# Assembly name: bCucCan1.pri # Organism name: Cuculus canorus (common cuckoo) # Isolate: bCucCan1 # Sex: female # Taxid: 55661 # BioSample: SAMN12629508 # BioProject: PRJNA562015 # Submitter: Vertebrate Genomes Project # Date: 2021-04-15 # Assembly type: haploid (principal pseudohaplotype of diploid) # Release type: major # Assembly level: Chromosome # Genome representation: full # WGS project: JAGIYT01 # Assembly method: FALCON v. DX 2.0.2; FALCON-Unzip v. DX 8.0.1; purge_dups v. DX 19-08-10; scaff10X v. DX 2.0.3; bionano Solve v. DX 3.4.0; Salsa2 HiC v. DX 2.2.0; pbalign v. 0.3.2; pbgcpp v. 1.9.0; Longranger Align v. DX 2.2.2.1; freebayes v. DX 19-07-11; gEVAL manual curation v. 2021-03-30; VGP assembly pipeline v. 1.5 # Expected final version: no # Genome coverage: 64.31x # Sequencing technology: PacBio Sequel II CLR; Illumina NovaSeq; Arima Genomics Hi-C; Bionano Genomics DLS # RefSeq category: Reference Genome # GenBank assembly accession: GCA_017976375.1 # RefSeq assembly accession: GCF_017976375.1 # RefSeq assembly and GenBank assemblies identical: no # Linked assembly: GCA_017976305.1 (alternate pseudohaplotype of diploid) # ## Assembly-Units: ## GenBank Unit Accession RefSeq Unit Accession Assembly-Unit name ## GCA_017976385.1 GCF_017976385.1 Primary Assembly ## GCA_017976395.1 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 CM030637.1 = NC_071401.1 Primary Assembly 209323829 na SUPER_2 assembled-molecule 2 Chromosome CM030638.1 = NC_071402.1 Primary Assembly 162173298 na SUPER_3 assembled-molecule 3 Chromosome CM030639.1 = NC_071403.1 Primary Assembly 122852502 na SUPER_4 assembled-molecule 4 Chromosome CM030640.1 = NC_071404.1 Primary Assembly 79991235 na SUPER_5 assembled-molecule 5 Chromosome CM030641.1 = NC_071405.1 Primary Assembly 69231175 na SUPER_6 assembled-molecule 6 Chromosome CM030642.1 = NC_071406.1 Primary Assembly 43035276 na SUPER_7 assembled-molecule 7 Chromosome CM030643.1 = NC_071407.1 Primary Assembly 39352363 na SUPER_8 assembled-molecule 8 Chromosome CM030644.1 = NC_071408.1 Primary Assembly 34799447 na SUPER_9 assembled-molecule 9 Chromosome CM030645.1 = NC_071409.1 Primary Assembly 28160375 na SUPER_10 assembled-molecule 10 Chromosome CM030646.1 = NC_071410.1 Primary Assembly 23373056 na SUPER_11 assembled-molecule 11 Chromosome CM030647.1 = NC_071411.1 Primary Assembly 22916006 na SUPER_12 assembled-molecule 12 Chromosome CM030648.1 = NC_071412.1 Primary Assembly 22578743 na SUPER_13 assembled-molecule 13 Chromosome CM030649.1 = NC_071413.1 Primary Assembly 21767650 na SUPER_14 assembled-molecule 14 Chromosome CM030650.1 = NC_071414.1 Primary Assembly 20807676 na SUPER_15 assembled-molecule 15 Chromosome CM030651.1 = NC_071415.1 Primary Assembly 18412470 na SUPER_16 assembled-molecule 16 Chromosome CM030652.1 = NC_071416.1 Primary Assembly 18083484 na SUPER_17 