiidae</th> <th>Ziphius cavirostris</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004364475.1/ target=_blank>GCA_004364475.1</a></th> <th>LC</th> </tr> <tr><th>79</th> <th>Tailed tailless bat</th> <th>CHIROPTERA</th> <th>Phyllostomidae</th> <th>Anoura caudifer</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004027475.1/ target=_blank>GCA_004027475.1</a></th> <th>LC</th> </tr> <tr><th>80</th> <th>Jamacian fruit-eating bat</th> <th>CHIROPTERA</th> <th>Phyllostomidae</th> <th>Artibeus jamaicensis</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004027435.1/ target=_blank>GCA_004027435.1</a></th> <th>LC</th> </tr> <tr><th>81</th> <th>Seba's short-tailed bat</th> <th>CHIROPTERA</th> <th>Phyllostomidae</th> <th>Carollia perspicillata</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004027735.1/ target=_blank>GCA_004027735.1</a></th> <th>LC</th> </tr> <tr><th>82</th> <th>Bumblebee bat</th> <th>CHIROPTERA</th> <th>Craseonycteridae</th> <th>Craseonycteris thonglongyai</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004027555.1/ target=_blank>GCA_004027555.1</a></th> <th>VU</th> </tr> <tr><th>83</th> <th>Common vampire bat</th> <th>CHIROPTERA</th> <th>Phyllostomidae</th> <th>Desmodus rotundus</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_002940915.2/ target=_blank>GCA_002940915.2</a></th> <th>LC</th> </tr> <tr><th>84</th> <th>Straw-colored fruit bat</th> <th>CHIROPTERA</th> <th>Pteropodidae</th> <th>Eidolon helvum</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_000465285.1/ target=_blank>GCA_000465285.1</a></th> <th>NT</th> </tr> <tr><th>85</th> <th>Big brown bat</th> <th>CHIROPTERA</th> <th>Vespertilionidae</th> <th>Eptesicus fuscus</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCF_000308155.1/ target=_blank>GCF_000308155.1</a></th> <th>LC</th> </tr> <tr><th>86</th> <th>Great roundleaf bat</th> <th>CHIROPTERA</th> <th>Hipposideridae</th> <th>Hipposideros armiger</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_001890085.1/ target=_blank>GCA_001890085.1</a></th> <th>LC</th> </tr> <tr><th>87</th> <th>Cantor's leaf-nosed bat</th> <th>CHIROPTERA</th> <th>Hipposideridae</th> <th>Hipposideros galeritus</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004027415.1/ target=_blank>GCA_004027415.1</a></th> <th>LC</th> </tr> <tr><th>88</th> <th>Eastern red bat</th> <th>CHIROPTERA</th> <th>Vespertilionidae</th> <th>Lasiurus borealis</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004026805.1/ target=_blank>GCA_004026805.1</a></th> <th>LC</th> </tr> <tr><th>89</th> <th>Long-tongued fruit bat</th> <th>CHIROPTERA</th> <th>Pteropodidae</th> <th>Macroglossus sobrinus</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004027375.1/ target=_blank>GCA_004027375.1</a></th> <th>LC</th> </tr> <tr><th>90</th> <th>Greater false vampire bat</th> <th>CHIROPTERA</th> <th>Megadermatidae</th> <th>Megaderma lyra</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004026885.1/ target=_blank>GCA_004026885.1</a></th> <th>LC</th> </tr> <tr><th>91</th> <th>Hairy big-eared bat</th> <th>CHIROPTERA</th> <th>Phyllostomidae</th> <th>Micronycteris hirsuta</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004026765.1/ target=_blank>GCA_004026765.1</a></th> <th>LC</th> </tr> <tr><th>92</th> <th>Natal long-fingered bat</th> <th>CHIROPTERA</th> <th>Vespertilionidae</th> <th>Miniopterus natalensis</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCF_001595765.1/ target=_blank>GCF_001595765.1</a></th> <th>LC</th> </tr> <tr><th>93</th> <th>Common bent-wing bat</th> <th>CHIROPTERA</th> <th>Vespertilionidae</th> <th>Miniopterus schreibersii</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004026525.1/ target=_blank>GCA_004026525.1</a></th> <th>NT</th> </tr> <tr><th>94</th> <th>Ghost-faced bat</th> <th>CHIROPTERA</th> <th>Mormoopidae</th> <th>Mormoops blainvillei</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004026545.1/ target=_blank>GCA_004026545.1</a></th> <th>LC</th> </tr> <tr><th>95</th> <th>Ashy-gray tube-nosed bat</th> <th>CHIROPTERA</th> <th>Vespertilionidae</th> <th>Murina feae</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004026665.1/ target=_blank>GCA_004026665.1</a></th> <th>LC</th> </tr> <tr><th>96</th> <th>Brandt's bat</th> <th>CHIROPTERA</th> <th>Vespertilionidae</th> <th>Myotis brandtii</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCF_000412655.1/ target=_blank>GCF_000412655.1</a></th> <th>LC</th> </tr> <tr><th>97</th> <th>David's myotis bat</th> <th>CHIROPTERA</th> <th>Vespertilionidae</th> <th>Myotis davidii</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCF_000327345.1/ target=_blank>GCF_000327345.1</a></th> <th>LC</th> </tr> <tr><th>98</th> <th>Little brown bat</th> <th>CHIROPTERA</th> <th>Vespertilionidae</th> <th>Myotis lucifugus</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCF_000147115.1/ target=_blank>GCF_000147115.1</a></th> <th>LC</th> </tr> <tr><th>99</th> <th>Greater mouse-eared bat</th> <th>CHIROPTERA</th> <th>Vespertilionidae</th> <th>Myotis myotis</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004026985.1/ target=_blank>GCA_004026985.1</a></th> <th>LC</th> </tr> <tr><th>100</th> <th>Greater bulldog bat</th> <th>CHIROPTERA</th> <th>Noctilionidae</th> <th>Noctilio leporinus</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004026585.1/ target=_blank>GCA_004026585.1</a></th> <th>LC</th> </tr> <tr><th>101</th> <th>Common pipistrelle</th> <th>CHIROPTERA</th> <th>Vespertilionidae</th> <th>Pipistrellus pipistrellus</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004026625.1/ target=_blank>GCA_004026625.1</a></th> <th>LC</th> </tr> <tr><th>102</th> <th>Parnell's mustached bat</th> <th>CHIROPTERA</th> <th>Mormoopidae</th> <th>Pteronotus parnellii</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_000465405.1/ target=_blank>GCA_000465405.1</a></th> <th>LC</th> </tr> <tr><th>103</th> <th>Black flying fox</th> <th>CHIROPTERA</th> <th>Pteropodidae</th> <th>Pteropus alecto</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCF_000325575.1/ target=_blank>GCF_000325575.1</a></th> <th>LC</th> </tr> <tr><th>104</th> <th>Large flying fox</th> <th>CHIROPTERA</th> <th>Pteropodidae</th> <th>Pteropus vampyrus</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCF_000151845.1/ target=_blank>GCF_000151845.1</a></th> <th>NT</th> </tr> <tr><th>105</th> <th>Chinese rufous horseshoe bat</th> <th>CHIROPTERA</th> <th>Rhinolophidae</th> <th>Rhinolophus sinicus</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_001888835.1/ target=_blank>GCA_001888835.1</a></th> <th>LC</th> </tr> <tr><th>106</th> <th>Egyptian fruit bat</th> <th>CHIROPTERA</th> <th>Pteropodidae</th> <th>Rousettus aegyptiacus</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004024865.1/ target=_blank>GCA_004024865.1</a></th> <th>LC</th> </tr> <tr><th>107</th> <th>Mexican free-tailed bat</th> <th>CHIROPTERA</th> <th>Molossidae</th> <th>Tadarida brasiliensis</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004025005.1/ target=_blank>GCA_004025005.1</a></th> <th>LC</th> </tr> <tr><th>108</th> <th>Stripe-headed round-eared bat</th> <th>CHIROPTERA</th> <th>Phyllostomidae</th> <th>Tonatia saurophila</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004024845.1/ target=_blank>GCA_004024845.1</a></th> <th>LC</th> </tr> <tr><th>109</th> <th>Screaming hairy armadillo</th> <th>CINGULATA</th> <th>Dasypodidae</th> <th>Chaetophractus vellerosus</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004027955.1/ target=_blank>GCA_004027955.1</a></th> <th>LC</th> </tr> <tr><th>110</th> <th>Nine-banded armadillo</th> <th>CINGULATA</th> <th>Dasypodidae</th> <th>Dasypus novemcinctus</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCF_000208655.1/ target=_blank>GCF_000208655.1</a></th> <th>LC</th> </tr> <tr><th>111</th> <th>Southern three-banded armadillo</th> <th>CINGULATA</th> <th>Dasypodidae</th> <th>Tolypeutes matacus</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004025125.1/ target=_blank>GCA_004025125.1</a></th> <th>NT</th> </tr> <tr><th>112</th> <th>Sunda flying lemur</th> <th>DERMOPTERA</th> <th>Cynocephalidae</th> <th>Galeopterus variegatus</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004027255.1/ target=_blank>GCA_004027255.1</a></th> <th>LC</th> </tr> <tr><th>113</th> <th>Star-nosed mole</th> <th>EULIPOTYPHLA</th> <th>Talpidae</th> <th>Condylura cristata</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCF_000260355.1/ target=_blank>GCF_000260355.1</a></th> <th>LC</th> </tr> <tr><th>114</th> <th>Indochinese shrew</th> <th>EULIPOTYPHLA</th> <th>Soricidae</th> <th>Crocidura indochinensis</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004027635.1/ target=_blank>GCA_004027635.1</a></th> <th>LC</th> </tr> <tr><th>115</th> <th>Western european hedgehog</th> <th>EULIPOTYPHLA</th> <th>Erinaceidae</th> <th>Erinaceus europaeus</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCF_000296755.1/ target=_blank>GCF_000296755.1</a></th> <th>LC</th> </tr> <tr><th>116</th> <th>Eastern mole</th> <th>EULIPOTYPHLA</th> <th>Talpidae</th> <th>Scalopus aquaticus</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004024925.1/ target=_blank>GCA_004024925.1</a></th> <th>LC</th> </tr> <tr><th>117</th> <th>Hispaniolan solenodon</th> <th>EULIPOTYPHLA</th> <th>Solenodontidae</th> <th>Solenodon paradoxus</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004363575.1/ target=_blank>GCA_004363575.1</a></th> <th>EN</th> </tr> <tr><th>118</th> <th>European shrew</th> <th>EULIPOTYPHLA</th> <th>Soricidae</th> <th>Sorex araneus</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCF_000181275.1/ target=_blank>GCF_000181275.1</a></th> <th>LC</th> </tr> <tr><th>119</th> <th>Gracile shrew-like mole</th> <th>EULIPOTYPHLA</th> <th>Talpidae</th> <th>Uropsilus gracilis</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004024945.1/ target=_blank>GCA_004024945.1</a></th> <th>LC</th> </tr> <tr><th>120</th> <th>African yellow-spotted rock hyrax</th> <th>HYRACOIDEA</th> <th>Procaviidae</th> <th>Heterohyrax brucei</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004026845.1/ target=_blank>GCA_004026845.1</a></th> <th>LC</th> </tr> <tr><th>121</th> <th>South African rock hyrax</th> <th>HYRACOIDEA</th> <th>Procaviidae</th> <th>Procavia capensis</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004026925.1/ target=_blank>GCA_004026925.1</a></th> <th>LC</th> </tr> <tr><th>122</th> <th>Snowshoe hare</th> <th>LAGOMORPHA</th> <th>Leporidae</th> <th>Lepus americanus</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004026855.1/ target=_blank>GCA_004026855.1</a></th> <th>LC</th> </tr> <tr><th>123</th> <th>American pika</th> <th>LAGOMORPHA</th> <th>Ochotonidae</th> <th>Ochotona princeps</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCF_000292845.1/ target=_blank>GCF_000292845.1</a></th> <th>LC</th> </tr> <tr><th>124</th> <th>Rabbit</th> <th>LAGOMORPHA</th> <th>Leporidae</th> <th>Oryctolagus cuniculus</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCF_000003625.3/ target=_blank>GCF_000003625.3</a></th> <th>NT</th> </tr> <tr><th>125</th> <th>Cape elephant shrew</th> <th>MACROSCELIDEA</th> <th>Macroscelididae</th> <th>Elephantulus edwardii</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004027355.1/ target=_blank>GCA_004027355.1</a></th> <th>LC</th> </tr> <tr><th>126</th> <th>Southern white rhinoceros</th> <th>PERISSODACTYLA</th> <th>Rhinocerotidae</th> <th>Ceratotherium simum</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCF_000283155.1/ target=_blank>GCF_000283155.1</a></th> <th>NT</th> </tr> <tr><th>127</th> <th>Northern white rhino</th> <th>PERISSODACTYLA</th> <th>Rhinocerotidae</th> <th>Ceratotherium simum cottoni</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004027795.1/ target=_blank>GCA_004027795.1</a></th> <th>CR</th> </tr> <tr><th>128</th> <th>Sumatran rhinoceros</th> <th>PERISSODACTYLA</th> <th>Rhinocerotidae</th> <th>Dicerorhinus sumatrensis</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_002844835.1/ target=_blank>GCA_002844835.1</a></th> <th>CR</th> </tr> <tr><th>129</th> <th>Black rhinocerous</th> <th>PERISSODACTYLA</th> <th>Rhinocerotidae</th> <th>Diceros bicornis</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004027315.1/ target=_blank>GCA_004027315.1</a></th> <th>CR</th> </tr> <tr><th>130</th> <th>Ass</th> <th>PERISSODACTYLA</th> <th>Equidae</th> <th>Equus asinus</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCF_001305755.1/ target=_blank>GCF_001305755.1</a></th> <th>LC</th> </tr> <tr><th>131</th> <th>Horse</th> <th>PERISSODACTYLA</th> <th>Equidae</th> <th>Equus caballus</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCF_000002305.2/ target=_blank>GCF_000002305.2</a></th> <th>LC</th> </tr> <tr><th>132</th> <th>Przewalski's horse</th> <th>PERISSODACTYLA</th> <th>Equidae</th> <th>Equus przewalskii</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCF_000696695.1/ target=_blank>GCF_000696695.1</a></th> <th>EN</th> </tr> <tr><th>133</th> <th>Malayan tapir</th> <th>PERISSODACTYLA</th> <th>Tapiridae</th> <th>Tapirus indicus</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004024905.1/ target=_blank>GCA_004024905.1</a></th> <th>EN</th> </tr> <tr><th>134</th> <th>South American tapir</th> <th>PERISSODACTYLA</th> <th>Tapiridae</th> <th>Tapirus terrestris</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004025025.1/ target=_blank>GCA_004025025.1</a></th> <th>VU</th> </tr> <tr><th>135</th> <th>Malayan pangolin</th> <th>PHOLIDOTA</th> <th>Manidae</th> <th>Manis