# Assembly name: bPorHoc1.mat.Z.cur # Organism name: Porphyrio hochstetteri (South Island takahe) # Isolate: bPorHoc1 # Sex: female # Taxid: 439704 # BioSample: SAMN22550412 # BioProject: PRJNA774331 # Submitter: Vertebrate Genomes Project # Date: 2021-11-08 # Assembly type: haploid (principal pseudohaplotype of diploid) # Release type: major # Assembly level: Chromosome # Genome representation: full # WGS project: JAJHSY01 # 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; VGP trio pipeline v. 2.0; cutadapt (done in beginning) v. 3.2; gEVAL manual curation v. 2021-11-06 # Expected final version: no # Genome coverage: 36.82x # Sequencing technology: PacBio Sequel II HiFi; Bionano Genomics DLS; Illumina HiSeq; Arima Genomics Hi-C v2 # RefSeq category: Representative Genome # GenBank assembly accession: GCA_020800305.1 # Linked assembly: GCA_020801775.1 (alternate pseudohaplotype of diploid) # ## Assembly-Units: ## GenBank Unit Accession RefSeq Unit Accession Assembly-Unit name ## GCA_020800315.1 Primary Assembly ## GCA_020800385.1 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 CM036905.1 <> na Primary Assembly 224114340 na SUPER_2 assembled-molecule 2 Chromosome CM036906.1 <> na Primary Assembly 171057732 na SUPER_3 assembled-molecule 3 Chromosome CM036907.1 <> na Primary Assembly 127874553 na SUPER_4 assembled-molecule 4 Chromosome CM036908.1 <> na Primary Assembly 71566193 na SUPER_5 assembled-molecule 5 Chromosome CM036909.1 <> na Primary Assembly 46767683 na SUPER_6 assembled-molecule 6 Chromosome CM036910.1 <> na Primary Assembly 44491086 na SUPER_7 assembled-molecule 7 Chromosome CM036911.1 <> na Primary Assembly 42323710 na SUPER_8 assembled-molecule 8 Chromosome CM036912.1 <> na Primary Assembly 36668294 na SUPER_9 assembled-molecule 9 Chromosome CM036913.1 <> na Primary Assembly 34454515 na SUPER_10 assembled-molecule 10 Chromosome CM036914.1 <> na Primary Assembly 29618820 na SUPER_11 assembled-molecule 11 Chromosome CM036915.1 <> na Primary Assembly 25337030 na SUPER_12 assembled-molecule 12 Chromosome CM036916.1 <> na Primary Assembly 24253456 na SUPER_13 assembled-molecule 13 Chromosome CM036917.1 <> na Primary Assembly 23991850 na SUPER_14 assembled-molecule 14 Chromosome CM036918.1 <> na Primary Assembly 22936666 na SUPER_15 assembled-molecule 15 Chromosome CM036919.1 <> na Primary Assembly 21684345 na SUPER_16 assembled-molecule 16 Chromosome CM036920.1 <> na Primary Assembly 19484417 na SUPER_17 assembled-molecule 17 Chromosome CM036921.1 <> na Primary Assembly 17566588 na SUPER_18 assembled-molecule 18 Chromosome CM036922.1 <> na Primary Assembly 16642641 na SUPER_19 assembled-molecule 19 Chromosome CM036923.1 <> na Primary Assembly 13871266 na SUPER_20 assembled-molecule 20 Chromosome CM036924.1 <> na Primary Assembly 13004814 na SUPER_21 assembled-molecule 21 Chromosome CM036925.1 <> na Primary Assembly 12827660 na SUPER_22 assembled-molecule 22 Chromosome CM036926.1 <> na Primary Assembly 10382098 na SUPER_23 assembled-molecule 23 Chromosome CM036927.1 <> na Primary Assembly 9284780 na SUPER_24 assembled-molecule 24 Chromosome CM036928.1 <> na Primary Assembly 8517493 na SUPER_25 assembled-molecule 25 Chromosome CM036929.1 <> na Primary Assembly 8300993 na SUPER_26 assembled-molecule 26 Chromosome CM036930.1 <> na Primary Assembly 7950778 na SUPER_27 assembled-molecule 27 Chromosome CM036931.1 <> na Primary Assembly 