# Assembly name: mTamHud3.hap1 # Organism name: Tamiasciurus hudsonicus (American red squirrel) # Isolate: mTamHud3 # Sex: female # Taxid: 10009 # BioSample: SAMN57316951 # BioProject: PRJNA1454672 # Submitter: Vertebrate Genomes Project # Date: 2026-05-15 # Assembly type: haploid (haplotype 1) # Release type: major # Assembly level: Chromosome # Genome representation: full # WGS project: JBXXPO01 # Assembly method: Hifiasm + Hi-C phasing v. 0.25.0 + galaxy0; yahs v. 1.2a.2 + galaxy3 # Expected final version: No # Genome coverage: 68.08x # Sequencing technology: PacBio Revio HiFi; Arima Hi-C v2 # RefSeq category: Reference Genome # GenBank assembly accession: GCA_057657825.1 # Linked assembly: GCA_057657875.1 (haplotype 2) # ## Assembly-Unit names: ## Primary Assembly ## non-nuclear # # 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 CM172909.1 <> na Primary Assembly 415215358 na SUPER_2 assembled-molecule 2 Chromosome CM172910.1 <> na Primary Assembly 349188028 na SUPER_3 assembled-molecule 3 Chromosome CM172911.1 <> na Primary Assembly 322707816 na SUPER_4 assembled-molecule 4 Chromosome CM172912.1 <> na Primary Assembly 312188552 na SUPER_5 assembled-molecule 5 Chromosome CM172913.1 <> na Primary Assembly 302432138 na SUPER_6 assembled-molecule 6 Chromosome CM172914.1 <> na Primary Assembly 257739901 na SUPER_7 assembled-molecule 7 Chromosome CM172915.1 <> na Primary Assembly 238758159 na SUPER_8 assembled-molecule 8 Chromosome CM172916.1 <> na Primary Assembly 237734749 na SUPER_9 assembled-molecule 9 Chromosome CM172917.1 <> na Primary Assembly 223513321 na SUPER_10 assembled-molecule 10 Chromosome CM172918.1 <> na Primary Assembly 213340194 na SUPER_11 assembled-molecule 11 Chromosome CM172919.1 <> na Primary Assembly 210882443 na SUPER_12 assembled-molecule 12 Chromosome CM172920.1 <> na Primary Assembly 209038856 na SUPER_13 assembled-molecule 13 Chromosome CM172921.1 <> na Primary Assembly 208047866 na SUPER_14 assembled-molecule 14 Chromosome CM172922.1 <> na Primary Assembly 202938266 na SUPER_15 assembled-molecule 15 Chromosome CM172923.1 <> na Primary Assembly 197389170 na SUPER_16 assembled-molecule 16 Chromosome CM172924.1 <> na Primary Assembly 194933259 na SUPER_17 assembled-molecule 17 Chromosome CM172925.1 <> na Primary Assembly 192964043 na SUPER_18 assembled-molecule 18 Chromosome CM172926.1 <> na Primary Assembly 188946619 na SUPER_19 assembled-molecule 19 Chromosome CM172927.1 <> na Primary Assembly 183413769 na SUPER_20 assembled-molecule 20 Chromosome CM172928.1 <> na Primary Assembly 172357615 na SUPER_21 assembled-molecule 21 Chromosome CM172929.1 <> na Primary Assembly 169970846 na SUPER_22 assembled-molecule 22 Chromosome CM172930.1 <> na Primary Assembly 125505891 na SUPER_X assembled-molecule X Chromosome CM172931.1 <> na Primary Assembly 152569893 na SUPER_1_unloc_1 unlocalized-scaffold 1 Chromosome JBXXPO010000033.1 <> na Primary Assembly 28074522 na SUPER_5_unloc_1 unlocalized-scaffold 5 Chromosome JBXXPO010000047.1 <> na Primary Assembly 989870 na SUPER_7_unloc_1 unlocalized-scaffold 7 Chromosome JBXXPO010000041.1 <> na Primary Assembly 8104944 na SUPER_8_unloc_1 unlocalized-scaffold 8 Chromosome JBXXPO010000027.1 <> na Primary Assembly 35012442 na SUPER_8_unloc_2 unlocalized-scaffold 8 Chromosome JBXXPO010000029.1 <> na Primary Assembly 30399714 na SUPER_17_unloc_1 unlocalized-scaffold 17 Chromosome JBXXPO010000026.1 <> na Primary Assembly 35841841 na SUPER_17_unloc_2 unlocalized-scaffold 17 Chromosome JBXXPO010000039.1 <> na Primary Assembly 12586152 na Scaffold_47 unplaced-scaffold na na JBXXPO010000025.1 <> na Primary Assembly 37241666 na Scaffold_63 unplaced-scaffold na na JBXXPO010000028.1 <> na Primary Assembly 30402483 na Scaffold_60 unplaced-scaffold na na JBXXPO010000030.1 <> na Primary Assembly 29743162 na Scaffold_59 unplaced-scaffold na na JBXXPO010000031.1 <> na Primary Assembly 29405436 na Scaffold_61 unplaced-scaffold na na JBXXPO010000032.1 <> na Primary Assembly 28956746 na Scaffold_49 unplaced-scaffold na na JBXXPO010000034.1 <> na Primary Assembly 26280673 na Scaffold_58 unplaced-scaffold na na JBXXPO010000035.1 <> na Primary Assembly 23941959 na Scaffold_68 unplaced-scaffold na na JBXXPO010000036.1 <> na Primary Assembly 19277679 na Scaffold_70 unplaced-scaffold na na JBXXPO010000037.1 <> na Primary Assembly 15466107 na Scaffold_56 unplaced-scaffold na na JBXXPO010000038.1 <> na Primary Assembly 14690212 na Scaffold_66 unplaced-scaffold na na JBXXPO010000040.1 <> na Primary Assembly 10405342 na Scaffold_50 unplaced-scaffold na na JBXXPO010000042.1 <> na Primary Assembly 3870097 na Scaffold_67 unplaced-scaffold na na JBXXPO010000043.1 <> na Primary Assembly 2301399 na Scaffold_74 unplaced-scaffold na na JBXXPO010000044.1 <> na Primary Assembly 1555285 na Scaffold_73 unplaced-scaffold na na JBXXPO010000045.1 <> na Primary Assembly 1041556 na Scaffold_53 unplaced-scaffold na na JBXXPO010000046.1 <> na Primary Assembly 1009939 na Scaffold_75 unplaced-scaffold na na JBXXPO010000048.1 <> na Primary Assembly 962087 na Scaffold_69 unplaced-scaffold na na JBXXPO010000049.1 <> na Primary Assembly 945158 na Scaffold_81 unplaced-scaffold na na JBXXPO010000050.1 <> na Primary Assembly 387478 na Scaffold_82 unplaced-scaffold na na JBXXPO010000051.1 <> na Primary Assembly 362035 na Scaffold_83 unplaced-scaffold na na JBXXPO010000052.1 <> na Primary Assembly 354702 na Scaffold_84 unplaced-scaffold na na JBXXPO010000053.1 <> na Primary Assembly 348046 na Scaffold_85 unplaced-scaffold na na JBXXPO010000054.1 <> na Primary Assembly 347788 na Scaffold_87 unplaced-scaffold na na JBXXPO010000055.1 <> na Primary Assembly 310264 na Scaffold_89 unplaced-scaffold na na JBXXPO010000056.1 <> na Primary Assembly 274256 na Scaffold_91 unplaced-scaffold na na JBXXPO010000057.1 <> na Primary Assembly 262090 na Scaffold_93 unplaced-scaffold na na JBXXPO010000058.1 <> na Primary Assembly 250280 na Scaffold_95 unplaced-scaffold na na JBXXPO010000059.1 <> na Primary Assembly 212601 na Scaffold_97 unplaced-scaffold na na JBXXPO010000060.1 <> na Primary Assembly 197547 na Scaffold_98 unplaced-scaffold na na JBXXPO010000061.1 <> na Primary Assembly 192706 na Scaffold_100 unplaced-scaffold na na JBXXPO010000062.1 <> na Primary Assembly 189021 na Scaffold_101 unplaced-scaffold na na JBXXPO010000063.1 <> na Primary Assembly 186245 na Scaffold_102 unplaced-scaffold na na JBXXPO010000064.1 <> na Primary Assembly 186165 na Scaffold_103 unplaced-scaffold na na JBXXPO010000065.1 <> na Primary Assembly 185422 na Scaffold_104 unplaced-scaffold na na JBXXPO010000066.1 <> na Primary Assembly 183779 na