javanica</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCF_001685135.1/ target=_blank>GCF_001685135.1</a></th> <th>CR</th> </tr> <tr><th>136</th> <th>Chinese pangolin</th> <th>PHOLIDOTA</th> <th>Manidae</th> <th>Manis pentadactyla</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_000738955.1/ target=_blank>GCA_000738955.1</a></th> <th>CR</th> </tr> <tr><th>137</th> <th>Linnaeus's two toed sloth</th> <th>PILOSA</th> <th>Megalonychidae</th> <th>Choloepus didactylus</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004027855.1/ target=_blank>GCA_004027855.1</a></th> <th>LC</th> </tr> <tr><th>138</th> <th>Hoffmann's two-fingered sloth</th> <th>PILOSA</th> <th>Megalonychidae</th> <th>Choloepus hoffmanni</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_000164785.2/ target=_blank>GCA_000164785.2</a></th> <th>LC</th> </tr> <tr><th>139</th> <th>Giant anteater</th> <th>PILOSA</th> <th>Myrmecophagidae</th> <th>Myrmecophaga tridactyla</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004026745.1/ target=_blank>GCA_004026745.1</a></th> <th>VU</th> </tr> <tr><th>140</th> <th>Southern tamandua</th> <th>PILOSA</th> <th>Myrmecophagidae</th> <th>Tamandua tetradactyla</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004025105.1/ target=_blank>GCA_004025105.1</a></th> <th>LC</th> </tr> <tr><th>141</th> <th>Mexican howler monkey</th> <th>PRIMATES</th> <th>Atelidae</th> <th>Alouatta palliata mexicana</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004027835.1/ target=_blank>GCA_004027835.1</a></th> <th>CR</th> </tr> <tr><th>142</th> <th>Ma's night monkey</th> <th>PRIMATES</th> <th>Aotidae</th> <th>Aotus nancymaae</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_000952055.2/ target=_blank>GCA_000952055.2</a></th> <th>VU</th> </tr> <tr><th>143</th> <th>Geoffroy's spider monkey</th> <th>PRIMATES</th> <th>Atelidae</th> <th>Ateles geoffroyi</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004024785.1/ target=_blank>GCA_004024785.1</a></th> <th>EN</th> </tr> <tr><th>144</th> <th>White-eared titi</th> <th>PRIMATES</th> <th>Pitheciidae</th> <th>Callicebus donacophilus</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004027715.1/ target=_blank>GCA_004027715.1</a></th> <th>LC</th> </tr> <tr><th>145</th> <th>White-tufted-ear marmoset</th> <th>PRIMATES</th> <th>Cebidae</th> <th>Callithrix jacchus</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_002754865.1/ target=_blank>GCA_002754865.1</a></th> <th>LC</th> </tr> <tr><th>146</th> <th>White-fronted capuchin</th> <th>PRIMATES</th> <th>Cebidae</th> <th>Cebus albifrons</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004027755.1/ target=_blank>GCA_004027755.1</a></th> <th>LC</th> </tr> <tr><th>147</th> <th>White-faced sapajou</th> <th>PRIMATES</th> <th>Cebidae</th> <th>Cebus capucinus</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCF_001604975.1/ target=_blank>GCF_001604975.1</a></th> <th>LC</th> </tr> <tr><th>148</th> <th>Sooty mangabey</th> <th>PRIMATES</th> <th>Cercopithecidae</th> <th>Cercocebus atys</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCF_000955945.1/ target=_blank>GCF_000955945.1</a></th> <th>NT</th> </tr> <tr><th>149</th> <th>De brazza's monkey</th> <th>PRIMATES</th> <th>Cercopithecidae</th> <th>Cercopithecus neglectus</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004027615.1/ target=_blank>GCA_004027615.1</a></th> <th>LC</th> </tr> <tr><th>150</th> <th>Fat-tailed dwarf lemur</th> <th>PRIMATES</th> <th>Cheirogaleidae</th> <th>Cheirogaleus medius</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004024725.1/ target=_blank>GCA_004024725.1</a></th> <th>LC</th> </tr> <tr><th>151</th> <th>Green monkey</th> <th>PRIMATES</th> <th>Cercopithecidae</th> <th>Chlorocebus sabaeus</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCF_000409795.2/ target=_blank>GCF_000409795.2</a></th> <th>LC</th> </tr> <tr><th>152</th> <th>Angolan colobus</th> <th>PRIMATES</th> <th>Cercopithecidae</th> <th>Colobus angolensis</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCF_000951035.1/ target=_blank>GCF_000951035.1</a></th> <th>VU</th> </tr> <tr><th>153</th> <th>Aye-aye</th> <th>PRIMATES</th> <th>Daubentoniidae</th> <th>Daubentonia madagascariensis</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004027145.1/ target=_blank>GCA_004027145.1</a></th> <th>EN</th> </tr> <tr><th>154</th> <th>Patas monkey</th> <th>PRIMATES</th> <th>Cercopithecidae</th> <th>Erythrocebus patas</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004027335.1/ target=_blank>GCA_004027335.1</a></th> <th>LC</th> </tr> <tr><th>155</th> <th>Sclater's lemur</th> <th>PRIMATES</th> <th>Lemuridae</th> <th>Eulemur flavifrons</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_001262665.1/ target=_blank>GCA_001262665.1</a></th> <th>CR</th> </tr> <tr><th>156</th> <th>Common brown lemur</th> <th>PRIMATES</th> <th>Lemuridae</th> <th>Eulemur fulvus</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004027275.1/ target=_blank>GCA_004027275.1</a></th> <th>NT</th> </tr> <tr><th>157</th> <th>Western lowland gorilla</th> <th>PRIMATES</th> <th>Hominidae</th> <th>Gorilla gorilla</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_900006655.3/ target=_blank>GCA_900006655.3</a></th> <th>CR</th> </tr> <tr><th>158</th> <th>Human</th> <th>PRIMATES</th> <th>Hominidae</th> <th>Homo sapiens</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_000001405.27/ target=_blank>GCA_000001405.27</a></th> <th>LC</th> </tr> <tr><th>159</th> <th>Indri</th> <th>PRIMATES</th> <th>Indridae</th> <th>Indri indri</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004363605.1/ target=_blank>GCA_004363605.1</a></th> <th>CR</th> </tr> <tr><th>160</th> <th>Ring tailed lemur</th> <th>PRIMATES</th> <th>Lemuridae</th> <th>Lemur catta</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004024665.1/ target=_blank>GCA_004024665.1</a></th> <th>EN</th> </tr> <tr><th>161</th> <th>Crab-eating macaque</th> <th>PRIMATES</th> <th>Cercopithecidae</th> <th>Macaca fascicularis</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCF_000364345.1/ target=_blank>GCF_000364345.1</a></th> <th>DD</th> </tr> <tr><th>162</th> <th>Rhesus monkey</th> <th>PRIMATES</th> <th>Cercopithecidae</th> <th>Macaca mulatta</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCF_000772875.2/ target=_blank>GCF_000772875.2</a></th> <th>LC</th> </tr> <tr><th>163</th> <th>Pig-tailed macaque</th> <th>PRIMATES</th> <th>Cercopithecidae</th> <th>Macaca nemestrina</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCF_000956065.1/ target=_blank>GCF_000956065.1</a></th> <th>VU</th> </tr> <tr><th>164</th> <th>Drill</th> <th>PRIMATES</th> <th>Cercopithecidae</th> <th>Mandrillus leucophaeus</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCF_000951045.1/ target=_blank>GCF_000951045.1</a></th> <th>EN</th> </tr> <tr><th>165</th> <th>Gray mouse lemur</th> <th>PRIMATES</th> <th>Cheirogaleidae</th> <th>Microcebus murinus</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_000165445.3/ target=_blank>GCA_000165445.3</a></th> <th>LC</th> </tr> <tr><th>166</th> <th>Coquerel's giant mouse lemur</th> <th>PRIMATES</th> <th>Cheirogaleidae</th> <th>Mirza coquereli</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004024645.1/ target=_blank>GCA_004024645.1</a></th> <th>EN</th> </tr> <tr><th>167</th> <th>Proboscis monkey</th> <th>PRIMATES</th> <th>Cercopithecidae</th> <th>Nasalis larvatus</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004027105.1/ target=_blank>GCA_004027105.1</a></th> <th>EN</th> </tr> <tr><th>168</th> <th>Northern white-cheeked gibbon</th> <th>PRIMATES</th> <th>Hylobatidae</th> <th>Nomascus leucogenys</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCF_000146795.2/ target=_blank>GCF_000146795.2</a></th> <th>CR</th> </tr> <tr><th>169</th> <th>Sunda slow loris</th> <th>PRIMATES</th> <th>Lorisidae</th> <th>Nycticebus coucang</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004027815.1/ target=_blank>GCA_004027815.1</a></th> <th>VU</th> </tr> <tr><th>170</th> <th>Small-eared galago</th> <th>PRIMATES</th> <th>Galagidae</th> <th>Otolemur garnettii</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCF_000181295.1/ target=_blank>GCF_000181295.1</a></th> <th>LC</th> </tr> <tr><th>171</th> <th>Pygmy chimpanzee</th> <th>PRIMATES</th> <th>Hominidae</th> <th>Pan paniscus</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCF_000258655.2/ target=_blank>GCF_000258655.2</a></th> <th>EN</th> </tr> <tr><th>172</th> <th>Chimpanzee</th> <th>PRIMATES</th> <th>Hominidae</th> <th>Pan troglodytes</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_002880755.3/ target=_blank>GCA_002880755.3</a></th> <th>EN</th> </tr> <tr><th>173</th> <th>Olive baboon</th> <th>PRIMATES</th> <th>Cercopithecidae</th> <th>Papio anubis</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_000264685.2/ target=_blank>GCA_000264685.2</a></th> <th>LC</th> </tr> <tr><th>174</th> <th>Ugandan red colobus</th> <th>PRIMATES</th> <th>Cercopithecidae</th> <th>Piliocolobus tephrosceles</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_002776525.1/ target=_blank>GCA_002776525.1</a></th> <th>EN</th> </tr> <tr><th>175</th> <th>White-faced saki</th> <th>PRIMATES</th> <th>Pitheciidae</th> <th>Pithecia pithecia</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004026645.1/ target=_blank>GCA_004026645.1</a></th> <th>LC</th> </tr> <tr><th>176</th> <th>Sumatran orangutan</th> <th>PRIMATES</th> <th>Hominidae</th> <th>Pongo abelii</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_002880775.3/ target=_blank>GCA_002880775.3</a></th> <th>CR</th> </tr> <tr><th>177</th> <th>Coquerel's sifaka</th> <th>PRIMATES</th> <th>Indridae</th> <th>Propithecus coquereli</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCF_000956105.1/ target=_blank>GCF_000956105.1</a></th> <th>EN</th> </tr> <tr><th>178</th> <th>Red-shanked douc</th> <th>PRIMATES</th> <th>Cercopithecidae</th> <th>Pygathrix nemaeus</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004024825.1/ target=_blank>GCA_004024825.1</a></th> <th>EN</th> </tr> <tr><th>179</th> <th>Black snub-nosed monkey</th> <th>PRIMATES</th> <th>Cercopithecidae</th> <th>Rhinopithecus bieti</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCF_001698545.1/ target=_blank>GCF_001698545.1</a></th> <th>EN</th> </tr> <tr><th>180</th> <th>Golden snub-nosed monkey</th> <th>PRIMATES</th> <th>Cercopithecidae</th> <th>Rhinopithecus roxellana</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCF_000769185.1/ target=_blank>GCF_000769185.1</a></th> <th>EN</th> </tr> <tr><th>181</th> <th>Emperor tamarin</th> <th>PRIMATES</th> <th>Cebidae</th> <th>Saguinus imperator</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004024885.1/ target=_blank>GCA_004024885.1</a></th> <th>LC</th> </tr> <tr><th>182</th> <th>Bolivian squirrel monkey</th> <th>PRIMATES</th> <th>Cebidae</th> <th>Saimiri boliviensis</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCF_000235385.1/ target=_blank>GCF_000235385.1</a></th> <th>LC</th> </tr> <tr><th>183</th> <th>Northern Plains gray langur</th> <th>PRIMATES</th> <th>Cercopithecidae</th> <th>Semnopithecus entellus</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004025065.1/ target=_blank>GCA_004025065.1</a></th> <th>LC</th> </tr> <tr><th>184</th> <th>African savanna elephant</th> <th>PROBOSCIDEA</th> <th>Elephantidae</th> <th>Loxodonta Africana</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCF_000001905.1/ target=_blank>GCF_000001905.1</a></th> <th>VU</th> </tr> <tr><th>185</th> <th>Cairo spiny mouse</th> <th>RODENTIA</th> <th>Muridae</th> <th>Acomys cahirinus</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004027535.1/ target=_blank>GCA_004027535.1</a></th> <th>LC</th> </tr> <tr><th>186</th> <th>Gobi jerboa</th> <th>RODENTIA</th> <th>Dipodidae</th> <th>Allactaga bullata</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004027895.1/ target=_blank>GCA_004027895.1</a></th> <th>LC</th> </tr> <tr><th>187</th> <th>Mountain beaver</th> <th>RODENTIA</th> <th>Aplodontiidae</th> <th>Aplodontia rufa</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004027875.1/ target=_blank>GCA_004027875.1</a></th> <th>LC</th> </tr> <tr><th>188</th> <th>Desmarest's hutia</th> <th>RODENTIA</th> <th>Capromyidae</th> <th>Capromys pilorides</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004027915.1/ target=_blank>GCA_004027915.1</a></th> <th>LC</th> </tr> <tr><th>189</th> <th>North American beaver</th> <th>RODENTIA</th> <th>Castoridae</th> <th>Castor canadensis</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004027675.1/ target=_blank>GCA_004027675.1</a></th> <th>LC</th> </tr> <tr><th>190</th> <th>Brazilian guinea pig</th> <th>RODENTIA</th> <th>Caviidae</th> <th>Cavia aperea</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_000688575.1/ target=_blank>GCA_000688575.1</a></th> <th>LC</th> </tr> <tr><th>191</th> <th>Domestic guinea pig</th> <th>RODENTIA</th> <th>Caviidae</th> <th>Cavia porcellus</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCF_000151735.1/ target=_blank>GCF_000151735.1</a></th> <th>LC</th> </tr> <tr><th>192</th> <th>Montane guinea pig</th> <th>RODENTIA</th> <th>Caviidae</th> <th>Cavia tschudii</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004027695.1/ target=_blank>GCA_004027695.1</a></th> <th>LC</th> </tr> <tr><th>193</th> <th>Long-tailed chinchilla</th> <th>RODENTIA</th> <th>Chinchillidae</th> <th>Chinchilla lanigera</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCF_000276665.1/ target=_blank>GCF_000276665.1</a></th> <th>EN</th> </tr> <tr><th>194</th> <th>Gambian pouched rat</th> <th>RODENTIA</th> <th>Nesomyidae</th> <th>Cricetomys gambianus</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004027575.1/ target=_blank>GCA_004027575.1</a></th> <th>LC</th> </tr> <tr><th>195</th> <th>Chinese hamster</th> <th>RODENTIA</th> <th>Nesomyidae</th> <th>Cricetulus griseus</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_900186095.1/ target=_blank>GCA_900186095.1</a></th> <th>LC</th> </tr> <tr><th>196</th> <th>Common gundi</th> <th>RODENTIA</th> <th>Ctenodactylidae</th> <th>Ctenodactylus gundi</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004027205.1/ target=_blank>GCA_004027205.1</a></th> <th>LC</th> </tr> <tr><th>197</th> <th>Social tuco-tuco</th> <th>RODENTIA</th> <th>Ctenomyidae</th> <th>Ctenomys sociabilis</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004027165.1/ target=_blank>GCA_004027165.1</a></th> <th>CR</th> </tr> <tr><th>198</th> <th>Lowland paca</th> <th>RODENTIA</th> <th>Cuniculidae</th> <th>Cuniculus paca</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004365215.1/ target=_blank>GCA_004365215.1</a></th> <th>LC</th> </tr> <tr><th>199</th> <th>Central American agouti</th> <th>RODENTIA</th> <th>Dasyproctidae</th> <th>Dasyprocta punctata</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004363535.1/ target=_blank>GCA_004363535.1</a></th> <th>LC</th> </tr> <tr><th>200</th> <th>Pacarana</th> <th>RODENTIA</th> <th>Dinomyidae</th> <th>Dinomys branickii</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004027595.1/ target=_blank>GCA_004027595.1</a></th> <th>LC</th> </tr> <tr><th>201</th> <th>Ord's kangaroo rat</th> <th>RODENTIA</th> <th>Heteromyidae</th> <th>Dipodomys ordii</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCF_000151885.1/ target=_blank>GCF_000151885.1</a></th> <th>LC</th> </tr> <tr><th>202</th> <th>Stephen's kangaroo rat</th> <th>RODENTIA</th> <th>Heteromyidae</th> <th>Dipodomys stephensi</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004024685.1/ target=_blank>GCA_004024685.1</a></th> <th>VU</th> </tr> <tr><th>203</th> <th>Patagonian mara</th> <th>RODENTIA</th> <th>Caviidae</th> <th>Dolichotis patagonum</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004027295.1/ target=_blank>GCA_004027295.1</a></th> <th>NT</th> </tr> <tr><th>204</th> <th>Transcaucasian mole vole</th> <th>RODENTIA</th> <th>Cricetidae</th> <th>Ellobius lutescens</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_001685075.1/ target=_blank>GCA_001685075.1</a></th> <th>LC</th> </tr> <tr><th>205</th> <th>Northern mole vole</th> <th>RODENTIA</th> <th>Cricetidae</th> <th>Ellobius talpinus</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_001685095.1/ target=_blank>GCA_001685095.1</a></th> <th>LC</th> </tr> <tr><th>206</th> <th>Damara mole-rat</th> <th>RODENTIA</th> <th>Bathyergidae</th> <th>Fukomys damarensis</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCF_000743615.1/ target=_blank>GCF_000743615.1</a></th> <th>LC</th> </tr> <tr><th>207</th> <th>Edible dormouse</th> <th>RODENTIA</th> <th>Gliridae</th> <th>Glis glis</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004027185.1/ target=_blank>GCA_004027185.1</a></th> <th>LC</th> </tr> <tr><th>208</th> <th>Woodland doormouse</th> <th>RODENTIA</th> <th>Gliridae</th> <th>Graphiurus murinus</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004027655.1/ target=_blank>GCA_004027655.1</a></th> <th>LC</th> </tr> <tr><th>209</th> <th>Naked mole-rat</th> <th>RODENTIA</th> <th>Bathyergidae</th> <th>Heterocephalus glaber</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCF_000247695.1/ target=_blank>GCF_000247695.1</a></th> <th>LC</th> </tr> <tr><th>210</th> <th>Capybara</th> <th>RODENTIA</th> <th>Caviidae</th> <th>Hydrochoerus hydrochaeris</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004027455.1/ target=_blank>GCA_004027455.1</a></th> <th>LC</th> </tr> <tr><th>211</th> <th>Northern crested porcupine</th> <th>RODENTIA</th> <th>Hystricidae</th> <th>Hystrix cristata</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004026905.1/ target=_blank>GCA_004026905.1</a></th> <th>LC</th> </tr> <tr><th>212</th> <th>Thirteen-lined ground squirrel</th> <th>RODENTIA</th> <th>Sciuridae</th> <th>Ictidomys tridecemlineatus</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCF_000236235.1/ target=_blank>GCF_000236235.1</a></th> <th>LC</th> </tr> <tr><th>213</th> <th>Lesser egyptian jerboa</th> <th>RODENTIA</th> <th>Dipodidae</th> <th>Jaculus jaculus</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCF_000280705.1/ target=_blank>GCF_000280705.1</a></th> <th>LC</th> </tr> <tr><th>214</th> <th>Alpine marmot</th> <th>RODENTIA</th> <th>Sciuridae</th> <th>Marmota marmota</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCF_001458135.1/ target=_blank>GCF_001458135.1</a></th> <th>LC</th> </tr> <tr><th>215</th> <th>Mongolian jird</th> <th>RODENTIA</th> <th>Muridae</th> <th>Meriones unguiculatus</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004026785.1/ target=_blank>GCA_004026785.1</a></th> <th>LC</th> </tr> <tr><th>216</th> <th>Golden hamster</th> <th>RODENTIA</th> <th>Cricetidae</th> <th>Mesocricetus auratus</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCF_000349665.1/ target=_blank>GCF_000349665.1</a></th> <th>VU</th> </tr> <tr><th>217</th> <th>Prairie vole</th> <th>RODENTIA</th> <th>Cricetidae</th> <th>Microtus ochrogaster</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCF_000317375.1/ target=_blank>GCF_000317375.1</a></th> <th>LC</th> </tr> <tr><th>218</th> <th>Ryukyu mouse</th> <th>RODENTIA</th> <th>Muridae</th> <th>Mus caroli</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_900094665.2/ target=_blank>GCA_900094665.2</a></th> <th>LC</th> </tr> <tr><th>219</th> <th>House mouse</th> <th>RODENTIA</th> <th>Muridae</th> <th>Mus musculus</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCF_000001635.26/ target=_blank>GCF_000001635.26</a></th> <th>LC</th> </tr> <tr><th>220</th> <th>Shrew mouse</th> <th>RODENTIA</th> <th>Muridae</th> <th>Mus pahari</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_900095145.2/ target=_blank>GCA_900095145.2</a></th> <th>LC</th> </tr> <tr><th>221</th> <th>Western wild mouse</th> <th>RODENTIA</th> <th>Muridae</th> <th>Mus spretus</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_001624865.1/ target=_blank>GCA_001624865.1</a></th> <th>LC</th> </tr> <tr><th>222</th> <th>Hazel dormouse</th> <th>RODENTIA</th> <th>Gliridae</th> <th>Muscardinus avellanarius</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004027005.1/ target=_blank>GCA_004027005.1</a></th> <th>LC</th> </tr> <tr><th>223</th> <th>Coypu</th> <th>RODENTIA</th> <th>Myocastoridae</th> <th>Myocastor