# Assembly name: rCroNil1.hap1 # Organism name: Crocodylus niloticus (Nile crocodile) # Isolate: rCroNil1 # Sex: female # Taxid: 8501 # BioSample: SAMN53135923 # BioProject: PRJNA1359027 # Submitter: Vertebrate Genomes Project # Date: 2026-01-29 # Assembly type: haploid (haplotype 1) # Release type: major # Assembly level: Chromosome # Genome representation: full # WGS project: JBTWWY01 # Assembly method: Hifiasm + Hi-C phasing v. 0.25.0 + galaxy0; yahs v. 1.2a.2 + galaxy2 # Expected final version: No # Genome coverage: 81.78x # Sequencing technology: PacBio Revio HiFi; Arima Hi-C v2 # GenBank assembly accession: GCA_054954115.1 # Linked assembly: GCA_054825085.1 (haplotype 2) # ## Assembly-Units: ## GenBank Unit Accession RefSeq Unit Accession Assembly-Unit name ## GCA_054954125.1 Primary Assembly ## GCA_054954135.1 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 CM143199.1 <> na Primary Assembly 484646003 na SUPER_2 assembled-molecule 2 Chromosome CM143200.1 <> na Primary Assembly 317502049 na SUPER_3 assembled-molecule 3 Chromosome CM143201.1 <> na Primary Assembly 259237453 na SUPER_4 assembled-molecule 4 Chromosome CM143202.1 <> na Primary Assembly 220680538 na SUPER_5 assembled-molecule 5 Chromosome CM143203.1 <> na Primary Assembly 177526641 na SUPER_6 assembled-molecule 6 Chromosome CM143204.1 <> na Primary Assembly 127497447 na SUPER_7 assembled-molecule 7 Chromosome CM143205.1 <> na Primary Assembly 126483728 na SUPER_8 assembled-molecule 8 Chromosome CM143206.1 <> na Primary Assembly 100598796 na SUPER_9 assembled-molecule 9 Chromosome CM143207.1 <> na Primary Assembly 82297260 na SUPER_10 assembled-molecule 10 Chromosome CM143208.1 <> na Primary Assembly 79125308 na SUPER_11 assembled-molecule 11 Chromosome CM143209.1 <> na Primary Assembly 76977712 na SUPER_12 assembled-molecule 12 Chromosome CM143210.1 <> na Primary Assembly 73968100 na SUPER_13 assembled-molecule 13 Chromosome CM143211.1 <> na Primary Assembly 69959104 na SUPER_14 assembled-molecule 14 Chromosome CM143212.1 <> na Primary Assembly 59195864 na SUPER_15 assembled-molecule 15 Chromosome CM143213.1 <> na Primary Assembly 41125267 na SUPER_16 assembled-molecule 16 Chromosome CM143214.1 <> na Primary Assembly 32112001 na SUPER_4_unloc_1 unlocalized-scaffold 4 Chromosome JBTWWY010000026.1 <> na Primary Assembly 291663 na SUPER_12_unloc_1 unlocalized-scaffold 12 Chromosome JBTWWY010000019.1 <> na Primary Assembly 515358 na SUPER_12_unloc_5 unlocalized-scaffold 12 Chromosome JBTWWY010000020.1 <> na Primary Assembly 430866 na SUPER_12_unloc_4 unlocalized-scaffold 12 Chromosome JBTWWY010000021.1 <> na Primary Assembly 429605 na SUPER_12_unloc_3 unlocalized-scaffold 12 Chromosome JBTWWY010000022.1 <> na Primary Assembly 427459 na SUPER_12_unloc_7 unlocalized-scaffold 12 Chromosome JBTWWY010000024.1 <> na Primary Assembly 315847 na SUPER_12_unloc_8 unlocalized-scaffold 12 Chromosome JBTWWY010000025.1 <> na