# Assembly name: rCroNil1.hap2 # Organism name: Crocodylus niloticus (Nile crocodile) # Isolate: rCroNil1 # Sex: female # Taxid: 8501 # BioSample: SAMN53135923 # BioProject: PRJNA1359028 # Submitter: Vertebrate Genomes Project # Date: 2026-01-29 # Assembly type: haploid (haplotype 2) # Release type: major # Assembly level: Chromosome # Genome representation: full # WGS project: JBTWWZ01 # 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 # RefSeq category: Reference Genome # GenBank assembly accession: GCA_054825085.1 # Linked assembly: GCA_054954115.1 (haplotype 1) # ## Assembly-Units: ## GenBank Unit Accession RefSeq Unit Accession Assembly-Unit name ## GCA_054825125.1 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 CM139663.1 <> na Primary Assembly 486965013 na SUPER_2 assembled-molecule 2 Chromosome CM139664.1 <> na Primary Assembly 318214715 na SUPER_3 assembled-molecule 3 Chromosome CM139665.1 <> na Primary Assembly 260608322 na SUPER_4 assembled-molecule 4 Chromosome CM139666.1 <> na Primary Assembly 222540633 na SUPER_5 assembled-molecule 5 Chromosome CM139667.1 <> na Primary Assembly 176718725 na SUPER_6 assembled-molecule 6 Chromosome CM139668.1 <> na Primary Assembly 125540988 na SUPER_7 assembled-molecule 7 Chromosome CM139669.1 <> na Primary Assembly 126112929 na SUPER_8 assembled-molecule 8 Chromosome CM139670.1 <> na Primary Assembly 100331355 na SUPER_9 assembled-molecule 9 Chromosome CM139671.1 <> na Primary Assembly 82334972 na SUPER_10 assembled-molecule 10 Chromosome CM139672.1 <> na Primary Assembly 79227702 na SUPER_11 assembled-molecule 11 Chromosome CM139673.1 <> na Primary Assembly 77560654 na SUPER_12 assembled-molecule 12 Chromosome CM139674.1 <> na Primary Assembly 71832305 na SUPER_13 assembled-molecule 13 Chromosome CM139675.1 <> na Primary Assembly 70819881 na SUPER_14 assembled-molecule 14 Chromosome CM139676.1 <> na Primary Assembly 61054772 na SUPER_15 assembled-molecule 15 Chromosome CM139677.1 <> na Primary Assembly 43467495 na SUPER_16 assembled-molecule 16 Chromosome CM139678.1 <> na Primary Assembly 31407134 na SUPER_7_unloc_1 unlocalized-scaffold 7 Chromosome JBTWWZ010000018.1 <> na Primary Assembly 675916 na SUPER_12_unloc_4 unlocalized-scaffold 12 Chromosome JBTWWZ010000019.1 <> na Primary Assembly 533495 na SUPER_12_unloc_3 unlocalized-scaffold 12 Chromosome JBTWWZ010000020.1 <> na Primary Assembly 511239 na SUPER_12_unloc_2 unlocalized-scaffold 12 Chromosome JBTWWZ010000021.1 <> na Primary Assembly 487689 na SUPER_12_unloc_5 unlocalized-scaffold 12 Chromosome JBTWWZ010000022.1 <> na Primary Assembly 353122 na SUPER_12_unloc_1 unlocalized-scaffold 12 Chromosome JBTWWZ010000023.1 <> na Primary Assembly 349009 na SUPER_12_unloc_6 unlocalized-scaffold 12 Chromosome JBTWWZ010000031.1 <> na Primary Assembly 174597 na Scaffold_105 unplaced-scaffold na na JBTWWZ010000017.1 <> na Primary Assembly 1888573 na Scaffold_33 unplaced-scaffold na na JBTWWZ010000024.1 <> na Primary Assembly 268571 na Scaffold_34 unplaced-scaffold na na JBTWWZ010000025.1 <> na Primary Assembly 238228 na Scaffold_35 unplaced-scaffold na na JBTWWZ010000026.1 <> na Primary Assembly 207375 na Scaffold_36 unplaced-scaffold na na JBTWWZ010000027.1 <> na Primary Assembly 198783 na Scaffold_38 unplaced-scaffold na na JBTWWZ010000028.1 <> na Primary Assembly 191432 na Scaffold_39 unplaced-scaffold na na JBTWWZ010000029.1 <> na Primary Assembly 188481 na Scaffold_40 unplaced-scaffold na na JBTWWZ010000030.1 <> na Primary Assembly 175170 na Scaffold_41 unplaced-scaffold na na JBTWWZ010000032.1 <> na Primary