coypus</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004027025.1/ target=_blank>GCA_004027025.1</a></th> <th>LC</th> </tr> <tr><th>224</th> <th>Upper galilee mountains blind mole rat</th> <th>RODENTIA</th> <th>Spalacidae</th> <th>Nannospalax galili</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCF_000622305.1/ target=_blank>GCF_000622305.1</a></th> <th>DD</th> </tr> <tr><th>225</th> <th>Degu</th> <th>RODENTIA</th> <th>Octodontidae</th> <th>Octodon degus</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCF_000260255.1/ target=_blank>GCF_000260255.1</a></th> <th>LC</th> </tr> <tr><th>226</th> <th>Muskrat</th> <th>RODENTIA</th> <th>Cricetidae</th> <th>Ondatra zibethicus</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004026605.1/ target=_blank>GCA_004026605.1</a></th> <th>LC</th> </tr> <tr><th>227</th> <th>Scorpion mouse</th> <th>RODENTIA</th> <th>Cricetidae</th> <th>Onychomys torridus</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004026725.1/ target=_blank>GCA_004026725.1</a></th> <th>LC</th> </tr> <tr><th>228</th> <th>Pacific pocket mouse</th> <th>RODENTIA</th> <th>Heteromyidae</th> <th>Perognathus longimembris pacificus</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004363475.1/ target=_blank>GCA_004363475.1</a></th> <th>LC</th> </tr> <tr><th>229</th> <th>Prairie deer mouse</th> <th>RODENTIA</th> <th>Cricetidae</th> <th>Peromyscus maniculatus</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCF_000500345.1/ target=_blank>GCF_000500345.1</a></th> <th>LC</th> </tr> <tr><th>230</th> <th>Dassie rat</th> <th>RODENTIA</th> <th>Petromuridae</th> <th>Petromus typicus</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004026965.1/ target=_blank>GCA_004026965.1</a></th> <th>LC</th> </tr> <tr><th>231</th> <th>Fat sand rat</th> <th>RODENTIA</th> <th>Muridae</th> <th>Psammomys obesus</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_002215935.1/ target=_blank>GCA_002215935.1</a></th> <th>LC</th> </tr> <tr><th>232</th> <th>Norway rat</th> <th>RODENTIA</th> <th>Muridae</th> <th>Rattus norvegicus</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCF_000001895.5/ target=_blank>GCF_000001895.5</a></th> <th>LC</th> </tr> <tr><th>233</th> <th>Hispid cotton rat</th> <th>RODENTIA</th> <th>Cricetidae</th> <th>Sigmodon hispidus</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004025045.1/ target=_blank>GCA_004025045.1</a></th> <th>LC</th> </tr> <tr><th>234</th> <th>Daurian ground squirrel</th> <th>RODENTIA</th> <th>Sciuridae</th> <th>Spermophilus dauricus</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_002406435.1/ target=_blank>GCA_002406435.1</a></th> <th>LC</th> </tr> <tr><th>235</th> <th>Greater cane rat</th> <th>RODENTIA</th> <th>Thryonomyidae</th> <th>Thryonomys swinderianus</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004025085.1/ target=_blank>GCA_004025085.1</a></th> <th>LC</th> </tr> <tr><th>236</th> <th>Cape ground squirrel</th> <th>RODENTIA</th> <th>Sciuridae</th> <th>Xerus inauris</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004024805.1/ target=_blank>GCA_004024805.1</a></th> <th>LC</th> </tr> <tr><th>237</th> <th>Meadow jumping mouse</th> <th>RODENTIA</th> <th>Dipodidae</th> <th>Zapus hudsonius</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004024765.1/ target=_blank>GCA_004024765.1</a></th> <th>LC</th> </tr> <tr><th>238</th> <th>Northern tree shrew</th> <th>SCANDENTIA</th> <th>Tupaiidae</th> <th>Tupaia belangeri chinensis</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCF_000334495.1/ target=_blank>GCF_000334495.1</a></th> <th>LC</th> </tr> <tr><th>239</th> <th>Large treeshrew</th> <th>SCANDENTIA</th> <th>Tupaiidae</th> <th>Tupaia tana</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004365275.1/ target=_blank>GCA_004365275.1</a></th> <th>LC</th> </tr> <tr><th>240</th> <th>Florida manatee</th> <th>SIRENIA</th> <th>Trichechidae</th> <th>Trichechus manatus</th> <th>2. Existing assembly</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCF_000243295.1/ target=_blank>GCF_000243295.1</a></th> <th>EN</th> </tr> <tr><th>241</th> <th>Aardvark</th> <th>TUBULIDENTATA</th> <th>Orycteropodidae</th> <th>Orycteropus afer</th> <th>1. Zoonomia</th> <th><a href=https://www.ncbi.nlm.nih.gov/assembly/GCA_004365145.1/ target=_blank>GCA_004365145.1</a></th> <th>LC</th> </tr> </table><br> <b>Table 1.</b> <em>Genome assemblies included in the 241-way Conservation track.</em><br> <b>Species status:</b>LC = Least Concern; NT = Near threatened; VU = Vulnerable; EN = Endangered; CR = Critically endangered<br> </blockquote></p> <h2>Display Conventions and Configuration</h2> <p> In full and pack display modes, conservation scores are displayed as a <em>wiggle track</em> (histogram) in which the height reflects the size of the score. The conservation wiggles can be configured in a variety of ways to highlight different aspects of the displayed information. Click the <a href="../goldenPath/help/hgWiggleTrackHelp.html" target=_blank>Graph configuration help</a> link for an explanation of the configuration options.</p> <p> Pairwise alignments of each species to the $organism genome are displayed below the conservation histogram as a grayscale density plot (in pack mode) or as a wiggle (in full mode) that indicates alignment quality. In dense display mode, conservation is shown in grayscale using darker values to indicate higher levels of overall conservation as scored by phastCons. </p> <p> Checkboxes on the track configuration page allow selection of the species to include in the pairwise display. +The names of selected species are colored according to their clade, +alternating between blue and green. Note that excluding species from the pairwise display does not alter the the conservation score display.</p> <p> To view detailed information about the alignments at a specific position, zoom the display in to 30,000 or fewer bases, then click on the alignment.</p> <h3>Gap Annotation</h3> <p> The <em>Display chains between alignments</em> configuration option enables display of gaps between alignment blocks in the pairwise alignments in a manner similar to the Chain track display. The following conventions are used: <ul> <li><b>Single line:</b> No bases in the aligned species. Possibly due to a lineage-specific insertion between the aligned blocks in the $organism genome or a lineage-specific deletion between the aligned blocks in the aligning species. <li><b>Double line:</b> Aligning species has one or more unalignable bases in the gap region. Possibly due to excessive evolutionary distance between species or independent indels in the region between the aligned blocks in both species. <li><b>Pale yellow coloring:</b> Aligning species has Ns in the gap region. Reflects uncertainty in the relationship between the DNA of both species, due to lack of sequence in relevant portions of the aligning species. </ul></p> <h3>Genomic Breaks</h3> <p> Discontinuities in the genomic context (chromosome, scaffold or region) of the aligned DNA in the aligning species are shown as follows: <ul> <li> <b>Vertical blue bar:</b> Represents a discontinuity that persists indefinitely on either side, <em>e.g.