# Assembly name: bCotChi1.hap2 # Organism name: Excalfactoria chinensis (birds) # Isolate: bCotChi1 # Sex: male # Taxid: 46218 # BioSample: SAMN41253798 # BioProject: PRJNA1108770 # Submitter: Vertebrate Genomes Project # Date: 2024-05-31 # Assembly type: haploid (haplotype 2) # Release type: major # Assembly level: Chromosome # Genome representation: full # WGS project: JBDMBA01 # Assembly method: Hifiasm + Hi-C phasing v. 0.16.1 + galaxy4; yahs v. 1.2a.2 + galaxy1 # Expected final version: no # Genome coverage: 52.0x # Sequencing technology: PacBio Sequel II HiFi; Arima Hi-C v2 # RefSeq category: Representative Genome # GenBank assembly accession: GCA_039878825.1 # Linked assembly: GCA_039878515.1 (haplotype 1) # ## Assembly-Units: ## GenBank Unit Accession RefSeq Unit Accession Assembly-Unit name ## GCA_039878875.1 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 CM078496.1 <> na Primary Assembly 183816686 na SUPER_2 assembled-molecule 2 Chromosome CM078497.1 <> na Primary Assembly 141754898 na SUPER_3 assembled-molecule 3 Chromosome CM078498.1 <> na Primary Assembly 105162541 na SUPER_4 assembled-molecule 4 Chromosome CM078499.1 <> na Primary Assembly 86361526 na SUPER_5 assembled-molecule 5 Chromosome CM078500.1 <> na Primary Assembly 57419292 na SUPER_6 assembled-molecule 6 Chromosome CM078501.1 <> na Primary Assembly 37708999 na SUPER_7 assembled-molecule 7 Chromosome CM078502.1 <> na Primary Assembly 34800168 na SUPER_8 assembled-molecule 8 Chromosome CM078503.1 <> na Primary Assembly 28131502 na SUPER_9 assembled-molecule 9 Chromosome CM078504.1 <> na Primary Assembly 19795197 na SUPER_10 assembled-molecule 10 Chromosome CM078505.1 <> na Primary Assembly 18938561 na SUPER_11 assembled-molecule 11 Chromosome CM078506.1 <> na Primary Assembly 18388147 na SUPER_12 assembled-molecule 12 Chromosome CM078507.1 <> na Primary Assembly 17991043 na SUPER_13 assembled-molecule 13 Chromosome CM078508.1 <> na Primary Assembly 16166991 na SUPER_14 assembled-molecule 14 Chromosome CM078509.1 <> na Primary Assembly 13636729 na SUPER_15 assembled-molecule 15 Chromosome CM078510.1 <> na Primary Assembly 12969056 na SUPER_16 assembled-molecule 16 Chromosome CM078511.1 <> na Primary Assembly 11730520 na SUPER_17 assembled-molecule 17 Chromosome CM078512.1 <> na Primary Assembly 9891760 na SUPER_18 assembled-molecule 18 Chromosome CM078513.1 <> na Primary Assembly 9217317 na SUPER_19 assembled-molecule 19 Chromosome CM078514.1 <> na Primary Assembly 8969914 na SUPER_20 assembled-molecule 20 Chromosome CM078515.1 <> na Primary Assembly 6368800 na SUPER_21 assembled-molecule 21 Chromosome CM078516.1 <> na Primary Assembly 5924505 na SUPER_22 assembled-molecule 22 Chromosome CM078517.1 <> na Primary Assembly 5289257 na SUPER_23 assembled-molecule 23 Chromosome CM078518.1 <> na Primary Assembly 4220735 na SUPER_24 assembled-molecule 24 Chromosome CM078519.1 <> na Primary Assembly 4582368 na SUPER_25 assembled-molecule 25 Chromosome CM078520.1 <> na Primary Assembly 4056396 na SUPER_26 