# Assembly name: mOliNig2.hap1 # Organism name: Oligoryzomys nigripes (Black-footed pygmy rice rat) # Isolate: mOliNig2 # Sex: female # Taxid: 37017 # BioSample: SAMN59321932 # BioProject: PRJNA1463265 # Submitter: Vertebrate Genomes Project # Date: 2026-06-03 # Assembly type: haploid (haplotype 1) # Release type: major # Assembly level: Chromosome # Genome representation: full # WGS project: JBYHCR01 # Assembly method: Hifiasm + Hi-C phasing v. 0.25.0 + galaxy0; yahs v. 1.2a.2 + galaxy2 # Expected final version: No # Genome coverage: 65.96x # Sequencing technology: PacBio Revio HiFi; Arima Hi-C v2 # RefSeq category: Reference Genome # GenBank assembly accession: GCA_057876635.1 # Linked assembly: GCA_057876665.1 (haplotype 2) # ## Assembly-Unit names: ## Primary Assembly # # Ordered by chromosome/plasmid; the chromosomes/plasmids are followed by # unlocalized scaffolds. # Unplaced scaffolds are listed at the end. # RefSeq is equal or derived from GenBank object. # # Sequence-Name Sequence-Role Assigned-Molecule Assigned-Molecule-Location/Type GenBank-Accn Relationship RefSeq-Accn Assembly-Unit Sequence-Length UCSC-style-name SUPER_1 assembled-molecule 1 Chromosome CM174561.1 <> na Primary Assembly 203674472 na SUPER_2 assembled-molecule 2 Chromosome CM174562.1 <> na Primary Assembly 162370047 na SUPER_3 assembled-molecule 3 Chromosome CM174563.1 <> na Primary Assembly 153444828 na SUPER_4 assembled-molecule 4 Chromosome CM174564.1 <> na Primary Assembly 129819452 na SUPER_5 assembled-molecule 5 Chromosome CM174565.1 <> na Primary Assembly 115591397 na SUPER_6 assembled-molecule 6 Chromosome CM174566.1 <> na Primary Assembly 100590121 na SUPER_7 assembled-molecule 7 Chromosome CM174567.1 <> na Primary Assembly 98835036 na SUPER_8 assembled-molecule 8 Chromosome CM174568.1 <> na Primary Assembly 90490158 na SUPER_9 assembled-molecule 9 Chromosome CM174569.1 <> na Primary Assembly 88759796 na SUPER_10 assembled-molecule 10 Chromosome CM174570.1 <> na Primary Assembly 79642056 na SUPER_11 assembled-molecule 11 Chromosome CM174571.1 <> na Primary Assembly 78255978 na SUPER_12 assembled-molecule 12 Chromosome CM174572.1 <> na Primary Assembly 76482418 na SUPER_13 assembled-molecule 13 Chromosome CM174573.1 <> na Primary Assembly 76031861 na SUPER_14 assembled-molecule 14 Chromosome CM174574.1 <> na Primary Assembly 73415663 na SUPER_15 assembled-molecule 15 Chromosome CM174575.1 <> na Primary Assembly 71934709 na SUPER_16 assembled-molecule 16 Chromosome CM174576.1 <> na Primary Assembly 69942259 na SUPER_17 assembled-molecule 17 Chromosome CM174577.1 <> na Primary Assembly 68345626 na SUPER_18 assembled-molecule 18 Chromosome CM174578.1 <> na Primary Assembly 66963445 na SUPER_19 assembled-molecule 19 Chromosome CM174579.1 <> na Primary Assembly 62903083 na SUPER_20 assembled-molecule 20 Chromosome CM174580.1 <> na Primary Assembly 60853453 na SUPER_21 assembled-molecule 21 Chromosome CM174581.1 <> na Primary Assembly 51342598 na SUPER_22 assembled-molecule 22 Chromosome CM174582.1 <> na Primary Assembly 49183573 na SUPER_23 assembled-molecule 23 Chromosome CM174583.1 <> na