</em> a large region of DNA on either side of the bar comes from a different chromosome in the aligned species due to a large scale rearrangement. <li> <b>Green square brackets:</b> Enclose shorter alignments consisting of DNA from one genomic context in the aligned species nested inside a larger chain of alignments from a different genomic context. The alignment within the brackets may represent a short misalignment, a lineage-specific insertion of a transposon in the $organism genome that aligns to a paralogous copy somewhere else in the aligned species, or other similar occurrence. </ul></p> <h3>Base Level</h3> <p> When zoomed-in to the base-level display, the track shows the base composition of each alignment. The numbers and symbols on the Gaps line indicate the lengths of gaps in the $organism sequence at those alignment positions relative to the longest non-$organism sequence. If there is sufficient space in the display, the size of the gap is shown. If the space is insufficient and the gap size is a multiple of 3, a "*" is displayed; other gap sizes are indicated by "+".</p> <p> Codon translation is available in base-level display mode if the displayed region is identified as a coding segment. To display this annotation, select the species for translation from the pull-down menu in the Codon Translation configuration section at the top of the page. Then, select one of the following modes: <ul> <li> <b>No codon translation:</b> The gene annotation is not used; the bases are displayed without translation. <li> <b>Use default species reading frames for translation:</b> The annotations from the genome displayed in the <em>Default species to establish reading frame</em> pull-down menu are used to translate all the aligned species present in the alignment. <li> <b>Use reading frames for species if available, otherwise no translation:</b> Codon translation is performed only for those species where the region is annotated as protein coding. <li><b>Use reading frames for species if available, otherwise use default species:</b> Codon translation is done on those species that are annotated as being protein coding over the aligned region using species-specific annotation; the remaining species are translated using the default species annotation. </ul></p> <p> Codon translation uses the following gene tracks as the basis for translation: <blockquote><table class="stdTbl"> <tr align=left><td><b>Gene Track</b></td><td><b>Species</b></td></tr> <tr align=left><td>UCSC Genes</td><td>Human</td></tr> <tr align=left><td>Ensembl Genes v104</td><td>Brazilian guinea pig, gibbon</td></tr> <tr align=left><td>RefSeq Genes</td><td>Angolan colobus, Balaenoptera acutorostrata, Bison bison, Black flying-fox, Brandt's myotis (bat), Bushbaby, Camelus bactrianus, Camelus ferus, Canis lupus familiaris, Cape elephant shrew, Capra hircus, Cavia porcellus, Ceratotherium simum, Cercocebus atys, Chinchilla, Chinese tree shrew, Chlorocebus sabaeus, Condylura cristata, Damara mole rat, Dasypus novemcinctus, David's myotis (bat), Delphinapterus leucas, Echinops telfairi, Enhydra lutris, Eptesicus fuscus, Equus asinus, Equus przewalskii, Erinaceus europaeus, Felis catus, Heterocephalus glaber, Jaculus jaculus, Kangaroo rat, Killer whale, Leptonychotes weddellii, Lipotes vexillifer, Little brown bat, Loxodonta africana, Macaca fascicularis, Macaca nemestrina, Mandrillus leucophaeus, Manis javanica, Marmota marmota, Mesocricetus auratus, Miniopterus natalensis, Mus musculus, Nannospalax galili, Ochotona princeps, Octodon degus, Oryctolagus cuniculus, Pacific walrus, Pan paniscus, Panthera tigris, Peromyscus maniculatus, Prairie vole, Propithecus coquereli, Pteropus vampyrus, Puma concolor, Rattus norvegicus, Rhinopithecus bieti, Shrew, Squirrel monkey, Squirrel, Sus scrofa, Trichechus manatus, Ursus maritimus, White-faced sapajou, Wild yak</td></tr> <tr align=left><td>no annotation</td><td>Acinonyx jubatus, Acomys cahirinus, Ailuropoda melanoleuca, Ailurus fulgens, Allactaga bullata, Alouatta palliata, Ammotragus lervia, Anoura caudifer, Antilocapra americana, Aotus nancymaae, Aplodontia rufa, Artibeus jamaicensis, Ateles geoffroyi, Balaenoptera bonaerensis, Beatragus hunteri, Bos indicus, Bos taurus, Bubalus bubalis, Callicebus donacophilus, Callithrix jacchus, Camelus dromedarius, Canis lupus, Capra aegagrus, Capromys pilorides, Carollia perspicillata, Castor canadensis, Catagonus wagneri, Cavia tschudii, Cebus albifrons, Ceratotherium simum cottoni, Cercopithecus neglectus, Chaetophractus vellerosus, Cheirogaleus medius, Choloepus didactylus, Choloepus hoffmanni, Chrysochloris asiatica, Craseonycteris thonglongyai, Cricetomys gambianus, Cricetulus griseus, Crocidura indochinensis, Cryptoprocta ferox, Ctenodactylus gundi, Ctenomys sociabilis, Cuniculus paca, Dasyprocta punctata, Daubentonia madagascariensis, Desmodus rotundus, Dicerorhinus sumatrensis, Diceros bicornis, Dinomys branickii, Dipodomys stephensi, Dolichotis patagonum, Elaphurus davidianus, Ellobius lutescens, Ellobius talpinus, Equus caballus, Erythrocebus patas, Eschrichtius robustus, Eubalaena japonica, Eulemur flavifrons, Eulemur fulvus, Felis nigripes, Galeopterus variegatus, Giraffa tippelskirchi, Glis glis, Gorilla gorilla, Graphiurus murinus, Helogale parvula, Hemitragus hylocrius, Heterohyrax brucei, Hippopotamus amphibius, Hipposideros armiger, Hipposideros galeritus, Hyaena hyaena, Hydrochoerus hydrochaeris, Hystrix cristata, Indri indri, Inia geoffrensis, Kogia breviceps, Lasiurus borealis, Lemur catta, Lepus americanus, Lycaon pictus, Macaca mulatta, Macroglossus sobrinus, Manis pentadactyla, Megaderma lyra, Mellivora capensis, Meriones unguiculatus, Mesoplodon bidens, Microcebus murinus, Microgale talazaci, Micronycteris hirsuta, Miniopterus schreibersii, Mirounga angustirostris, Mirza coquereli, Monodon monoceros, Mormoops blainvillei, Moschus moschiferus, Mungos mungo, Murina feae, Mus caroli, Mus pahari, Mus spretus, Muscardinus avellanarius, Mustela putorius, Myocastor coypus, Myotis myotis, Myrmecophaga tridactyla, Nasalis larvatus, Neomonachus schauinslandi, Neophocaena asiaeorientalis, Noctilio leporinus, Nycticebus coucang, Odocoileus virginianus, Okapia johnstoni, Ondatra zibethicus, Onychomys torridus, Orycteropus afer, Ovis aries, Ovis canadensis, Pan troglodytes, Panthera onca, Panthera pardus, Pantholops hodgsonii, Papio anubis, Paradoxurus hermaphroditus</td></tr> </table> <b>Table 2.