assembled-molecule 26 Chromosome CM078521.1 <> na Primary Assembly 2260391 na SUPER_27 assembled-molecule 27 Chromosome CM078522.1 <> na Primary Assembly 1173491 na SUPER_28 assembled-molecule 28 Chromosome CM078523.1 <> na Primary Assembly 1772183 na SUPER_29 assembled-molecule 29 Chromosome CM078524.1 <> na Primary Assembly 963199 na SUPER_30 assembled-molecule 30 Chromosome CM078525.1 <> na Primary Assembly 849968 na SUPER_31 assembled-molecule 31 Chromosome CM078526.1 <> na Primary Assembly 1144065 na SUPER_32 assembled-molecule 32 Chromosome CM078527.1 <> na Primary Assembly 1127101 na SUPER_Z assembled-molecule Z Chromosome CM078528.1 <> na Primary Assembly 75051344 na SUPER_1_unloc_1 unlocalized-scaffold 1 Chromosome JBDMBA010000057.1 <> na Primary Assembly 147757 na SUPER_1_unloc_2 unlocalized-scaffold 1 Chromosome JBDMBA010000058.1 <> na Primary Assembly 137334 na SUPER_1_unloc_3 unlocalized-scaffold 1 Chromosome JBDMBA010000064.1 <> na Primary Assembly 113809 na SUPER_2_unloc_1 unlocalized-scaffold 2 Chromosome JBDMBA010000051.1 <> na Primary Assembly 207078 na SUPER_14_unloc_1 unlocalized-scaffold 14 Chromosome JBDMBA010000086.1 <> na Primary Assembly 70626 na SUPER_Z_unloc_1 unlocalized-scaffold Z Chromosome JBDMBA010000030.1 <> na Primary Assembly 1532350 na SUPER_Z_unloc_2 unlocalized-scaffold Z Chromosome JBDMBA010000037.1 <> na Primary Assembly 789929 na SUPER_Z_unloc_3 unlocalized-scaffold Z Chromosome JBDMBA010000038.1 <> na Primary Assembly 758220 na SUPER_Z_unloc_4 unlocalized-scaffold Z Chromosome JBDMBA010000040.1 <> na Primary Assembly 588137 na SUPER_Z_unloc_5 unlocalized-scaffold Z Chromosome JBDMBA010000043.1 <> na Primary Assembly 376858 na SUPER_Z_unloc_6 unlocalized-scaffold Z Chromosome JBDMBA010000044.1 <> na Primary Assembly 375744 na SUPER_Z_unloc_9 unlocalized-scaffold Z Chromosome JBDMBA010000046.1 <> na Primary Assembly 328024 na SUPER_Z_unloc_10 unlocalized-scaffold Z Chromosome JBDMBA010000047.1 <> na Primary Assembly 324475 na SUPER_Z_unloc_11 unlocalized-scaffold Z Chromosome JBDMBA010000053.1 <> na Primary Assembly 160491 na SUPER_Z_unloc_7 unlocalized-scaffold Z Chromosome JBDMBA010000056.1 <> na Primary Assembly 153000 na SUPER_Z_unloc_8 unlocalized-scaffold Z Chromosome JBDMBA010000061.1 <> na Primary Assembly 123527 na Scaffold_85 unplaced-scaffold na na JBDMBA010000029.1 <> na Primary Assembly 1603572 na Scaffold_68 unplaced-scaffold na na JBDMBA010000031.1 <> na Primary Assembly 1468237 na Scaffold_84 unplaced-scaffold na na JBDMBA010000039.1 <> na Primary Assembly 699237 na Scaffold_81 unplaced-scaffold na na JBDMBA010000041.1 <> na Primary Assembly 538338 na Scaffold_71 unplaced-scaffold na na JBDMBA010000042.1 <> na Primary Assembly 468147 na Scaffold_82 unplaced-scaffold na na JBDMBA010000045.1 <> na Primary Assembly 356734 na Scaffold_74 unplaced-scaffold na na JBDMBA010000048.1 <> na Primary Assembly 294038 na Scaffold_88 unplaced-scaffold na na JBDMBA010000049.1 <> na Primary Assembly 227256 na Scaffold_331 unplaced-scaffold