# Assembly name: bPorHoc1.pat.decon # Organism name: Porphyrio hochstetteri (South Island takahe) # Isolate: bPorHoc1 # Sex: female # Taxid: 439704 # BioSample: SAMN22550412 # BioProject: PRJNA774332 # Submitter: Vertebrate Genomes Project # Date: 2021-11-08 # Assembly type: alternate-pseudohaplotype # Release type: major # Assembly level: Scaffold # Genome representation: full # WGS project: JAJHSZ01 # Assembly method: Trio HiFiasm v. 0.15.1-r329; purge_dups v. 1.2.5; Bionano Solve v. 3.6.1_11162020; Salsa v. 2.3; gEVAL manual curation v. 2021-07-20; cutadapt (done in beginning) v. 3.2 # Expected final version: no # Genome coverage: 36.82x # Sequencing technology: PacBio Sequel II HiFi; Bionano Genomics DLS; Illumina HiSeq; Arima Genomics Hi-C v2 # GenBank assembly accession: GCA_020801775.1 # Linked assembly: GCA_020800305.1 (principal pseudohaplotype of diploid) # ## Assembly-Units: ## GenBank Unit Accession RefSeq Unit Accession Assembly-Unit name ## GCA_020801785.1 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 scaffold_1 unplaced-scaffold na na JAJHSZ010000001.1 <> na Primary Assembly 168782532 na scaffold_10 unplaced-scaffold na na JAJHSZ010000010.1 <> na Primary Assembly 41511999 na scaffold_100 unplaced-scaffold na na JAJHSZ010000100.1 <> na Primary Assembly 131830 na scaffold_101 unplaced-scaffold na na JAJHSZ010000101.1 <> na Primary Assembly 128685 na scaffold_102 unplaced-scaffold na na JAJHSZ010000102.1 <> na Primary Assembly 116994 na scaffold_103 unplaced-scaffold na na JAJHSZ010000103.1 <> na Primary Assembly 109785 na scaffold_104 unplaced-scaffold na na JAJHSZ010000104.1 <> na Primary Assembly 108490 na scaffold_105 unplaced-scaffold na na JAJHSZ010000105.1 <> na Primary Assembly 105989 na scaffold_106 unplaced-scaffold na na JAJHSZ010000106.1 <> na Primary Assembly 104601 na scaffold_107 unplaced-scaffold na na JAJHSZ010000107.1 <> na Primary Assembly 103498 na scaffold_108 unplaced-scaffold na na JAJHSZ010000108.1 <> na Primary Assembly 101214 na scaffold_109 unplaced-scaffold na na JAJHSZ010000109.1 <> na Primary Assembly 98465 na scaffold_11 unplaced-scaffold na na JAJHSZ010000011.1 <> na Primary Assembly 36798447 na scaffold_110 unplaced-scaffold na na JAJHSZ010000110.1 <> na Primary Assembly 92575 na scaffold_111 unplaced-scaffold na na JAJHSZ010000111.1 <> na Primary Assembly 89631 na scaffold_112 unplaced-scaffold na na JAJHSZ010000112.1 <> na Primary Assembly 87500 na scaffold_113 unplaced-scaffold na na JAJHSZ010000113.1 <> na Primary Assembly 86484 na scaffold_114 unplaced-scaffold na na JAJHSZ010000114.1 <> na Primary Assembly 84429 na scaffold_115 unplaced-scaffold na na JAJHSZ010000115.1 <> na Primary Assembly 83431 na scaffold_116 unplaced-scaffold na na JAJHSZ010000116.1 <> na Primary Assembly 83476 na scaffold_117 unplaced-scaffold na na JAJHSZ010000117.1 <> na Primary Assembly 82534 na scaffold_118 unplaced-scaffold na na JAJHSZ010000118.1 <> na Primary Assembly 76555 na scaffold_119 unplaced-scaffold na na JAJHSZ010000119.1 <> na Primary Assembly 74681 na scaffold_12 unplaced-scaffold na na JAJHSZ010000012.1 <> na Primary Assembly 34211606 na scaffold_120 unplaced-scaffold na na JAJHSZ010000120.1 <> na Primary Assembly 73357 na scaffold_121 unplaced-scaffold na na JAJHSZ010000121.1 <> na Primary Assembly 70496 na