Primary Assembly 45588415 na SUPER_24 assembled-molecule 24 Chromosome CM174584.1 <> na Primary Assembly 45329183 na SUPER_25 assembled-molecule 25 Chromosome CM174585.1 <> na Primary Assembly 44595010 na SUPER_26 assembled-molecule 26 Chromosome CM174586.1 <> na Primary Assembly 41065285 na SUPER_27 assembled-molecule 27 Chromosome CM174587.1 <> na Primary Assembly 35295474 na SUPER_28 assembled-molecule 28 Chromosome CM174588.1 <> na Primary Assembly 34557590 na SUPER_29 assembled-molecule 29 Chromosome CM174589.1 <> na Primary Assembly 31996290 na SUPER_30 assembled-molecule 30 Chromosome CM174590.1 <> na Primary Assembly 30907379 na SUPER_X assembled-molecule X Chromosome CM174591.1 <> na Primary Assembly 276892379 na SUPER_5_unloc_1 unlocalized-scaffold 5 Chromosome JBYHCR010000035.1 <> na Primary Assembly 516105 na SUPER_16_unloc_1 unlocalized-scaffold 16 Chromosome JBYHCR010000032.1 <> na Primary Assembly 5004353 na Scaffold_73 unplaced-scaffold na na JBYHCR010000033.1 <> na Primary Assembly 2141559 na Scaffold_67 unplaced-scaffold na na JBYHCR010000034.1 <> na Primary Assembly 534701 na Scaffold_72 unplaced-scaffold na na JBYHCR010000036.1 <> na Primary Assembly 492181 na Scaffold_75 unplaced-scaffold na na JBYHCR010000037.1 <> na Primary Assembly 409229 na Scaffold_78 unplaced-scaffold na na JBYHCR010000038.1 <> na Primary Assembly 379127 na Scaffold_79 unplaced-scaffold na na JBYHCR010000039.1 <> na Primary Assembly 352314 na Scaffold_82 unplaced-scaffold na na JBYHCR010000040.1 <> na Primary Assembly 315203 na Scaffold_88 unplaced-scaffold na na JBYHCR010000041.1 <> na Primary Assembly 246249 na Scaffold_89 unplaced-scaffold na na JBYHCR010000042.1 <> na Primary Assembly 245688 na Scaffold_91 unplaced-scaffold na na JBYHCR010000043.1 <> na Primary Assembly 240324 na Scaffold_71 unplaced-scaffold na na JBYHCR010000044.1 <> na Primary Assembly 207005 na Scaffold_66 unplaced-scaffold na na JBYHCR010000045.1 <> na Primary Assembly 181249 na Scaffold_101 unplaced-scaffold na na JBYHCR010000046.1 <> na Primary Assembly 165601 na Scaffold_102 unplaced-scaffold na na JBYHCR010000047.1 <> na Primary Assembly 158660 na Scaffold_103 unplaced-scaffold na na JBYHCR010000048.1 <> na Primary Assembly 156732 na Scaffold_105 unplaced-scaffold na na JBYHCR010000049.1 <> na Primary Assembly 141914 na Scaffold_108 unplaced-scaffold na na JBYHCR010000050.1 <> na Primary Assembly 131160 na Scaffold_109 unplaced-scaffold na na JBYHCR010000051.1 <> na Primary Assembly 124259 na Scaffold_110 unplaced-scaffold na na JBYHCR010000052.1 <> na Primary Assembly 116051 na Scaffold_111 unplaced-scaffold na na JBYHCR010000053.1 <> na Primary Assembly 112047 na Scaffold_268 unplaced-scaffold na na JBYHCR010000054.1 <> na Primary Assembly 105570 na Scaffold_269 unplaced-scaffold na na JBYHCR010000055.1 <> na Primary Assembly 95961 na Scaffold_114 unplaced-scaffold na na JBYHCR010000056.1 <> na Primary Assembly 95444 na Scaffold_259 unplaced-scaffold na na JBYHCR010000057.1 <> na Primary Assembly 94255 na Scaffold_115 unplaced-scaffold na na JBYHCR010000058.1 <> na Primary Assembly 93997 na