na na JBDMBA010000050.1 <> na Primary Assembly 222628 na Scaffold_72 unplaced-scaffold na na JBDMBA010000052.1 <> na Primary Assembly 200750 na Scaffold_324 unplaced-scaffold na na JBDMBA010000054.1 <> na Primary Assembly 157110 na Scaffold_325 unplaced-scaffold na na JBDMBA010000055.1 <> na Primary Assembly 154519 na Scaffold_326 unplaced-scaffold na na JBDMBA010000059.1 <> na Primary Assembly 127464 na Scaffold_327 unplaced-scaffold na na JBDMBA010000060.1 <> na Primary Assembly 124824 na Scaffold_328 unplaced-scaffold na na JBDMBA010000062.1 <> na Primary Assembly 122722 na Scaffold_329 unplaced-scaffold na na JBDMBA010000063.1 <> na Primary Assembly 114527 na Scaffold_332 unplaced-scaffold na na JBDMBA010000065.1 <> na Primary Assembly 107855 na Scaffold_330 unplaced-scaffold na na JBDMBA010000066.1 <> na Primary Assembly 107749 na Scaffold_333 unplaced-scaffold na na JBDMBA010000067.1 <> na Primary Assembly 106856 na Scaffold_335 unplaced-scaffold na na JBDMBA010000068.1 <> na Primary Assembly 105642 na Scaffold_339 unplaced-scaffold na na JBDMBA010000069.1 <> na Primary Assembly 102644 na Scaffold_336 unplaced-scaffold na na JBDMBA010000070.1 <> na Primary Assembly 98979 na Scaffold_337 unplaced-scaffold na na JBDMBA010000071.1 <> na Primary Assembly 98526 na Scaffold_338 unplaced-scaffold na na JBDMBA010000072.1 <> na Primary Assembly 97566 na Scaffold_340 unplaced-scaffold na na JBDMBA010000073.1 <> na Primary Assembly 96879 na Scaffold_341 unplaced-scaffold na na JBDMBA010000074.1 <> na Primary Assembly 96319 na Scaffold_342 unplaced-scaffold na na JBDMBA010000075.1 <> na Primary Assembly 94103 na Scaffold_343 unplaced-scaffold na na JBDMBA010000076.1 <> na Primary Assembly 93833 na Scaffold_344 unplaced-scaffold na na JBDMBA010000077.1 <> na Primary Assembly 92309 na Scaffold_345 unplaced-scaffold na na JBDMBA010000078.1 <> na Primary Assembly 84699 na Scaffold_346 unplaced-scaffold na na JBDMBA010000079.1 <> na Primary Assembly 82990 na Scaffold_347 unplaced-scaffold na na JBDMBA010000080.1 <> na Primary Assembly 82756 na Scaffold_348 unplaced-scaffold na na JBDMBA010000081.1 <> na Primary Assembly 81698 na Scaffold_349 unplaced-scaffold na na JBDMBA010000082.1 <> na Primary Assembly 78762 na Scaffold_350 unplaced-scaffold na na JBDMBA010000083.1 <> na Primary Assembly 73998 na Scaffold_351 unplaced-scaffold na na JBDMBA010000084.1 <> na Primary Assembly 71269 na Scaffold_352 unplaced-scaffold na na JBDMBA010000085.1 <> na Primary Assembly 70944 na Scaffold_353 unplaced-scaffold na na JBDMBA010000087.1 <> na Primary Assembly 70367 na Scaffold_354 unplaced-scaffold na na JBDMBA010000088.1 <> na Primary Assembly 69413 na Scaffold_355 unplaced-scaffold na na JBDMBA010000089.1 <> na Primary Assembly 68910 na Scaffold_356 unplaced-scaffold na na JBDMBA010000090.1 <> na Primary Assembly 68825 na Scaffold_357 unplaced-scaffold na na JBDMBA010000091.1 <> na Primary Assembly 68654 na Scaffold_358 unplaced-scaffold na na JBDMBA010000092.1 <> na Primary Assembly 65636 na