assembled-molecule 17 Chromosome CM030653.1 = NC_071417.1 Primary Assembly 15626348 na SUPER_18 assembled-molecule 18 Chromosome CM030654.1 = NC_071418.1 Primary Assembly 13571377 na SUPER_19 assembled-molecule 19 Chromosome CM030655.1 = NC_071419.1 Primary Assembly 12779522 na SUPER_20 assembled-molecule 20 Chromosome CM030656.1 = NC_071420.1 Primary Assembly 12566544 na SUPER_21 assembled-molecule 21 Chromosome CM030657.1 = NC_071421.1 Primary Assembly 9296794 na SUPER_22 assembled-molecule 22 Chromosome CM030658.1 = NC_071422.1 Primary Assembly 9131761 na SUPER_23 assembled-molecule 23 Chromosome CM030659.1 = NC_071423.1 Primary Assembly 8474506 na SUPER_24 assembled-molecule 24 Chromosome CM030660.1 = NC_071424.1 Primary Assembly 8007972 na SUPER_25 assembled-molecule 25 Chromosome CM030661.1 = NC_071425.1 Primary Assembly 7729152 na SUPER_26 assembled-molecule 26 Chromosome CM030662.1 = NC_071426.1 Primary Assembly 7209170 na SUPER_27 assembled-molecule 27 Chromosome CM030663.1 = NC_071427.1 Primary Assembly 7090994 na SUPER_28 assembled-molecule 28 Chromosome CM030664.1 = NC_071428.1 Primary Assembly 3982923 na SUPER_29 assembled-molecule 29 Chromosome CM030665.1 = NC_071429.1 Primary Assembly 3644481 na SUPER_30 assembled-molecule 30 Chromosome CM030666.1 = NC_071430.1 Primary Assembly 1819002 na SUPER_31 assembled-molecule 31 Chromosome CM030667.1 = NC_071431.1 Primary Assembly 1761595 na SUPER_32 assembled-molecule 32 Chromosome CM030668.1 = NC_071432.1 Primary Assembly 1577804 na SUPER_33 assembled-molecule 33 Chromosome CM030669.1 = NC_071433.1 Primary Assembly 1484757 na SUPER_34 assembled-molecule 34 Chromosome CM030670.1 = NC_071434.1 Primary Assembly 1409890 na SUPER_35 assembled-molecule 35 Chromosome CM030671.1 = NC_071435.1 Primary Assembly 1344321 na SUPER_36 assembled-molecule 36 Chromosome CM030672.1 = NC_071436.1 Primary Assembly 1248072 na SUPER_37 assembled-molecule 37 Chromosome CM030673.1 = NC_071437.1 Primary Assembly 1235818 na SUPER_38 assembled-molecule 38 Chromosome CM030674.1 = NC_071438.1 Primary Assembly 1056872 na SUPER_39 assembled-molecule 39 Chromosome CM030675.1 = NC_071439.1 Primary Assembly 1003585 na SUPER_W assembled-molecule W Chromosome CM030676.1 = NC_071440.1 Primary Assembly 22312972 na SUPER_Z assembled-molecule Z Chromosome CM030677.1 = NC_071441.1 Primary Assembly 78325852 na SUPER_2_unloc_1 unlocalized-scaffold 2 Chromosome JAGIYT010000005.1 = NW_026527752.1 Primary Assembly 64408 na subtelo1 unplaced-scaffold na na JAGIYT010000043.1 = NW_026527860.1 Primary Assembly 1396503 na scaffold_65_arrow_ctg1 unplaced-scaffold na na JAGIYT010000044.1 = NW_026527845.1 Primary Assembly 530816 na scaffold_54_arrow_ctg1 unplaced-scaffold na na JAGIYT010000045.1 = NW_026527841.1 Primary Assembly 508192 na scaffold_62_arrow_ctg1 unplaced-scaffold na na JAGIYT010000046.1 = NW_026527843.1 Primary Assembly 771316 na scaffold_63_arrow_ctg1 unplaced-scaffold na na JAGIYT010000047.1 = NW_026527844.1 Primary Assembly 295228 na scaffold_67_arrow_ctg1a unplaced-scaffold na na JAGIYT010000048.1 = NW_026527846.1 Primary Assembly 335892 na scaffold_68_arrow_ctg1 unplaced-scaffold na na JAGIYT010000049.1 = NW_026527847.1 Primary Assembly 119971 na scaffold_69_arrow_ctg1 unplaced-scaffold na na JAGIYT010000050.1 = NW_026527848.1 Primary Assembly 393257 na scaffold_71_arrow_ctg1 unplaced-scaffold na na JAGIYT010000051.1 = NW_026527849.1 Primary Assembly 373182 na scaffold_73_arrow_ctg1 unplaced-scaffold na na JAGIYT010000052.1 = NW_026527850.1 Primary Assembly 353272 na scaffold_78_arrow_ctg1 unplaced-scaffold na na JAGIYT010000053.1 = NW_026527851.1 Primary Assembly 263990 na scaffold_79_arrow_ctg1 unplaced-scaffold na na JAGIYT010000054.1 = NW_026527852.1 Primary Assembly 245188 na scaffold_82_arrow_ctg1 unplaced-scaffold na na JAGIYT010000055.1 = NW_026527853.1 Primary Assembly 228907 na scaffold_85_arrow_ctg1 unplaced-scaffold na na JAGIYT010000056.1 = NW_026527854.1 Primary Assembly 136714 na scaffold_88_arrow_ctg1 unplaced-scaffold na na JAGIYT010000057.1 = NW_026527855.1 Primary Assembly 190092 na scaffold_91_arrow_ctg1 unplaced-scaffold na na JAGIYT010000058.1 = NW_026527856.1 Primary Assembly 175439 na scaffold_93_arrow_ctg1 unplaced-scaffold na na JAGIYT010000059.1 = NW_026527857.1 Primary Assembly 165713 na scaffold_94_multi_2_16 unplaced-scaffold na na JAGIYT010000060.1 = NW_026527858.1 Primary Assembly 162649 na scaffold_97_arrow_ctg1 unplaced-scaffold na na JAGIYT010000061.1 = NW_026527859.1 Primary Assembly 132978 na scaffold_103_arrow_ctg1 unplaced-scaffold na na JAGIYT010000062.1 = NW_026527753.1 Primary Assembly 108175 na scaffold_105_arrow_ctg1 unplaced-scaffold na na JAGIYT010000063.1 = NW_026527754.1 Primary Assembly 99518 na scaffold_106_arrow_ctg1 unplaced-scaffold na na JAGIYT010000064.1 = NW_026527755.1 Primary Assembly 98199 na scaffold_108_arrow_ctg1 unplaced-scaffold na na JAGIYT010000065.1 = NW_026527756.1 Primary Assembly 91605 na scaffold_111_arrow_ctg1 unplaced-scaffold na na JAGIYT010000066.1 = NW_026527757.1 Primary Assembly 87937 na scaffold_112_arrow_ctg1 unplaced-scaffold na na JAGIYT010000067.1 = NW_026527758.1 Primary Assembly 85354 na scaffold_113_arrow_ctg1 unplaced-scaffold na na JAGIYT010000068.1 = NW_026527759.1 Primary Assembly 80318 na scaffold_114_arrow_ctg1 unplaced-scaffold na na JAGIYT010000069.1 = NW_026527760.1 Primary Assembly 79735 na scaffold_116_arrow_ctg1 unplaced-scaffold na na JAGIYT010000070.1 = NW_026527761.1 Primary Assembly 73757 na scaffold_118_arrow_ctg1 unplaced-scaffold na na JAGIYT010000071.1 = NW_026527762.1 Primary Assembly 71750 na scaffold_119_arrow_ctg1 unplaced-scaffold na na JAGIYT010000072.1 = NW_026527763.1 Primary