Assembly 172154 na Scaffold_43 unplaced-scaffold na na JBTWWZ010000033.1 <> na Primary Assembly 169054 na Scaffold_44 unplaced-scaffold na na JBTWWZ010000034.1 <> na Primary Assembly 142020 na Scaffold_45 unplaced-scaffold na na JBTWWZ010000035.1 <> na Primary Assembly 141345 na Scaffold_49 unplaced-scaffold na na JBTWWZ010000036.1 <> na Primary Assembly 126248 na Scaffold_50 unplaced-scaffold na na JBTWWZ010000037.1 <> na Primary Assembly 125265 na Scaffold_256 unplaced-scaffold na na JBTWWZ010000038.1 <> na Primary Assembly 123182 na Scaffold_255 unplaced-scaffold na na JBTWWZ010000039.1 <> na Primary Assembly 114956 na Scaffold_57 unplaced-scaffold na na JBTWWZ010000040.1 <> na Primary Assembly 113710 na Scaffold_58 unplaced-scaffold na na JBTWWZ010000041.1 <> na Primary Assembly 111725 na Scaffold_252 unplaced-scaffold na na JBTWWZ010000042.1 <> na Primary Assembly 111321 na Scaffold_60 unplaced-scaffold na na JBTWWZ010000043.1 <> na Primary Assembly 111121 na Scaffold_61 unplaced-scaffold na na JBTWWZ010000044.1 <> na Primary Assembly 110115 na Scaffold_62 unplaced-scaffold na na JBTWWZ010000045.1 <> na Primary Assembly 109270 na Scaffold_63 unplaced-scaffold na na JBTWWZ010000046.1 <> na Primary Assembly 104377 na Scaffold_64 unplaced-scaffold na na JBTWWZ010000047.1 <> na Primary Assembly 103081 na Scaffold_70 unplaced-scaffold na na JBTWWZ010000048.1 <> na Primary Assembly 90036 na Scaffold_72 unplaced-scaffold na na JBTWWZ010000049.1 <> na Primary Assembly 86926 na Scaffold_244 unplaced-scaffold na na JBTWWZ010000050.1 <> na Primary Assembly 86595 na Scaffold_75 unplaced-scaffold na na JBTWWZ010000051.1 <> na Primary Assembly 80955 na Scaffold_242 unplaced-scaffold na na JBTWWZ010000052.1 <> na Primary Assembly 79116 na Scaffold_241 unplaced-scaffold na na JBTWWZ010000053.1 <> na Primary Assembly 74404 na Scaffold_80 unplaced-scaffold na na JBTWWZ010000054.1 <> na Primary Assembly 67395 na Scaffold_81 unplaced-scaffold na na JBTWWZ010000055.1 <> na Primary Assembly 64895 na Scaffold_278 unplaced-scaffold na na JBTWWZ010000056.1 <> na Primary Assembly 62688 na Scaffold_83 unplaced-scaffold na na JBTWWZ010000057.1 <> na Primary Assembly 61993 na Scaffold_84 unplaced-scaffold na na JBTWWZ010000058.1 <> na Primary Assembly 59694 na Scaffold_275 unplaced-scaffold na na JBTWWZ010000059.1 <> na Primary Assembly 55536 na Scaffold_88 unplaced-scaffold na na JBTWWZ010000060.1 <> na Primary Assembly 54148 na Scaffold_273 unplaced-scaffold na na JBTWWZ010000061.1 <> na Primary Assembly 51714 na Scaffold_90 unplaced-scaffold na na JBTWWZ010000062.1 <> na Primary Assembly 51017 na Scaffold_271 unplaced-scaffold na na JBTWWZ010000063.1 <> na Primary Assembly 43980 na Scaffold_94 unplaced-scaffold na na JBTWWZ010000064.1 <> na Primary Assembly 42799 na Scaffold_269 unplaced-scaffold na na JBTWWZ010000065.1 <> na Primary Assembly 41941 na Scaffold_268 unplaced-scaffold na na JBTWWZ010000066.1 <> na Primary Assembly 39856 na Scaffold_267 unplaced-scaffold na na JBTWWZ010000067.1 <> na Primary Assembly 39307 na Scaffold_97 unplaced-scaffold na na JBTWWZ010000068.1 <> na Primary Assembly 37564 na Scaffold_265 unplaced-scaffold na na JBTWWZ010000069.1 <> na Primary Assembly 36029 na Scaffold_264 unplaced-scaffold na na JBTWWZ010000070.1 <> na Primary Assembly 33985 na Scaffold_263 unplaced-scaffold na na JBTWWZ010000071.1 <> na Primary Assembly 31306 na Scaffold_262 unplaced-scaffold na na JBTWWZ010000072.1 <> na Primary Assembly 27813 na Scaffold_261 unplaced-scaffold na na JBTWWZ010000073.1 <> na Primary Assembly 23095 na