Primary Assembly 312291 na SUPER_12_unloc_9 unlocalized-scaffold 12 Chromosome JBTWWY010000027.1 <> na Primary Assembly 276742 na SUPER_12_unloc_10 unlocalized-scaffold 12 Chromosome JBTWWY010000028.1 <> na Primary Assembly 272257 na SUPER_12_unloc_6 unlocalized-scaffold 12 Chromosome JBTWWY010000030.1 <> na Primary Assembly 249559 na SUPER_12_unloc_2 unlocalized-scaffold 12 Chromosome JBTWWY010000033.1 <> na Primary Assembly 195758 na SUPER_13_unloc_1 unlocalized-scaffold 13 Chromosome JBTWWY010000029.1 <> na Primary Assembly 268535 na Scaffold_104 unplaced-scaffold na na JBTWWY010000018.1 <> na Primary Assembly 1045915 na Scaffold_106 unplaced-scaffold na na JBTWWY010000023.1 <> na Primary Assembly 352539 na Scaffold_108 unplaced-scaffold na na JBTWWY010000031.1 <> na Primary Assembly 237187 na Scaffold_109 unplaced-scaffold na na JBTWWY010000032.1 <> na Primary Assembly 219656 na Scaffold_37 unplaced-scaffold na na JBTWWY010000034.1 <> na Primary Assembly 193740 na Scaffold_107 unplaced-scaffold na na JBTWWY010000035.1 <> na Primary Assembly 188485 na Scaffold_42 unplaced-scaffold na na JBTWWY010000036.1 <> na Primary Assembly 171358 na Scaffold_46 unplaced-scaffold na na JBTWWY010000037.1 <> na Primary Assembly 134977 na Scaffold_47 unplaced-scaffold na na JBTWWY010000038.1 <> na Primary Assembly 130231 na Scaffold_48 unplaced-scaffold na na JBTWWY010000039.1 <> na Primary Assembly 129863 na Scaffold_51 unplaced-scaffold na na JBTWWY010000040.1 <> na Primary Assembly 122633 na Scaffold_52 unplaced-scaffold na na JBTWWY010000041.1 <> na Primary Assembly 120667 na Scaffold_53 unplaced-scaffold na na JBTWWY010000042.1 <> na Primary Assembly 120417 na Scaffold_54 unplaced-scaffold na na JBTWWY010000043.1 <> na Primary Assembly 116122 na Scaffold_55 unplaced-scaffold na na JBTWWY010000044.1 <> na Primary Assembly 115653 na Scaffold_56 unplaced-scaffold na na JBTWWY010000045.1 <> na Primary Assembly 114251 na Scaffold_59 unplaced-scaffold na na JBTWWY010000046.1 <> na Primary Assembly 111662 na Scaffold_220 unplaced-scaffold na na JBTWWY010000047.1 <> na Primary Assembly 107989 na Scaffold_65 unplaced-scaffold na na JBTWWY010000048.1 <> na Primary Assembly 101984 na Scaffold_218 unplaced-scaffold na na JBTWWY010000049.1 <> na Primary Assembly 100846 na Scaffold_66 unplaced-scaffold na na JBTWWY010000050.1 <> na Primary Assembly 100742 na Scaffold_67 unplaced-scaffold na na JBTWWY010000051.1 <> na Primary Assembly 96863 na Scaffold_215 unplaced-scaffold na na JBTWWY010000052.1 <> na Primary Assembly 95595 na Scaffold_68 unplaced-scaffold na na JBTWWY010000053.1 <> na Primary Assembly 92268 na Scaffold_69 unplaced-scaffold na na JBTWWY010000054.1 <> na Primary Assembly 92026 na Scaffold_212 unplaced-scaffold na na JBTWWY010000055.1 <> na Primary Assembly 90036 na Scaffold_71 unplaced-scaffold na na JBTWWY010000056.1 <> na Primary Assembly 88916 na Scaffold_210 unplaced-scaffold na na