</b> <em>Gene tracks used for codon translation.</em> </blockquote></p> <h2>Methods</h2> <p> The Zoonomia alignment was composed of two sets of mammalian genomes: newly assembled DISCOVAR assemblies and GenBank assemblies. The DISCOVAR genomes were masked with RepeatMasker (commit 2d947604), using Repbase version 20170127 as the repeat library and CrossMatch as the alignment engine. The pipeline used is available at <a href="https://github.com/joelarmstrong/repeatMaskerPipeline">repeatMaskerPipeline</a> (commit a6ad966). The guide-tree topology was taken from the TimeTree database (using release current in October 2018), and the branch lengths were estimated using the least-squares-fit mode of <a href="https://evolution.genetics.washington.edu/phylip/getme-new1.html">PHYLIP</a>, version 3.695. The distance matrix used was largely based on distances from the 4d site trees from the UCSC browser. To add those species not present in the UCSC tree, approximate distances estimated by <a href="https://github.com/marbl/Mash">Mash</a> (commit 541971b) to the closest UCSC species were added to the distance between the two closest UCSC species. We used the <a href="https://github.com/ComparativeGenomicsToolkit/hal">HAL package</a> (commit 68db41d) produce the HAL file. </p> <p> </p> <p> </p> <h3> Phylogenetic Tree Model</h3> <p> The <em>phyloP</em> are phylogenetic methods that rely on a tree model containing the tree topology, branch lengths representing evolutionary distance at neutrally evolving sites, the background distribution of nucleotides, and a substitution rate matrix. The <a href="https://hgdownload.soe.ucsc.edu/goldenPath/hg38/cactus241way/phyloP241way/" target=_blank>all-species tree model</a> for this track was generated using the <em>phyloFit</em> program from the PHAST package (REV model, EM algorithm, medium precision) using multiple alignments of 4-fold degenerate sites extracted from the 241-way alignment (msa_view). The 4d sites were derived from the RefSeq (Reviewed+Coding) gene set, filtered to select single-coverage long transcripts. </p> <p> This same tree model was used in the phyloP calculations; however, the background frequencies were modified to maintain reversibility. The resulting tree model: <a href="http://hgdownload.soe.ucsc.edu/goldenPath/hg38/phyloP241way/hg38.phyloP241way.mod" target=_blank>all species</a>. </p> <h3> PhyloP Conservation </h3> <p> The phyloP program supports several different methods for computing p-values of conservation or acceleration, for individual nucleotides or larger elements (<a href="http://compgen.cshl.edu/phast/" target="_blank"> http://compgen.cshl.edu/phast/</a>). Here it was used to produce separate scores at each base (--wig-scores option), considering all branches of the phylogeny rather than a particular subtree or lineage (i.e., the --subtree option was not used). The scores were computed by performing a likelihood ratio test at each alignment column (--method LRT), and scores for both conservation and acceleration were produced (--mode CONACC). </p> <h2>References</h2> <h3>Zoonomia:</h3> <p> Zoonomia Consortium.. <a href="https://www.ncbi.nlm.nih.gov/pubmed/33177664" target="_blank"> A comparative genomics multitool for scientific discovery and conservation</a>. <em>Nature</em>. 2020 Nov;587(7833):240-245. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/33177664" target="_blank">33177664</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7759459/" target="_blank">PMC7759459</a>; DOI: <a href="https://doi.org/10.1038/s41586-020-2876-6" target="_blank">10.1038/s41586-020-2876-6</a> </p> <h3>Cactus:</h3> <p> Armstrong J, Hickey G, Diekhans M, Fiddes IT, Novak AM, Deran A, Fang Q, Xie D, Feng S, Stiller J <em>et al</em>. <a href="https://www.ncbi.nlm.nih.gov/pubmed/33177663" target="_blank"> Progressive Cactus is a multiple-genome aligner for the thousand-genome era</a>. <em>Nature</em>. 2020 Nov;587(7833):246-251. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/33177663" target="_blank">33177663</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7673649/" target="_blank">PMC7673649</a>; DOI: <a href="https://doi.org/10.1038/s41586-020-2871-y" target="_blank">10.1038/s41586-020-2871-y</a> </p> <p> Paten B, Earl D, Nguyen N, Diekhans M, Zerbino D, Haussler D. <a href="https://www.ncbi.nlm.nih.gov/pubmed/21665927" target="_blank"> Cactus: Algorithms for genome multiple sequence alignment</a>. <em>Genome Res</em>. 2011 Sep;21(9):1512-28. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/21665927" target="_blank">21665927</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3166836/" target="_blank">PMC3166836</a>; DOI: <a href="https://doi.org/10.1101/gr.123356.111" target="_blank">10.1101/gr.123356.111</a> </p> <p> Harris RS. <a href="http://www.bx.psu.edu/~rsharris/rsharris_phd_thesis_2007.pdf" target="_blank">Improved pairwise alignment of genomic DNA</a>. <em>Ph.D. Thesis</em>. Pennsylvania State University, USA. 2007. </p> <h3>PhyloP:</h3> <p> Cooper GM, Stone EA, Asimenos G, NISC Comparative Sequencing Program., Green ED, Batzoglou S, Sidow A. <a href="https://www.ncbi.nlm.nih.gov/pubmed/15965027" target="_blank"> Distribution and intensity of constraint in mammalian genomic sequence</a>. <em>Genome Res</em>. 2005 Jul;15(7):901-13. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/15965027" target="_blank">15965027</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1172034/" target="_blank">PMC1172034</a>; DOI: <a href="https://doi.org/10.1101/gr.3577405" target="_blank">10.1101/gr.3577405</a> </p> <p> Pollard KS, Hubisz MJ, Rosenbloom KR, Siepel A. <a href="https://genome.cshlp.org/content/20/1/110.long" target="_blank"> Detection of nonneutral substitution rates on mammalian phylogenies</a>. <em>Genome Res</em>. 2010 Jan;20(1):110-21. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/19858363" target="_blank">19858363</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2798823/" target="_blank">PMC2798823</a> </p> <p> Siepel A, Haussler D. <a href="https://link.springer.com/content/pdf/10.1007%2F0-387-27733-1_12.pdf" target="_blank">Phylogenetic Hidden Markov Models</a>. In: Nielsen R, editor. Statistical Methods in Molecular Evolution. New York: Springer; 2005. pp. 325-351. DOI: <a href="https://doi.org/10.1007/0-387-27733-1_12" target="_blank">10.1007/0-387-27733-1_12</a> </p> <p> Siepel A, Pollard KS, and Haussler D. New methods for detecting lineage-specific selection. In Proceedings of the 10th International Conference on Research in Computational Molecular Biology (RECOMB 2006), pp. 190-205. DOI: <a href="https://doi.org/10.1007/11732990_17" target="_blank">10.1007/11732990_17</a> </p>