Scaffold_273 unplaced-scaffold na na JBYHCR010000059.1 <> na Primary Assembly 93069 na Scaffold_117 unplaced-scaffold na na JBYHCR010000060.1 <> na Primary Assembly 92250 na Scaffold_63 unplaced-scaffold na na JBYHCR010000061.1 <> na Primary Assembly 89436 na Scaffold_276 unplaced-scaffold na na JBYHCR010000062.1 <> na Primary Assembly 88576 na Scaffold_118 unplaced-scaffold na na JBYHCR010000063.1 <> na Primary Assembly 87108 na Scaffold_119 unplaced-scaffold na na JBYHCR010000064.1 <> na Primary Assembly 86538 na Scaffold_120 unplaced-scaffold na na JBYHCR010000065.1 <> na Primary Assembly 79076 na Scaffold_280 unplaced-scaffold na na JBYHCR010000066.1 <> na Primary Assembly 73548 na Scaffold_281 unplaced-scaffold na na JBYHCR010000067.1 <> na Primary Assembly 73010 na Scaffold_283 unplaced-scaffold na na JBYHCR010000068.1 <> na Primary Assembly 64046 na Scaffold_123 unplaced-scaffold na na JBYHCR010000069.1 <> na Primary Assembly 64011 na Scaffold_198 unplaced-scaffold na na JBYHCR010000070.1 <> na Primary Assembly 63702 na Scaffold_157 unplaced-scaffold na na JBYHCR010000071.1 <> na Primary Assembly 62378 na Scaffold_124 unplaced-scaffold na na JBYHCR010000072.1 <> na Primary Assembly 62144 na Scaffold_159 unplaced-scaffold na na JBYHCR010000073.1 <> na Primary Assembly 58518 na Scaffold_160 unplaced-scaffold na na JBYHCR010000074.1 <> na Primary Assembly 52608 na Scaffold_161 unplaced-scaffold na na JBYHCR010000075.1 <> na Primary Assembly 51572 na Scaffold_162 unplaced-scaffold na na JBYHCR010000076.1 <> na Primary Assembly 51540 na Scaffold_128 unplaced-scaffold na na JBYHCR010000077.1 <> na Primary Assembly 51451 na Scaffold_164 unplaced-scaffold na na JBYHCR010000078.1 <> na Primary Assembly 51324 na Scaffold_165 unplaced-scaffold na na JBYHCR010000079.1 <> na Primary Assembly 51172 na Scaffold_166 unplaced-scaffold na na JBYHCR010000080.1 <> na Primary Assembly 46509 na Scaffold_130 unplaced-scaffold na na JBYHCR010000081.1 <> na Primary Assembly 45694 na Scaffold_168 unplaced-scaffold na na JBYHCR010000082.1 <> na Primary Assembly 45370 na Scaffold_156 unplaced-scaffold na na JBYHCR010000083.1 <> na Primary Assembly 45282 na Scaffold_131 unplaced-scaffold na na JBYHCR010000084.1 <> na Primary Assembly 44833 na Scaffold_171 unplaced-scaffold na na JBYHCR010000085.1 <> na Primary Assembly 44808 na Scaffold_132 unplaced-scaffold na na JBYHCR010000086.1 <> na Primary Assembly 43593 na Scaffold_173 unplaced-scaffold na na JBYHCR010000087.1 <> na Primary Assembly 42167 na Scaffold_174 unplaced-scaffold na na JBYHCR010000088.1 <> na Primary Assembly 42149 na Scaffold_133 unplaced-scaffold na na JBYHCR010000089.1 <> na Primary Assembly 41911 na Scaffold_176 unplaced-scaffold na na JBYHCR010000090.1 <> na Primary Assembly 40826 na Scaffold_177 unplaced-scaffold na na JBYHCR010000091.1 <> na Primary Assembly 40668 na Scaffold_134 unplaced-scaffold na na JBYHCR010000092.1 <> na Primary Assembly 40189 na Scaffold_179 unplaced-scaffold na na JBYHCR010000093.1 <> na Primary Assembly 40063 na Scaffold_180 unplaced-scaffold na na JBYHCR010000094.1 <> na Primary Assembly 39799 na