7416271 na SUPER_28 assembled-molecule 28 Chromosome CM036932.1 <> na Primary Assembly 7391111 na SUPER_29 assembled-molecule 29 Chromosome CM036933.1 <> na Primary Assembly 3703963 na SUPER_30 assembled-molecule 30 Chromosome CM036934.1 <> na Primary Assembly 2277785 na SUPER_31 assembled-molecule 31 Chromosome CM036935.1 <> na Primary Assembly 1051076 na SUPER_32 assembled-molecule 32 Chromosome CM036936.1 <> na Primary Assembly 811784 na SUPER_W assembled-molecule W Chromosome CM036937.1 <> na Primary Assembly 5278612 na SUPER_Z assembled-molecule Z Chromosome CM036938.1 <> na Primary Assembly 92514803 na SUPER_W_unloc_13 unlocalized-scaffold W Chromosome JAJHSY010000011.1 <> na Primary Assembly 199704 na SUPER_W_unloc_14 unlocalized-scaffold W Chromosome JAJHSY010000016.1 <> na Primary Assembly 131177 na SUPER_W_unloc_1 unlocalized-scaffold W Chromosome JAJHSY010000128.1 <> na Primary Assembly 2718983 na SUPER_W_unloc_3 unlocalized-scaffold W Chromosome JAJHSY010000135.1 <> na Primary Assembly 1650850 na SUPER_W_unloc_4 unlocalized-scaffold W Chromosome JAJHSY010000137.1 <> na Primary Assembly 1611078 na SUPER_W_unloc_5 unlocalized-scaffold W Chromosome JAJHSY010000140.1 <> na Primary Assembly 1232123 na SUPER_W_unloc_2 unlocalized-scaffold W Chromosome JAJHSY010000141.1 <> na Primary Assembly 2375983 na SUPER_W_unloc_6 unlocalized-scaffold W Chromosome JAJHSY010000148.1 <> na Primary Assembly 963014 na SUPER_W_unloc_7 unlocalized-scaffold W Chromosome JAJHSY010000149.1 <> na Primary Assembly 881820 na SUPER_W_unloc_8 unlocalized-scaffold W Chromosome JAJHSY010000156.1 <> na Primary Assembly 630623 na SUPER_W_unloc_9 unlocalized-scaffold W Chromosome JAJHSY010000157.1 <> na Primary Assembly 612710 na SUPER_W_unloc_10 unlocalized-scaffold W Chromosome JAJHSY010000160.1 <> na Primary Assembly 558139 na SUPER_W_unloc_11 unlocalized-scaffold W Chromosome JAJHSY010000164.1 <> na Primary Assembly 435950 na SUPER_W_unloc_12 unlocalized-scaffold W Chromosome JAJHSY010000172.1 <> na Primary Assembly 293284 na SUPER_Z_unloc_1 unlocalized-scaffold Z Chromosome JAJHSY010000002.1 <> na Primary Assembly 46083 na SUPER_Z_unloc_2 unlocalized-scaffold Z Chromosome JAJHSY010000003.1 <> na Primary Assembly 45309 na SUPER_Z_unloc_3 unlocalized-scaffold Z Chromosome JAJHSY010000004.1 <> na Primary Assembly 32794 na SUPER_Z_unloc_4 unlocalized-scaffold Z Chromosome JAJHSY010000005.1 <> na Primary Assembly 26269 na SUPER_Z_unloc_5 unlocalized-scaffold Z Chromosome JAJHSY010000006.1 <> na Primary Assembly 25768 na scaffold_100_ctg1 unplaced-scaffold na na JAJHSY010000008.1 <> na Primary Assembly 270834 na scaffold_107_ctg1 unplaced-scaffold na na JAJHSY010000009.1 <> na Primary Assembly 212682 na scaffold_111_ctg1 unplaced-scaffold na na JAJHSY010000012.1 <> na Primary Assembly 196947 na scaffold_113_ctg1 unplaced-scaffold na na JAJHSY010000013.1 <> na Primary Assembly 188731 na scaffold_114_ctg1 unplaced-scaffold na na JAJHSY010000014.1 <> na Primary Assembly 182299 na scaffold_123_ctg1 unplaced-scaffold na na JAJHSY010000017.1 <> na Primary Assembly 129168 na scaffold_128_ctg1 unplaced-scaffold na na JAJHSY010000018.1 <> na Primary Assembly 109950 na scaffold_129_ctg1 unplaced-scaffold na na JAJHSY010000019.1 <> na Primary Assembly 109785 na scaffold_131_ctg1 unplaced-scaffold na na JAJHSY010000021.1 <> na Primary Assembly 108248 na scaffold_132_ctg1 unplaced-scaffold