JBTWWY010000057.1 <> na Primary Assembly 88625 na Scaffold_73 unplaced-scaffold na na JBTWWY010000058.1 <> na Primary Assembly 85045 na Scaffold_74 unplaced-scaffold na na JBTWWY010000059.1 <> na Primary Assembly 84266 na Scaffold_158 unplaced-scaffold na na JBTWWY010000060.1 <> na Primary Assembly 81415 na Scaffold_76 unplaced-scaffold na na JBTWWY010000061.1 <> na Primary Assembly 78856 na Scaffold_140 unplaced-scaffold na na JBTWWY010000062.1 <> na Primary Assembly 76541 na Scaffold_77 unplaced-scaffold na na JBTWWY010000063.1 <> na Primary Assembly 76337 na Scaffold_138 unplaced-scaffold na na JBTWWY010000064.1 <> na Primary Assembly 75230 na Scaffold_78 unplaced-scaffold na na JBTWWY010000065.1 <> na Primary Assembly 74528 na Scaffold_79 unplaced-scaffold na na JBTWWY010000066.1 <> na Primary Assembly 73793 na Scaffold_135 unplaced-scaffold na na JBTWWY010000067.1 <> na Primary Assembly 68513 na Scaffold_134 unplaced-scaffold na na JBTWWY010000068.1 <> na Primary Assembly 65568 na Scaffold_133 unplaced-scaffold na na JBTWWY010000069.1 <> na Primary Assembly 63673 na Scaffold_82 unplaced-scaffold na na JBTWWY010000070.1 <> na Primary Assembly 63297 na Scaffold_131 unplaced-scaffold na na JBTWWY010000071.1 <> na Primary Assembly 61220 na Scaffold_130 unplaced-scaffold na na JBTWWY010000072.1 <> na Primary Assembly 61129 na Scaffold_129 unplaced-scaffold na na JBTWWY010000073.1 <> na Primary Assembly 58295 na Scaffold_85 unplaced-scaffold na na JBTWWY010000074.1 <> na Primary Assembly 58061 na Scaffold_119 unplaced-scaffold na na JBTWWY010000075.1 <> na Primary Assembly 57642 na Scaffold_111 unplaced-scaffold na na JBTWWY010000076.1 <> na Primary Assembly 57354 na Scaffold_86 unplaced-scaffold na na JBTWWY010000077.1 <> na Primary Assembly 56976 na Scaffold_113 unplaced-scaffold na na JBTWWY010000078.1 <> na Primary Assembly 56728 na Scaffold_87 unplaced-scaffold na na JBTWWY010000079.1 <> na Primary Assembly 56368 na Scaffold_115 unplaced-scaffold na na JBTWWY010000080.1 <> na Primary Assembly 54929 na Scaffold_116 unplaced-scaffold na na JBTWWY010000081.1 <> na Primary Assembly 53088 na Scaffold_89 unplaced-scaffold na na JBTWWY010000082.1 <> na Primary Assembly 52704 na Scaffold_118 unplaced-scaffold na na JBTWWY010000083.1 <> na Primary Assembly 52635 na Scaffold_110 unplaced-scaffold na na JBTWWY010000084.1 <> na Primary Assembly 49824 na Scaffold_120 unplaced-scaffold na na JBTWWY010000085.1 <> na Primary Assembly 48960 na Scaffold_91 unplaced-scaffold na na JBTWWY010000086.1 <> na Primary Assembly 48754 na Scaffold_122 unplaced-scaffold na na JBTWWY010000087.1 <> na Primary Assembly 48390 na Scaffold_123 unplaced-scaffold na na JBTWWY010000088.1 <> na Primary Assembly 47758 na Scaffold_92 unplaced-scaffold na na JBTWWY010000089.1 <> na Primary Assembly 47509 na Scaffold_125 unplaced-scaffold na na JBTWWY010000090.1 <> na Primary Assembly 47089 na Scaffold_126 unplaced-scaffold