Scaffold_105 unplaced-scaffold na na JBXXPO010000067.1 <> na Primary Assembly 183166 na Scaffold_106 unplaced-scaffold na na JBXXPO010000068.1 <> na Primary Assembly 178731 na Scaffold_107 unplaced-scaffold na na JBXXPO010000069.1 <> na Primary Assembly 176398 na Scaffold_108 unplaced-scaffold na na JBXXPO010000070.1 <> na Primary Assembly 173265 na Scaffold_110 unplaced-scaffold na na JBXXPO010000071.1 <> na Primary Assembly 165150 na Scaffold_111 unplaced-scaffold na na JBXXPO010000072.1 <> na Primary Assembly 161516 na Scaffold_112 unplaced-scaffold na na JBXXPO010000073.1 <> na Primary Assembly 159744 na Scaffold_118 unplaced-scaffold na na JBXXPO010000074.1 <> na Primary Assembly 134971 na Scaffold_218 unplaced-scaffold na na JBXXPO010000075.1 <> na Primary Assembly 131991 na Scaffold_119 unplaced-scaffold na na JBXXPO010000076.1 <> na Primary Assembly 131517 na Scaffold_120 unplaced-scaffold na na JBXXPO010000077.1 <> na Primary Assembly 130933 na Scaffold_179 unplaced-scaffold na na JBXXPO010000078.1 <> na Primary Assembly 127547 na Scaffold_122 unplaced-scaffold na na JBXXPO010000079.1 <> na Primary Assembly 123109 na Scaffold_124 unplaced-scaffold na na JBXXPO010000080.1 <> na Primary Assembly 112675 na Scaffold_182 unplaced-scaffold na na JBXXPO010000081.1 <> na Primary Assembly 111432 na Scaffold_126 unplaced-scaffold na na JBXXPO010000082.1 <> na Primary Assembly 102917 na Scaffold_127 unplaced-scaffold na na JBXXPO010000083.1 <> na Primary Assembly 96411 na Scaffold_176 unplaced-scaffold na na JBXXPO010000084.1 <> na Primary Assembly 94926 na Scaffold_128 unplaced-scaffold na na JBXXPO010000085.1 <> na Primary Assembly 93165 na Scaffold_187 unplaced-scaffold na na JBXXPO010000086.1 <> na Primary Assembly 92389 na Scaffold_129 unplaced-scaffold na na JBXXPO010000087.1 <> na Primary Assembly 92177 na Scaffold_189 unplaced-scaffold na na JBXXPO010000088.1 <> na Primary Assembly 89893 na Scaffold_130 unplaced-scaffold na na JBXXPO010000089.1 <> na Primary Assembly 88138 na Scaffold_191 unplaced-scaffold na na JBXXPO010000090.1 <> na Primary Assembly 87965 na Scaffold_192 unplaced-scaffold na na JBXXPO010000091.1 <> na Primary Assembly 85707 na Scaffold_132 unplaced-scaffold na na JBXXPO010000092.1 <> na Primary Assembly 81090 na Scaffold_159 unplaced-scaffold na na JBXXPO010000093.1 <> na Primary Assembly 80027 na Scaffold_133 unplaced-scaffold na na JBXXPO010000094.1 <> na Primary Assembly 76480 na Scaffold_161 unplaced-scaffold na na JBXXPO010000095.1 <> na Primary Assembly 75313 na Scaffold_162 unplaced-scaffold na na JBXXPO010000096.1 <> na Primary Assembly 70896 na Scaffold_136 unplaced-scaffold na na JBXXPO010000097.1 <> na Primary Assembly 67979 na Scaffold_137 unplaced-scaffold na na JBXXPO010000098.1 <> na Primary Assembly 62676 na Scaffold_140 unplaced-scaffold na na JBXXPO010000099.1 <> na Primary Assembly 55538 na Scaffold_166 unplaced-scaffold na na JBXXPO010000100.1 <> na Primary Assembly 55202 na Scaffold_158 unplaced-scaffold na na JBXXPO010000101.1 <> na Primary Assembly 54176 na Scaffold_168 unplaced-scaffold na na JBXXPO010000102.1 <> na Primary Assembly 54126 na Scaffold_169 unplaced-scaffold na na JBXXPO010000103.1 <> na Primary Assembly 52444 na Scaffold_143 unplaced-scaffold na na JBXXPO010000104.1 <> na Primary Assembly 50579 