Scaffold_359 unplaced-scaffold na na JBDMBA010000093.1 <> na Primary Assembly 64977 na Scaffold_360 unplaced-scaffold na na JBDMBA010000094.1 <> na Primary Assembly 63822 na Scaffold_361 unplaced-scaffold na na JBDMBA010000095.1 <> na Primary Assembly 63581 na Scaffold_362 unplaced-scaffold na na JBDMBA010000096.1 <> na Primary Assembly 63450 na Scaffold_363 unplaced-scaffold na na JBDMBA010000097.1 <> na Primary Assembly 59730 na Scaffold_364 unplaced-scaffold na na JBDMBA010000098.1 <> na Primary Assembly 58804 na Scaffold_365 unplaced-scaffold na na JBDMBA010000099.1 <> na Primary Assembly 57597 na Scaffold_366 unplaced-scaffold na na JBDMBA010000100.1 <> na Primary Assembly 57574 na Scaffold_367 unplaced-scaffold na na JBDMBA010000101.1 <> na Primary Assembly 56372 na Scaffold_368 unplaced-scaffold na na JBDMBA010000102.1 <> na Primary Assembly 55192 na Scaffold_369 unplaced-scaffold na na JBDMBA010000103.1 <> na Primary Assembly 55089 na Scaffold_370 unplaced-scaffold na na JBDMBA010000104.1 <> na Primary Assembly 54800 na Scaffold_372 unplaced-scaffold na na JBDMBA010000105.1 <> na Primary Assembly 54211 na Scaffold_371 unplaced-scaffold na na JBDMBA010000106.1 <> na Primary Assembly 52941 na Scaffold_981 unplaced-scaffold na na JBDMBA010000107.1 <> na Primary Assembly 52829 na Scaffold_374 unplaced-scaffold na na JBDMBA010000108.1 <> na Primary Assembly 52353 na Scaffold_373 unplaced-scaffold na na JBDMBA010000109.1 <> na Primary Assembly 51724 na Scaffold_375 unplaced-scaffold na na JBDMBA010000110.1 <> na Primary Assembly 51010 na Scaffold_376 unplaced-scaffold na na JBDMBA010000111.1 <> na Primary Assembly 50979 na Scaffold_377 unplaced-scaffold na na JBDMBA010000112.1 <> na Primary Assembly 49682 na Scaffold_987 unplaced-scaffold na na JBDMBA010000113.1 <> na Primary Assembly 49254 na Scaffold_378 unplaced-scaffold na na JBDMBA010000114.1 <> na Primary Assembly 48885 na Scaffold_379 unplaced-scaffold na na JBDMBA010000115.1 <> na Primary Assembly 48599 na Scaffold_380 unplaced-scaffold na na JBDMBA010000116.1 <> na Primary Assembly 48342 na Scaffold_381 unplaced-scaffold na na JBDMBA010000117.1 <> na Primary Assembly 48267 na Scaffold_382 unplaced-scaffold na na JBDMBA010000118.1 <> na Primary Assembly 48223 na Scaffold_383 unplaced-scaffold na na JBDMBA010000119.1 <> na Primary Assembly 47413 na Scaffold_994 unplaced-scaffold na na JBDMBA010000120.1 <> na Primary Assembly 47402 na Scaffold_384 unplaced-scaffold na na JBDMBA010000121.1 <> na Primary Assembly 46943 na Scaffold_385 unplaced-scaffold na na JBDMBA010000122.1 <> na Primary Assembly 45695 na Scaffold_386 unplaced-scaffold na na JBDMBA010000123.1 <> na Primary Assembly 45287 na Scaffold_998 unplaced-scaffold na na JBDMBA010000124.1 <> na Primary Assembly 45175 na Scaffold_387 unplaced-scaffold na na JBDMBA010000125.1 <> na Primary Assembly 44942 na Scaffold_388 unplaced-scaffold na na JBDMBA010000126.1 <> na Primary Assembly 43955 na Scaffold_389 unplaced-scaffold na na JBDMBA010000127.1 <> na Primary