scaffold_122 unplaced-scaffold na na JAJHSZ010000122.1 <> na Primary Assembly 69950 na scaffold_123 unplaced-scaffold na na JAJHSZ010000123.1 <> na Primary Assembly 69816 na scaffold_124 unplaced-scaffold na na JAJHSZ010000124.1 <> na Primary Assembly 69666 na scaffold_125 unplaced-scaffold na na JAJHSZ010000125.1 <> na Primary Assembly 67232 na scaffold_126 unplaced-scaffold na na JAJHSZ010000126.1 <> na Primary Assembly 66666 na scaffold_127 unplaced-scaffold na na JAJHSZ010000127.1 <> na Primary Assembly 66588 na scaffold_128 unplaced-scaffold na na JAJHSZ010000128.1 <> na Primary Assembly 64255 na scaffold_129 unplaced-scaffold na na JAJHSZ010000129.1 <> na Primary Assembly 61824 na scaffold_13 unplaced-scaffold na na JAJHSZ010000013.1 <> na Primary Assembly 29804360 na scaffold_130 unplaced-scaffold na na JAJHSZ010000130.1 <> na Primary Assembly 59890 na scaffold_131 unplaced-scaffold na na JAJHSZ010000131.1 <> na Primary Assembly 57666 na scaffold_132 unplaced-scaffold na na JAJHSZ010000132.1 <> na Primary Assembly 55563 na scaffold_133 unplaced-scaffold na na JAJHSZ010000133.1 <> na Primary Assembly 52290 na scaffold_134 unplaced-scaffold na na JAJHSZ010000134.1 <> na Primary Assembly 51638 na scaffold_135 unplaced-scaffold na na JAJHSZ010000135.1 <> na Primary Assembly 50789 na scaffold_136 unplaced-scaffold na na JAJHSZ010000136.1 <> na Primary Assembly 49746 na scaffold_137 unplaced-scaffold na na JAJHSZ010000137.1 <> na Primary Assembly 46083 na scaffold_138 unplaced-scaffold na na JAJHSZ010000138.1 <> na Primary Assembly 45309 na scaffold_139 unplaced-scaffold na na JAJHSZ010000139.1 <> na Primary Assembly 44268 na scaffold_14 unplaced-scaffold na na JAJHSZ010000014.1 <> na Primary Assembly 24292989 na scaffold_140 unplaced-scaffold na na JAJHSZ010000140.1 <> na Primary Assembly 42197 na scaffold_141 unplaced-scaffold na na JAJHSZ010000141.1 <> na Primary Assembly 41349 na scaffold_142 unplaced-scaffold na na JAJHSZ010000142.1 <> na Primary Assembly 41332 na scaffold_143 unplaced-scaffold na na JAJHSZ010000143.1 <> na Primary Assembly 40525 na scaffold_144 unplaced-scaffold na na JAJHSZ010000144.1 <> na Primary Assembly 38666 na scaffold_145 unplaced-scaffold na na JAJHSZ010000145.1 <> na Primary Assembly 36554 na scaffold_146 unplaced-scaffold na na JAJHSZ010000146.1 <> na Primary Assembly 35737 na scaffold_147 unplaced-scaffold na na JAJHSZ010000147.1 <> na Primary Assembly 35291 na scaffold_148 unplaced-scaffold na na JAJHSZ010000148.1 <> na Primary Assembly 34498 na scaffold_149 unplaced-scaffold na na JAJHSZ010000149.1 <> na Primary Assembly 34271 na scaffold_15 unplaced-scaffold na na JAJHSZ010000015.1 <> na Primary Assembly 23961441 na scaffold_150 unplaced-scaffold na na JAJHSZ010000150.1 <> na Primary Assembly 33295 na scaffold_151 unplaced-scaffold na na JAJHSZ010000151.1 <> na Primary Assembly 33262 na scaffold_152 unplaced-scaffold na na JAJHSZ010000152.1 <> na Primary Assembly 32949 na scaffold_153 unplaced-scaffold na na JAJHSZ010000153.1 <> na Primary Assembly 32794 na scaffold_154 unplaced-scaffold na na JAJHSZ010000154.1 <> na Primary Assembly 32075 na scaffold_155 unplaced-scaffold na na JAJHSZ010000155.1 <> na Primary Assembly 31839 na scaffold_156 unplaced-scaffold na na JAJHSZ010000156.1 <> na Primary Assembly 31073 na scaffold_157 