na na JBTWWY010000091.1 <> na Primary Assembly 46222 na Scaffold_93 unplaced-scaffold na na JBTWWY010000092.1 <> na Primary Assembly 45173 na Scaffold_173 unplaced-scaffold na na JBTWWY010000093.1 <> na Primary Assembly 43557 na Scaffold_172 unplaced-scaffold na na JBTWWY010000094.1 <> na Primary Assembly 42642 na Scaffold_171 unplaced-scaffold na na JBTWWY010000095.1 <> na Primary Assembly 42452 na Scaffold_95 unplaced-scaffold na na JBTWWY010000096.1 <> na Primary Assembly 41879 na Scaffold_169 unplaced-scaffold na na JBTWWY010000097.1 <> na Primary Assembly 41587 na Scaffold_168 unplaced-scaffold na na JBTWWY010000098.1 <> na Primary Assembly 41188 na Scaffold_96 unplaced-scaffold na na JBTWWY010000099.1 <> na Primary Assembly 40998 na Scaffold_166 unplaced-scaffold na na JBTWWY010000100.1 <> na Primary Assembly 38579 na Scaffold_165 unplaced-scaffold na na JBTWWY010000101.1 <> na Primary Assembly 37157 na Scaffold_164 unplaced-scaffold na na JBTWWY010000102.1 <> na Primary Assembly 36366 na Scaffold_98 unplaced-scaffold na na JBTWWY010000103.1 <> na Primary Assembly 35433 na Scaffold_162 unplaced-scaffold na na JBTWWY010000104.1 <> na Primary Assembly 33872 na Scaffold_161 unplaced-scaffold na na JBTWWY010000105.1 <> na Primary Assembly 33530 na Scaffold_99 unplaced-scaffold na na JBTWWY010000106.1 <> na Primary Assembly 33429 na Scaffold_159 unplaced-scaffold na na JBTWWY010000107.1 <> na Primary Assembly 32747 na Scaffold_142 unplaced-scaffold na na JBTWWY010000108.1 <> na Primary Assembly 32398 na Scaffold_157 unplaced-scaffold na na JBTWWY010000109.1 <> na Primary Assembly 32326 na Scaffold_100 unplaced-scaffold na na JBTWWY010000110.1 <> na Primary Assembly 32211 na Scaffold_155 unplaced-scaffold na na JBTWWY010000111.1 <> na Primary Assembly 31689 na Scaffold_154 unplaced-scaffold na na JBTWWY010000112.1 <> na Primary Assembly 30520 na Scaffold_153 unplaced-scaffold na na JBTWWY010000113.1 <> na Primary Assembly 30477 na Scaffold_101 unplaced-scaffold na na JBTWWY010000114.1 <> na Primary Assembly 28294 na Scaffold_151 unplaced-scaffold na na JBTWWY010000115.1 <> na Primary Assembly 27828 na Scaffold_150 unplaced-scaffold na na JBTWWY010000116.1 <> na Primary Assembly 26844 na Scaffold_149 unplaced-scaffold na na JBTWWY010000117.1 <> na Primary Assembly 26820 na Scaffold_102 unplaced-scaffold na na JBTWWY010000118.1 <> na Primary Assembly 25073 na Scaffold_147 unplaced-scaffold na na JBTWWY010000119.1 <> na Primary Assembly 25017 na Scaffold_146 unplaced-scaffold na na JBTWWY010000120.1 <> na Primary Assembly 23807 na Scaffold_145 unplaced-scaffold na na JBTWWY010000121.1 <> na Primary Assembly 22659 na Scaffold_144 unplaced-scaffold na na JBTWWY010000122.1 <> na Primary Assembly 22550 na Scaffold_103 unplaced-scaffold na na JBTWWY010000123.1 <> na Primary Assembly 19942 na ptg000001l_rc_rotated assembled-molecule MT Mitochondrion CM143215.1 <> na non-nuclear 16827 na