Assembly 67215 na scaffold_120_arrow_ctg1 unplaced-scaffold na na JAGIYT010000073.1 = NW_026527764.1 Primary Assembly 39114 na scaffold_121_arrow_ctg1 unplaced-scaffold na na JAGIYT010000074.1 = NW_026527765.1 Primary Assembly 64993 na scaffold_123_arrow_ctg1 unplaced-scaffold na na JAGIYT010000075.1 = NW_026527766.1 Primary Assembly 61968 na scaffold_124_arrow_ctg1 unplaced-scaffold na na JAGIYT010000076.1 = NW_026527767.1 Primary Assembly 59730 na scaffold_127_arrow_ctg1 unplaced-scaffold na na JAGIYT010000077.1 = NW_026527768.1 Primary Assembly 50250 na scaffold_130_arrow_ctg1 unplaced-scaffold na na JAGIYT010000078.1 = NW_026527769.1 Primary Assembly 48453 na scaffold_131_arrow_ctg1 unplaced-scaffold na na JAGIYT010000079.1 = NW_026527770.1 Primary Assembly 45552 na scaffold_132_arrow_ctg1 unplaced-scaffold na na JAGIYT010000080.1 = NW_026527771.1 Primary Assembly 45440 na scaffold_133_arrow_ctg1 unplaced-scaffold na na JAGIYT010000081.1 = NW_026527772.1 Primary Assembly 42775 na scaffold_134_arrow_ctg1 unplaced-scaffold na na JAGIYT010000082.1 = NW_026527773.1 Primary Assembly 42404 na scaffold_135_arrow_ctg1 unplaced-scaffold na na JAGIYT010000083.1 = NW_026527774.1 Primary Assembly 41206 na scaffold_136_arrow_ctg1 unplaced-scaffold na na JAGIYT010000084.1 = NW_026527775.1 Primary Assembly 40599 na scaffold_137_arrow_ctg1 unplaced-scaffold na na JAGIYT010000085.1 = NW_026527776.1 Primary Assembly 40900 na scaffold_138_arrow_ctg1 unplaced-scaffold na na JAGIYT010000086.1 = NW_026527777.1 Primary Assembly 40369 na scaffold_5_unloc1 unplaced-scaffold na na JAGIYT010000087.1 = NW_026527842.1 Primary Assembly 40290 na scaffold_140_arrow_ctg1 unplaced-scaffold na na JAGIYT010000088.1 = NW_026527778.1 Primary Assembly 38657 na scaffold_141_arrow_ctg1 unplaced-scaffold na na JAGIYT010000089.1 = NW_026527779.1 Primary Assembly 38204 na scaffold_143_muti_telo unplaced-scaffold na na JAGIYT010000090.1 = NW_026527780.1 Primary Assembly 36357 na scaffold_144_arrow_ctg1 unplaced-scaffold na na JAGIYT010000091.1 = NW_026527781.1 Primary Assembly 34833 na scaffold_146_maybe8 unplaced-scaffold na na JAGIYT010000092.1 = NW_026527782.1 Primary Assembly 31241 na scaffold_147_arrow_ctg1 unplaced-scaffold na na JAGIYT010000093.1 = NW_026527783.1 Primary Assembly 31032 na scaffold_148_arrow_ctg1 unplaced-scaffold na na JAGIYT010000094.1 = NW_026527784.1 Primary Assembly 30401 na scaffold_149_arrow_ctg1 unplaced-scaffold na na JAGIYT010000095.1 = NW_026527785.1 Primary Assembly 30726 na scaffold_150_arrow_ctg1 unplaced-scaffold na na JAGIYT010000096.1 = NW_026527786.1 Primary Assembly 29857 na scaffold_152_arrow_ctg1 unplaced-scaffold na na JAGIYT010000097.1 = NW_026527787.1 Primary Assembly 28406 na scaffold_153_arrow_ctg1 unplaced-scaffold na na JAGIYT010000098.1 = NW_026527788.1 Primary Assembly 28088 na scaffold_155_arrow_ctg1 