unplaced-scaffold na na JAJHSZ010000157.1 <> na Primary Assembly 30895 na scaffold_158 unplaced-scaffold na na JAJHSZ010000158.1 <> na Primary Assembly 30545 na scaffold_159 unplaced-scaffold na na JAJHSZ010000159.1 <> na Primary Assembly 29585 na scaffold_16 unplaced-scaffold na na JAJHSZ010000016.1 <> na Primary Assembly 23886002 na scaffold_160 unplaced-scaffold na na JAJHSZ010000160.1 <> na Primary Assembly 29416 na scaffold_161 unplaced-scaffold na na JAJHSZ010000161.1 <> na Primary Assembly 28652 na scaffold_162 unplaced-scaffold na na JAJHSZ010000162.1 <> na Primary Assembly 27071 na scaffold_163 unplaced-scaffold na na JAJHSZ010000163.1 <> na Primary Assembly 26812 na scaffold_164 unplaced-scaffold na na JAJHSZ010000164.1 <> na Primary Assembly 26722 na scaffold_165 unplaced-scaffold na na JAJHSZ010000165.1 <> na Primary Assembly 26269 na scaffold_166 unplaced-scaffold na na JAJHSZ010000166.1 <> na Primary Assembly 26125 na scaffold_167 unplaced-scaffold na na JAJHSZ010000167.1 <> na Primary Assembly 25768 na scaffold_168 unplaced-scaffold na na JAJHSZ010000168.1 <> na Primary Assembly 25348 na scaffold_169 unplaced-scaffold na na JAJHSZ010000169.1 <> na Primary Assembly 25227 na scaffold_17 unplaced-scaffold na na JAJHSZ010000017.1 <> na Primary Assembly 21761025 na scaffold_170 unplaced-scaffold na na JAJHSZ010000170.1 <> na Primary Assembly 25216 na scaffold_171 unplaced-scaffold na na JAJHSZ010000171.1 <> na Primary Assembly 24349 na scaffold_172 unplaced-scaffold na na JAJHSZ010000172.1 <> na Primary Assembly 23641 na scaffold_173 unplaced-scaffold na na JAJHSZ010000173.1 <> na Primary Assembly 23260 na scaffold_174 unplaced-scaffold na na JAJHSZ010000174.1 <> na Primary Assembly 22430 na scaffold_175 unplaced-scaffold na na JAJHSZ010000175.1 <> na Primary Assembly 22293 na scaffold_176 unplaced-scaffold na na JAJHSZ010000176.1 <> na Primary Assembly 20617 na scaffold_177 unplaced-scaffold na na JAJHSZ010000177.1 <> na Primary Assembly 17795 na scaffold_178 unplaced-scaffold na na JAJHSZ010000178.1 <> na Primary Assembly 11797 na scaffold_18 unplaced-scaffold na na JAJHSZ010000018.1 <> na Primary Assembly 21297119 na scaffold_19 unplaced-scaffold na na JAJHSZ010000019.1 <> na Primary Assembly 19491750 na scaffold_2 unplaced-scaffold na na JAJHSZ010000002.1 <> na Primary Assembly 125965682 na scaffold_20 unplaced-scaffold na na JAJHSZ010000020.1 <> na Primary Assembly 17627792 na scaffold_21 unplaced-scaffold na na JAJHSZ010000021.1 <> na Primary Assembly 16652972 na scaffold_22 unplaced-scaffold na na JAJHSZ010000022.1 <> na Primary Assembly 13981293 na scaffold_23 unplaced-scaffold na na JAJHSZ010000023.1 <> na Primary Assembly 13485052 na scaffold_24 unplaced-scaffold na na JAJHSZ010000024.1 <> na Primary Assembly 13188206 na scaffold_25 unplaced-scaffold na na JAJHSZ010000025.1 <> na Primary Assembly 10390277 na scaffold_26 unplaced-scaffold na na JAJHSZ010000026.1 <> na Primary Assembly 9754967 na scaffold_27 unplaced-scaffold na na JAJHSZ010000027.1 <> na Primary Assembly 8444406 na scaffold_28 unplaced-scaffold na na JAJHSZ010000028.1 <> na Primary Assembly 8308031 na scaffold_29 unplaced-scaffold na na JAJHSZ010000029.1 <> na Primary Assembly 8294305 na scaffold_3 unplaced-scaffold na na JAJHSZ010000003.1 <> na Primary Assembly 92686875 