na Scaffold_171 unplaced-scaffold na na JBXXPO010000105.1 <> na Primary Assembly 50541 na Scaffold_172 unplaced-scaffold na na JBXXPO010000106.1 <> na Primary Assembly 50442 na Scaffold_144 unplaced-scaffold na na JBXXPO010000107.1 <> na Primary Assembly 50329 na Scaffold_174 unplaced-scaffold na na JBXXPO010000108.1 <> na Primary Assembly 50116 na Scaffold_145 unplaced-scaffold na na JBXXPO010000109.1 <> na Primary Assembly 48721 na Scaffold_185 unplaced-scaffold na na JBXXPO010000110.1 <> na Primary Assembly 48309 na Scaffold_210 unplaced-scaffold na na JBXXPO010000111.1 <> na Primary Assembly 47779 na Scaffold_211 unplaced-scaffold na na JBXXPO010000112.1 <> na Primary Assembly 47376 na Scaffold_212 unplaced-scaffold na na JBXXPO010000113.1 <> na Primary Assembly 46869 na Scaffold_213 unplaced-scaffold na na JBXXPO010000114.1 <> na Primary Assembly 46294 na Scaffold_147 unplaced-scaffold na na JBXXPO010000115.1 <> na Primary Assembly 46231 na Scaffold_215 unplaced-scaffold na na JBXXPO010000116.1 <> na Primary Assembly 45828 na Scaffold_216 unplaced-scaffold na na JBXXPO010000117.1 <> na Primary Assembly 45659 na Scaffold_217 unplaced-scaffold na na JBXXPO010000118.1 <> na Primary Assembly 45449 na Scaffold_149 unplaced-scaffold na na JBXXPO010000119.1 <> na Primary Assembly 44463 na Scaffold_219 unplaced-scaffold na na JBXXPO010000120.1 <> na Primary Assembly 44431 na Scaffold_220 unplaced-scaffold na na JBXXPO010000121.1 <> na Primary Assembly 44237 na Scaffold_150 unplaced-scaffold na na JBXXPO010000122.1 <> na Primary Assembly 43298 na Scaffold_222 unplaced-scaffold na na JBXXPO010000123.1 <> na Primary Assembly 43186 na Scaffold_223 unplaced-scaffold na na JBXXPO010000124.1 <> na Primary Assembly 42922 na Scaffold_151 unplaced-scaffold na na JBXXPO010000125.1 <> na Primary Assembly 42315 na Scaffold_202 unplaced-scaffold na na JBXXPO010000126.1 <> na Primary Assembly 41681 na Scaffold_194 unplaced-scaffold na na JBXXPO010000127.1 <> na Primary Assembly 39780 na Scaffold_195 unplaced-scaffold na na JBXXPO010000128.1 <> na Primary Assembly 39664 na Scaffold_196 unplaced-scaffold na na JBXXPO010000129.1 <> na Primary Assembly 37232 na Scaffold_197 unplaced-scaffold na na JBXXPO010000130.1 <> na Primary Assembly 37177 na Scaffold_153 unplaced-scaffold na na JBXXPO010000131.1 <> na Primary Assembly 37156 na Scaffold_199 unplaced-scaffold na na JBXXPO010000132.1 <> na Primary Assembly 37141 na Scaffold_200 unplaced-scaffold na na JBXXPO010000133.1 <> na Primary Assembly 37138 na Scaffold_201 unplaced-scaffold na na JBXXPO010000134.1 <> na Primary Assembly 37085 na Scaffold_193 unplaced-scaffold na na JBXXPO010000135.1 <> na Primary Assembly 36793 na Scaffold_203 unplaced-scaffold na na JBXXPO010000136.1 <> na Primary Assembly 36429 na Scaffold_204 unplaced-scaffold na na JBXXPO010000137.1 <> na Primary Assembly 35273 na Scaffold_156 unplaced-scaffold na na JBXXPO010000138.1 <> na Primary Assembly 31853 na Scaffold_206 unplaced-scaffold na na JBXXPO010000139.1 <> na Primary Assembly 30995 na Scaffold_207 unplaced-scaffold na na JBXXPO010000140.1 <> na Primary Assembly 30036 na Scaffold_157 unplaced-scaffold na na JBXXPO010000141.1 <> na Primary Assembly 26215 na ptg000020l_rc_rotated assembled-molecule MT Mitochondrion CM172932.1 <> na non-nuclear 16499 na