unplaced-scaffold na na JAGIYT010000099.1 = NW_026527789.1 Primary Assembly 27093 na scaffold_156_arrow_ctg1 unplaced-scaffold na na JAGIYT010000100.1 = NW_026527790.1 Primary Assembly 26798 na scaffold_157_arrow_ctg1 unplaced-scaffold na na JAGIYT010000101.1 = NW_026527791.1 Primary Assembly 25978 na scaffold_158_arrow_ctg1 unplaced-scaffold na na JAGIYT010000102.1 = NW_026527792.1 Primary Assembly 25614 na scaffold_160_arrow_ctg1 unplaced-scaffold na na JAGIYT010000103.1 = NW_026527793.1 Primary Assembly 25135 na scaffold_161_arrow_ctg1 unplaced-scaffold na na JAGIYT010000104.1 = NW_026527794.1 Primary Assembly 24945 na scaffold_163_arrow_ctg1 unplaced-scaffold na na JAGIYT010000105.1 = NW_026527795.1 Primary Assembly 24846 na scaffold_164_arrow_ctg1 unplaced-scaffold na na JAGIYT010000106.1 = NW_026527796.1 Primary Assembly 21768 na scaffold_165_arrow_ctg1 unplaced-scaffold na na JAGIYT010000107.1 = NW_026527797.1 Primary Assembly 22031 na scaffold_166_arrow_ctg1 unplaced-scaffold na na JAGIYT010000108.1 = NW_026527798.1 Primary Assembly 21720 na scaffold_167_arrow_ctg1 unplaced-scaffold na na JAGIYT010000109.1 = NW_026527799.1 Primary Assembly 19702 na scaffold_168_arrow_ctg1 unplaced-scaffold na na JAGIYT010000110.1 = NW_026527800.1 Primary Assembly 19681 na scaffold_169_arrow_ctg1 unplaced-scaffold na na JAGIYT010000111.1 = NW_026527801.1 Primary Assembly 19099 na scaffold_170_arrow_ctg1 unplaced-scaffold na na JAGIYT010000112.1 = NW_026527802.1 Primary Assembly 18732 na scaffold_171_arrow_ctg1 unplaced-scaffold na na JAGIYT010000113.1 = NW_026527803.1 Primary Assembly 17617 na scaffold_172_arrow_ctg1 unplaced-scaffold na na JAGIYT010000114.1 = NW_026527804.1 Primary Assembly 17450 na scaffold_173_arrow_ctg1 unplaced-scaffold na na JAGIYT010000115.1 = NW_026527805.1 Primary Assembly 17451 na scaffold_174_arrow_ctg1 unplaced-scaffold na na JAGIYT010000116.1 = NW_026527806.1 Primary Assembly 17141 na scaffold_175_arrow_ctg1 unplaced-scaffold na na JAGIYT010000117.1 = NW_026527807.1 Primary Assembly 16300 na scaffold_176_arrow_ctg1 unplaced-scaffold na na JAGIYT010000118.1 = NW_026527808.1 Primary Assembly 16195 na scaffold_177_arrow_ctg1 unplaced-scaffold na na JAGIYT010000119.1 = NW_026527809.1 Primary Assembly 15823 na scaffold_178_arrow_ctg1 unplaced-scaffold na na JAGIYT010000120.1 = NW_026527810.1 Primary Assembly 15728 na scaffold_179_arrow_ctg1 unplaced-scaffold na na JAGIYT010000121.1 = NW_026527811.1 Primary Assembly 15117 na scaffold_180_arrow_ctg1 unplaced-scaffold na na JAGIYT010000122.1 = NW_026527812.1 Primary Assembly 14956 na scaffold_181_arrow_ctg1 unplaced-scaffold na na JAGIYT010000123.1 = NW_026527813.1 Primary Assembly 14925 na scaffold_182_arrow_ctg1 unplaced-scaffold na na JAGIYT010000124.1 = NW_026527814.1 Primary Assembly 14127 na scaffold_183_arrow_ctg1 unplaced-scaffold