na scaffold_30 unplaced-scaffold na na JAJHSZ010000030.1 <> na Primary Assembly 7704898 na scaffold_31 unplaced-scaffold na na JAJHSZ010000031.1 <> na Primary Assembly 5812062 na scaffold_32 unplaced-scaffold na na JAJHSZ010000032.1 <> na Primary Assembly 5240437 na scaffold_33 unplaced-scaffold na na JAJHSZ010000033.1 <> na Primary Assembly 3887628 na scaffold_34 unplaced-scaffold na na JAJHSZ010000034.1 <> na Primary Assembly 3176178 na scaffold_35 unplaced-scaffold na na JAJHSZ010000035.1 <> na Primary Assembly 2745658 na scaffold_36 unplaced-scaffold na na JAJHSZ010000036.1 <> na Primary Assembly 2436035 na scaffold_37 unplaced-scaffold na na JAJHSZ010000037.1 <> na Primary Assembly 1901171 na scaffold_38 unplaced-scaffold na na JAJHSZ010000038.1 <> na Primary Assembly 1896686 na scaffold_39 unplaced-scaffold na na JAJHSZ010000039.1 <> na Primary Assembly 1852113 na scaffold_4 unplaced-scaffold na na JAJHSZ010000004.1 <> na Primary Assembly 85217687 na scaffold_40 unplaced-scaffold na na JAJHSZ010000040.1 <> na Primary Assembly 1839311 na scaffold_41 unplaced-scaffold na na JAJHSZ010000041.1 <> na Primary Assembly 1780835 na scaffold_42 unplaced-scaffold na na JAJHSZ010000042.1 <> na Primary Assembly 1064455 na scaffold_43 unplaced-scaffold na na JAJHSZ010000043.1 <> na Primary Assembly 1286950 na scaffold_44 unplaced-scaffold na na JAJHSZ010000044.1 <> na Primary Assembly 1100142 na scaffold_45 unplaced-scaffold na na JAJHSZ010000045.1 <> na Primary Assembly 999725 na scaffold_46 unplaced-scaffold na na JAJHSZ010000046.1 <> na Primary Assembly 994863 na scaffold_47 unplaced-scaffold na na JAJHSZ010000047.1 <> na Primary Assembly 984135 na scaffold_48 unplaced-scaffold na na JAJHSZ010000048.1 <> na Primary Assembly 976614 na scaffold_49 unplaced-scaffold na na JAJHSZ010000049.1 <> na Primary Assembly 963363 na scaffold_5 unplaced-scaffold na na JAJHSZ010000005.1 <> na Primary Assembly 77818260 na scaffold_50 unplaced-scaffold na na JAJHSZ010000050.1 <> na Primary Assembly 943492 na scaffold_51 unplaced-scaffold na na JAJHSZ010000051.1 <> na Primary Assembly 940085 na scaffold_52 unplaced-scaffold na na JAJHSZ010000052.1 <> na Primary Assembly 900341 na scaffold_53 unplaced-scaffold na na JAJHSZ010000053.1 <> na Primary Assembly 846085 na scaffold_54 unplaced-scaffold na na JAJHSZ010000054.1 <> na Primary Assembly 820536 na scaffold_55 unplaced-scaffold na na JAJHSZ010000055.1 <> na Primary Assembly 812425 na scaffold_56 unplaced-scaffold na na JAJHSZ010000056.1 <> na Primary Assembly 749987 na scaffold_57 unplaced-scaffold na na JAJHSZ010000057.1 <> na Primary Assembly 726005 na scaffold_58 unplaced-scaffold na na JAJHSZ010000058.1 <> na Primary Assembly 720116 na scaffold_59 unplaced-scaffold na na JAJHSZ010000059.1 <> na Primary Assembly 457350 na scaffold_6 unplaced-scaffold na na JAJHSZ010000006.1 <> na Primary Assembly 71521518 na scaffold_60 unplaced-scaffold na na JAJHSZ010000060.1 <> na Primary Assembly 679269 na scaffold_61 unplaced-scaffold na na JAJHSZ010000061.1 <> na Primary Assembly 656363 na scaffold_62 unplaced-scaffold na na JAJHSZ010000062.1 <> na Primary Assembly 656465 na scaffold_63 unplaced-scaffold na na JAJHSZ010000063.1 <> na Primary Assembly 621322 na scaffold_64 unplaced-scaffold na na JAJHSZ010000064.1 <> na Primary Assembly 