na na JAJHSY010000022.1 <> na Primary Assembly 108606 na scaffold_136_ctg1 unplaced-scaffold na na JAJHSY010000023.1 <> na Primary Assembly 97268 na scaffold_138_ctg1 unplaced-scaffold na na JAJHSY010000024.1 <> na Primary Assembly 89746 na scaffold_140_ctg1 unplaced-scaffold na na JAJHSY010000026.1 <> na Primary Assembly 85294 na scaffold_143_ctg1 unplaced-scaffold na na JAJHSY010000027.1 <> na Primary Assembly 78801 na scaffold_144_ctg1 unplaced-scaffold na na JAJHSY010000028.1 <> na Primary Assembly 77472 na scaffold_145_ctg1 unplaced-scaffold na na JAJHSY010000029.1 <> na Primary Assembly 76655 na scaffold_146_ctg1 unplaced-scaffold na na JAJHSY010000030.1 <> na Primary Assembly 75740 na scaffold_148_ctg1 unplaced-scaffold na na JAJHSY010000031.1 <> na Primary Assembly 72380 na scaffold_150_ctg1 unplaced-scaffold na na JAJHSY010000033.1 <> na Primary Assembly 66588 na scaffold_152_ctg1 unplaced-scaffold na na JAJHSY010000034.1 <> na Primary Assembly 64342 na scaffold_153_ctg1 unplaced-scaffold na na JAJHSY010000035.1 <> na Primary Assembly 63656 na scaffold_154_ctg1 unplaced-scaffold na na JAJHSY010000036.1 <> na Primary Assembly 62017 na scaffold_157_ctg1 unplaced-scaffold na na JAJHSY010000037.1 <> na Primary Assembly 59303 na scaffold_158_ctg1 unplaced-scaffold na na JAJHSY010000038.1 <> na Primary Assembly 59258 na scaffold_159_ctg1 unplaced-scaffold na na JAJHSY010000039.1 <> na Primary Assembly 57758 na scaffold_160_ctg1 unplaced-scaffold na na JAJHSY010000041.1 <> na Primary Assembly 56777 na scaffold_162_ctg1 unplaced-scaffold na na JAJHSY010000042.1 <> na Primary Assembly 54854 na scaffold_163_ctg1 unplaced-scaffold na na JAJHSY010000043.1 <> na Primary Assembly 54356 na scaffold_164_ctg1 unplaced-scaffold na na JAJHSY010000044.1 <> na Primary Assembly 53695 na scaffold_165_ctg1 unplaced-scaffold na na JAJHSY010000045.1 <> na Primary Assembly 53466 na scaffold_166_ctg1 unplaced-scaffold na na JAJHSY010000046.1 <> na Primary Assembly 52290 na scaffold_167_ctg1 unplaced-scaffold na na JAJHSY010000047.1 <> na Primary Assembly 51638 na scaffold_169_ctg1 unplaced-scaffold na na JAJHSY010000048.1 <> na Primary Assembly 50312 na scaffold_170_ctg1 unplaced-scaffold na na JAJHSY010000050.1 <> na Primary Assembly 50146 na scaffold_171_ctg1 unplaced-scaffold na na JAJHSY010000051.1 <> na Primary Assembly 49429 na scaffold_172_ctg1 unplaced-scaffold na na JAJHSY010000052.1 <> na Primary Assembly 48640 na scaffold_173_ctg1 unplaced-scaffold na na JAJHSY010000053.1 <> na Primary Assembly 48325 na scaffold_174_ctg1 unplaced-scaffold na na JAJHSY010000054.1 <> na Primary Assembly 47428 na scaffold_175_ctg1 unplaced-scaffold na na JAJHSY010000055.1 <> na Primary Assembly 47156 na scaffold_178_ctg1 unplaced-scaffold na na JAJHSY010000056.1 <> na Primary Assembly 45167 na scaffold_179_ctg1 unplaced-scaffold na na JAJHSY010000057.1 <> na Primary Assembly 44800 na scaffold_180_ctg1 unplaced-scaffold na na JAJHSY010000059.1 <> na Primary Assembly 44300 na scaffold_181_ctg1 unplaced-scaffold na na JAJHSY010000060.1 <> na Primary Assembly 44054 na scaffold_182_ctg1 unplaced-scaffold na na JAJHSY010000061.1 <> na Primary Assembly 42291 na scaffold_183_ctg1 unplaced-scaffold na na JAJHSY010000062.1 <> na Primary Assembly 42197 na scaffold_184_ctg1 unplaced-scaffold na na JAJHSY010000063.1 <> na Primary Assembly 41525 na scaffold_185_ctg1 unplaced-scaffold na na