na na JAGIYT010000125.1 = NW_026527815.1 Primary Assembly 13624 na scaffold_184_arrow_ctg1 unplaced-scaffold na na JAGIYT010000126.1 = NW_026527816.1 Primary Assembly 13205 na scaffold_185_arrow_ctg1 unplaced-scaffold na na JAGIYT010000127.1 = NW_026527817.1 Primary Assembly 13086 na scaffold_187_arrow_ctg1 unplaced-scaffold na na JAGIYT010000128.1 = NW_026527818.1 Primary Assembly 12540 na scaffold_188_arrow_ctg1 unplaced-scaffold na na JAGIYT010000129.1 = NW_026527819.1 Primary Assembly 12339 na scaffold_189_arrow_ctg1 unplaced-scaffold na na JAGIYT010000130.1 = NW_026527820.1 Primary Assembly 12553 na scaffold_190_arrow_ctg1 unplaced-scaffold na na JAGIYT010000131.1 = NW_026527821.1 Primary Assembly 10775 na scaffold_191_arrow_ctg1 unplaced-scaffold na na JAGIYT010000132.1 = NW_026527822.1 Primary Assembly 10390 na scaffold_192_arrow_ctg1 unplaced-scaffold na na JAGIYT010000133.1 = NW_026527823.1 Primary Assembly 9823 na scaffold_193_arrow_ctg1 unplaced-scaffold na na JAGIYT010000134.1 = NW_026527824.1 Primary Assembly 9772 na scaffold_194_arrow_ctg1 unplaced-scaffold na na JAGIYT010000135.1 = NW_026527825.1 Primary Assembly 9305 na scaffold_195_arrow_ctg1 unplaced-scaffold na na JAGIYT010000136.1 = NW_026527826.1 Primary Assembly 9191 na scaffold_196_arrow_ctg1 unplaced-scaffold na na JAGIYT010000137.1 = NW_026527827.1 Primary Assembly 9306 na scaffold_197_arrow_ctg1 unplaced-scaffold na na JAGIYT010000138.1 = NW_026527828.1 Primary Assembly 9062 na scaffold_198_arrow_ctg1 unplaced-scaffold na na JAGIYT010000139.1 = NW_026527829.1 Primary Assembly 8776 na scaffold_199_arrow_ctg1 unplaced-scaffold na na JAGIYT010000140.1 = NW_026527830.1 Primary Assembly 8743 na scaffold_200_arrow_ctg1 unplaced-scaffold na na JAGIYT010000141.1 = NW_026527831.1 Primary Assembly 8084 na scaffold_201_arrow_ctg1 unplaced-scaffold na na JAGIYT010000142.1 = NW_026527832.1 Primary Assembly 8264 na scaffold_202_arrow_ctg1 unplaced-scaffold na na JAGIYT010000143.1 = NW_026527833.1 Primary Assembly 8168 na scaffold_203_arrow_ctg1 unplaced-scaffold na na JAGIYT010000144.1 = NW_026527834.1 Primary Assembly 5659 na scaffold_204_arrow_ctg1 unplaced-scaffold na na JAGIYT010000145.1 = NW_026527835.1 Primary Assembly 4968 na scaffold_205_arrow_ctg1 unplaced-scaffold na na JAGIYT010000146.1 = NW_026527836.1 Primary Assembly 3776 na scaffold_206_arrow_ctg1 unplaced-scaffold na na JAGIYT010000147.1 = NW_026527837.1 Primary Assembly 3342 na scaffold_207_arrow_ctg1 unplaced-scaffold na na JAGIYT010000148.1 = NW_026527838.1 Primary Assembly 3143 na scaffold_208_arrow_ctg1 unplaced-scaffold na na JAGIYT010000149.1 = NW_026527839.1 Primary Assembly 2338 na scaffold_209_arrow_ctg1 unplaced-scaffold na na JAGIYT010000150.1 = NW_026527840.1 Primary Assembly 587 na bCucCan1_MT assembled-molecule MT Mitochondrion CM030679.1 <> na non-nuclear 19698 na