617550 na scaffold_65 unplaced-scaffold na na JAJHSZ010000065.1 <> na Primary Assembly 590940 na scaffold_66 unplaced-scaffold na na JAJHSZ010000066.1 <> na Primary Assembly 585888 na scaffold_67 unplaced-scaffold na na JAJHSZ010000067.1 <> na Primary Assembly 571350 na scaffold_68 unplaced-scaffold na na JAJHSZ010000068.1 <> na Primary Assembly 557078 na scaffold_69 unplaced-scaffold na na JAJHSZ010000069.1 <> na Primary Assembly 552505 na scaffold_7 unplaced-scaffold na na JAJHSZ010000007.1 <> na Primary Assembly 58902102 na scaffold_70 unplaced-scaffold na na JAJHSZ010000070.1 <> na Primary Assembly 539192 na scaffold_71 unplaced-scaffold na na JAJHSZ010000071.1 <> na Primary Assembly 530023 na scaffold_72 unplaced-scaffold na na JAJHSZ010000072.1 <> na Primary Assembly 520834 na scaffold_73 unplaced-scaffold na na JAJHSZ010000073.1 <> na Primary Assembly 470432 na scaffold_74 unplaced-scaffold na na JAJHSZ010000074.1 <> na Primary Assembly 461569 na scaffold_75 unplaced-scaffold na na JAJHSZ010000075.1 <> na Primary Assembly 434059 na scaffold_76 unplaced-scaffold na na JAJHSZ010000076.1 <> na Primary Assembly 423724 na scaffold_77 unplaced-scaffold na na JAJHSZ010000077.1 <> na Primary Assembly 384184 na scaffold_78 unplaced-scaffold na na JAJHSZ010000078.1 <> na Primary Assembly 373823 na scaffold_79 unplaced-scaffold na na JAJHSZ010000079.1 <> na Primary Assembly 360215 na scaffold_8 unplaced-scaffold na na JAJHSZ010000008.1 <> na Primary Assembly 46840750 na scaffold_80 unplaced-scaffold na na JAJHSZ010000080.1 <> na Primary Assembly 317768 na scaffold_81 unplaced-scaffold na na JAJHSZ010000081.1 <> na Primary Assembly 311023 na scaffold_82 unplaced-scaffold na na JAJHSZ010000082.1 <> na Primary Assembly 295844 na scaffold_83 unplaced-scaffold na na JAJHSZ010000083.1 <> na Primary Assembly 292643 na scaffold_84 unplaced-scaffold na na JAJHSZ010000084.1 <> na Primary Assembly 275083 na scaffold_85 unplaced-scaffold na na JAJHSZ010000085.1 <> na Primary Assembly 275078 na scaffold_86 unplaced-scaffold na na JAJHSZ010000086.1 <> na Primary Assembly 255993 na scaffold_87 unplaced-scaffold na na JAJHSZ010000087.1 <> na Primary Assembly 251805 na scaffold_88 unplaced-scaffold na na JAJHSZ010000088.1 <> na Primary Assembly 239191 na scaffold_89 unplaced-scaffold na na JAJHSZ010000089.1 <> na Primary Assembly 235975 na scaffold_9 unplaced-scaffold na na JAJHSZ010000009.1 <> na Primary Assembly 44262735 na scaffold_90 unplaced-scaffold na na JAJHSZ010000090.1 <> na Primary Assembly 206711 na scaffold_91 unplaced-scaffold na na JAJHSZ010000091.1 <> na Primary Assembly 203258 na scaffold_92 unplaced-scaffold na na JAJHSZ010000092.1 <> na Primary Assembly 198910 na scaffold_93 unplaced-scaffold na na JAJHSZ010000093.1 <> na Primary Assembly 193177 na scaffold_94 unplaced-scaffold na na JAJHSZ010000094.1 <> na Primary Assembly 188731 na scaffold_95 unplaced-scaffold na na JAJHSZ010000095.1 <> na Primary Assembly 187808 na scaffold_96 unplaced-scaffold na na JAJHSZ010000096.1 <> na Primary Assembly 172415 na scaffold_97 unplaced-scaffold na na JAJHSZ010000097.1 <> na Primary Assembly 151312 na scaffold_98 unplaced-scaffold na na JAJHSZ010000098.1 <> na Primary Assembly 145825 na scaffold_99 unplaced-scaffold na na JAJHSZ010000099.1 <> na Primary Assembly 139939 na