Scaffold_135 unplaced-scaffold na na JBYHCR010000095.1 <> na Primary Assembly 39616 na Scaffold_145 unplaced-scaffold na na JBYHCR010000096.1 <> na Primary Assembly 38820 na Scaffold_136 unplaced-scaffold na na JBYHCR010000097.1 <> na Primary Assembly 38136 na Scaffold_147 unplaced-scaffold na na JBYHCR010000098.1 <> na Primary Assembly 36644 na Scaffold_137 unplaced-scaffold na na JBYHCR010000099.1 <> na Primary Assembly 35877 na Scaffold_149 unplaced-scaffold na na JBYHCR010000100.1 <> na Primary Assembly 35385 na Scaffold_150 unplaced-scaffold na na JBYHCR010000101.1 <> na Primary Assembly 34056 na Scaffold_151 unplaced-scaffold na na JBYHCR010000102.1 <> na Primary Assembly 33634 na Scaffold_152 unplaced-scaffold na na JBYHCR010000103.1 <> na Primary Assembly 32347 na Scaffold_139 unplaced-scaffold na na JBYHCR010000104.1 <> na Primary Assembly 28384 na Scaffold_154 unplaced-scaffold na na JBYHCR010000105.1 <> na Primary Assembly 28166 na Scaffold_155 unplaced-scaffold na na JBYHCR010000106.1 <> na Primary Assembly 27769 na Scaffold_169 unplaced-scaffold na na JBYHCR010000107.1 <> na Primary Assembly 27698 na Scaffold_192 unplaced-scaffold na na JBYHCR010000108.1 <> na Primary Assembly 27665 na Scaffold_193 unplaced-scaffold na na JBYHCR010000109.1 <> na Primary Assembly 26470 na Scaffold_140 unplaced-scaffold na na JBYHCR010000110.1 <> na Primary Assembly 26359 na Scaffold_195 unplaced-scaffold na na JBYHCR010000111.1 <> na Primary Assembly 25920 na Scaffold_196 unplaced-scaffold na na JBYHCR010000112.1 <> na Primary Assembly 25538 na Scaffold_197 unplaced-scaffold na na JBYHCR010000113.1 <> na Primary Assembly 25275 na Scaffold_141 unplaced-scaffold na na JBYHCR010000114.1 <> na Primary Assembly 23944 na Scaffold_200 unplaced-scaffold na na JBYHCR010000115.1 <> na Primary Assembly 23821 na Scaffold_201 unplaced-scaffold na na JBYHCR010000116.1 <> na Primary Assembly 23721 na Scaffold_202 unplaced-scaffold na na JBYHCR010000117.1 <> na Primary Assembly 22972 na Scaffold_203 unplaced-scaffold na na JBYHCR010000118.1 <> na Primary Assembly 21965 na Scaffold_204 unplaced-scaffold na na JBYHCR010000119.1 <> na Primary Assembly 21405 na Scaffold_142 unplaced-scaffold na na JBYHCR010000120.1 <> na Primary Assembly 19035 na Scaffold_182 unplaced-scaffold na na JBYHCR010000121.1 <> na Primary Assembly 18662 na Scaffold_183 unplaced-scaffold na na JBYHCR010000122.1 <> na Primary Assembly 18215 na Scaffold_184 unplaced-scaffold na na JBYHCR010000123.1 <> na Primary Assembly 16478 na Scaffold_185 unplaced-scaffold na na JBYHCR010000124.1 <> na Primary Assembly 15366 na Scaffold_186 unplaced-scaffold na na JBYHCR010000125.1 <> na Primary Assembly 15117 na Scaffold_187 unplaced-scaffold na na JBYHCR010000126.1 <> na Primary Assembly 14975 na Scaffold_188 unplaced-scaffold na na JBYHCR010000127.1 <> na Primary Assembly 14902 na Scaffold_189 unplaced-scaffold na na JBYHCR010000128.1 <> na Primary Assembly 14621 na Scaffold_190 unplaced-scaffold na na JBYHCR010000129.1 <> na Primary Assembly 14228 na Scaffold_143 unplaced-scaffold na na JBYHCR010000130.1 <> na Primary Assembly 12698 na