JAJHSY010000064.1 <> na Primary Assembly 41058 na scaffold_186_ctg1 unplaced-scaffold na na JAJHSY010000065.1 <> na Primary Assembly 40189 na scaffold_187_ctg1 unplaced-scaffold na na JAJHSY010000066.1 <> na Primary Assembly 39890 na scaffold_188_ctg1 unplaced-scaffold na na JAJHSY010000067.1 <> na Primary Assembly 39668 na scaffold_189_ctg1 unplaced-scaffold na na JAJHSY010000068.1 <> na Primary Assembly 39035 na scaffold_190_ctg1 unplaced-scaffold na na JAJHSY010000070.1 <> na Primary Assembly 38257 na scaffold_191_ctg1 unplaced-scaffold na na JAJHSY010000071.1 <> na Primary Assembly 36779 na scaffold_192_ctg1 unplaced-scaffold na na JAJHSY010000072.1 <> na Primary Assembly 36090 na scaffold_193_ctg1 unplaced-scaffold na na JAJHSY010000073.1 <> na Primary Assembly 35925 na scaffold_194_ctg1 unplaced-scaffold na na JAJHSY010000074.1 <> na Primary Assembly 35693 na scaffold_195_ctg1 unplaced-scaffold na na JAJHSY010000075.1 <> na Primary Assembly 35668 na scaffold_196_ctg1 unplaced-scaffold na na JAJHSY010000076.1 <> na Primary Assembly 34104 na scaffold_197_ctg1 unplaced-scaffold na na JAJHSY010000077.1 <> na Primary Assembly 34088 na scaffold_198_ctg1 unplaced-scaffold na na JAJHSY010000078.1 <> na Primary Assembly 34015 na scaffold_199_ctg1 unplaced-scaffold na na JAJHSY010000079.1 <> na Primary Assembly 33602 na scaffold_200_ctg1 unplaced-scaffold na na JAJHSY010000082.1 <> na Primary Assembly 33276 na scaffold_201_ctg1 unplaced-scaffold na na JAJHSY010000083.1 <> na Primary Assembly 33269 na scaffold_202_ctg1 unplaced-scaffold na na JAJHSY010000084.1 <> na Primary Assembly 32979 na scaffold_203_ctg1 unplaced-scaffold na na JAJHSY010000085.1 <> na Primary Assembly 32103 na scaffold_205_ctg1 unplaced-scaffold na na JAJHSY010000086.1 <> na Primary Assembly 31481 na scaffold_206_ctg1 unplaced-scaffold na na JAJHSY010000087.1 <> na Primary Assembly 30791 na scaffold_207_ctg1 unplaced-scaffold na na JAJHSY010000088.1 <> na Primary Assembly 30216 na scaffold_208_ctg1 unplaced-scaffold na na JAJHSY010000089.1 <> na Primary Assembly 29861 na scaffold_209_ctg1 unplaced-scaffold na na JAJHSY010000090.1 <> na Primary Assembly 28730 na scaffold_210_ctg1 unplaced-scaffold na na JAJHSY010000092.1 <> na Primary Assembly 28461 na scaffold_211_ctg1 unplaced-scaffold na na JAJHSY010000093.1 <> na Primary Assembly 27929 na scaffold_212_ctg1 unplaced-scaffold na na JAJHSY010000094.1 <> na Primary Assembly 27786 na scaffold_213_ctg1 unplaced-scaffold na na JAJHSY010000095.1 <> na Primary Assembly 26977 na scaffold_214_ctg1 unplaced-scaffold na na JAJHSY010000096.1 <> na Primary Assembly 26838 na scaffold_215_ctg1 unplaced-scaffold na na JAJHSY010000097.1 <> na Primary Assembly 26679 na scaffold_216_ctg1 unplaced-scaffold na na JAJHSY010000098.1 <> na Primary Assembly 26018 na scaffold_218_ctg1 unplaced-scaffold na na JAJHSY010000099.1 <> na Primary Assembly 24701 na scaffold_219_ctg1 unplaced-scaffold na na JAJHSY010000100.1 <> na Primary Assembly 24438 na scaffold_220_ctg1 unplaced-scaffold na na JAJHSY010000102.1 <> na Primary Assembly 23178 na scaffold_221_ctg1 unplaced-scaffold na na JAJHSY010000103.1 <> na Primary Assembly 23103 na scaffold_222_ctg1 unplaced-scaffold na na JAJHSY010000104.1 <> na Primary Assembly 20551 na scaffold_223_ctg1 unplaced-scaffold na na JAJHSY010000105.1 <> na Primary Assembly 18681 na scaffold_224_ctg1 unplaced-scaffold na na JAJHSY010000106.1 <> na Primary Assembly 18566 na scaffold_225_ctg1 unplaced-scaffold na na JAJHSY010000107.1 <> na Primary Assembly 18437 na scaffold_226_ctg1 unplaced-scaffold na na JAJHSY010000108.1 <> na Primary Assembly 17090 na scaffold_227_ctg1 unplaced-scaffold na na JAJHSY010000109.1 <> na Primary Assembly 17034 na scaffold_228_ctg1 unplaced-scaffold na na JAJHSY010000110.1 <> na Primary Assembly 16925 na scaffold_229_ctg1 unplaced-scaffold na na JAJHSY010000111.1 <> na Primary Assembly 16882 na scaffold_230_ctg1 unplaced-scaffold na na JAJHSY010000113.1 <> na Primary Assembly 3912 na scaffold_29_ctg1 unplaced-scaffold na na JAJHSY010000120.1 <> na Primary Assembly 4326848 na S29 unplaced-scaffold na na JAJHSY010000124.1 <> na Primary Assembly 4961870 na S30 unplaced-scaffold na na JAJHSY010000125.1 <> na Primary Assembly 4842099 na scaffold_35_ctg1A unplaced-scaffold na na JAJHSY010000126.1 <> na Primary Assembly 964262 na S31 unplaced-scaffold na na JAJHSY010000127.1 <> na Primary Assembly 3938414 na scaffold_38_ctg1 unplaced-scaffold na na JAJHSY010000129.1 <> na Primary Assembly 2424255 na scaffold_39_ctg1 unplaced-scaffold na na JAJHSY010000130.1 <> na Primary Assembly 2370205 na scaffold_40_ctg1 unplaced-scaffold na na JAJHSY010000132.1 <> na Primary Assembly 2334336 na scaffold_41_ctg1 unplaced-scaffold na na JAJHSY010000133.1 <> na Primary Assembly 1975675 na scaffold_43_ctg1 unplaced-scaffold na na JAJHSY010000134.1 <> na Primary Assembly 1732335 na scaffold_45_ctg1 unplaced-scaffold na na JAJHSY010000136.1 <> na Primary Assembly 1427341 na scaffold_47_ctg1 unplaced-scaffold na na JAJHSY010000138.1 <> na Primary Assembly 1551850 na scaffold_50_ctg1 unplaced-scaffold na na JAJHSY010000139.1 <> na Primary Assembly 1409182 na scaffold_55_ctg1 unplaced-scaffold na na JAJHSY010000142.1 <> na Primary Assembly 1211431 na scaffold_59_ctg1 unplaced-scaffold na na JAJHSY010000143.1 <> na Primary Assembly 1113332 na scaffold_61_ctg1 unplaced-scaffold na na JAJHSY010000144.1 <> na Primary Assembly 1052899 na scaffold_62_ctg1 unplaced-scaffold na na JAJHSY010000145.1 <> na Primary Assembly 1032228 na scaffold_63_ctg1 unplaced-scaffold na na JAJHSY010000146.1 <> na Primary Assembly 991413 na scaffold_64_ctg1 unplaced-scaffold na na JAJHSY010000147.1 <> na Primary Assembly 545730 na scaffold_71_ctg1 unplaced-scaffold na na JAJHSY010000154.1 <> na Primary Assembly 755913 na scaffold_73_ctg1 unplaced-scaffold na na JAJHSY010000155.1 <> na Primary Assembly 732600 na scaffold_84_ctg1 unplaced-scaffold na na JAJHSY010000161.1 <> na Primary Assembly 519743 na scaffold_85_ctg1 unplaced-scaffold na na JAJHSY010000162.1 <> na Primary Assembly 503326 na scaffold_86_ctg1 unplaced-scaffold na na JAJHSY010000163.1 <> na Primary Assembly 322194 na scaffold_88_ctg1 unplaced-scaffold na na JAJHSY010000165.1 <> na Primary Assembly 430829 na scaffold_89_ctg1 unplaced-scaffold na na JAJHSY010000166.1 <> na Primary Assembly 424344 na scaffold_90_ctg1 unplaced-scaffold na na JAJHSY010000168.1 <> na Primary Assembly 395886 na scaffold_91_ctg1 unplaced-scaffold na na JAJHSY010000169.1 <> na Primary Assembly 375387 na scaffold_92_ctg1 unplaced-scaffold na na JAJHSY010000170.1 <> na Primary Assembly 369531 na scaffold_93_ctg1 unplaced-scaffold na na JAJHSY010000171.1 <> na Primary Assembly 353713 na h1tg000195l assembled-molecule MT Mitochondrion CM036939.1 <> na non-nuclear 16988 na