Assembly 43693 na Scaffold_1002 unplaced-scaffold na na JBDMBA010000128.1 <> na Primary Assembly 43456 na Scaffold_390 unplaced-scaffold na na JBDMBA010000129.1 <> na Primary Assembly 42948 na Scaffold_391 unplaced-scaffold na na JBDMBA010000130.1 <> na Primary Assembly 42857 na Scaffold_1005 unplaced-scaffold na na JBDMBA010000131.1 <> na Primary Assembly 42250 na Scaffold_392 unplaced-scaffold na na JBDMBA010000132.1 <> na Primary Assembly 40992 na Scaffold_393 unplaced-scaffold na na JBDMBA010000133.1 <> na Primary Assembly 40146 na Scaffold_1008 unplaced-scaffold na na JBDMBA010000134.1 <> na Primary Assembly 40098 na Scaffold_394 unplaced-scaffold na na JBDMBA010000135.1 <> na Primary Assembly 39748 na Scaffold_395 unplaced-scaffold na na JBDMBA010000136.1 <> na Primary Assembly 38462 na Scaffold_1011 unplaced-scaffold na na JBDMBA010000137.1 <> na Primary Assembly 38228 na Scaffold_396 unplaced-scaffold na na JBDMBA010000138.1 <> na Primary Assembly 38130 na Scaffold_334 unplaced-scaffold na na JBDMBA010000139.1 <> na Primary Assembly 37845 na Scaffold_1014 unplaced-scaffold na na JBDMBA010000140.1 <> na Primary Assembly 37640 na Scaffold_397 unplaced-scaffold na na JBDMBA010000141.1 <> na Primary Assembly 36584 na Scaffold_398 unplaced-scaffold na na JBDMBA010000142.1 <> na Primary Assembly 36476 na Scaffold_1018 unplaced-scaffold na na JBDMBA010000143.1 <> na Primary Assembly 36143 na Scaffold_399 unplaced-scaffold na na JBDMBA010000144.1 <> na Primary Assembly 35577 na Scaffold_1020 unplaced-scaffold na na JBDMBA010000145.1 <> na Primary Assembly 34358 na Scaffold_400 unplaced-scaffold na na JBDMBA010000146.1 <> na Primary Assembly 34032 na Scaffold_1022 unplaced-scaffold na na JBDMBA010000147.1 <> na Primary Assembly 33973 na Scaffold_401 unplaced-scaffold na na JBDMBA010000148.1 <> na Primary Assembly 33862 na Scaffold_1024 unplaced-scaffold na na JBDMBA010000149.1 <> na Primary Assembly 33765 na Scaffold_402 unplaced-scaffold na na JBDMBA010000150.1 <> na Primary Assembly 33608 na Scaffold_1026 unplaced-scaffold na na JBDMBA010000151.1 <> na Primary Assembly 32669 na Scaffold_403 unplaced-scaffold na na JBDMBA010000152.1 <> na Primary Assembly 32634 na Scaffold_1028 unplaced-scaffold na na JBDMBA010000153.1 <> na Primary Assembly 32403 na Scaffold_404 unplaced-scaffold na na JBDMBA010000154.1 <> na Primary Assembly 32375 na Scaffold_1030 unplaced-scaffold na na JBDMBA010000155.1 <> na Primary Assembly 32110 na Scaffold_405 unplaced-scaffold na na JBDMBA010000156.1 <> na Primary Assembly 32012 na Scaffold_406 unplaced-scaffold na na JBDMBA010000157.1 <> na Primary Assembly 31265 na Scaffold_1033 unplaced-scaffold na na JBDMBA010000158.1 <> na Primary Assembly 30754 na Scaffold_407 unplaced-scaffold na na JBDMBA010000159.1 <> na Primary Assembly 30751 na Scaffold_1035 unplaced-scaffold na na JBDMBA010000160.1 <> na Primary Assembly 30736 na Scaffold_408 unplaced-scaffold na na JBDMBA010000161.1 <> na Primary Assembly 30609 na Scaffold_1037 unplaced-scaffold na na JBDMBA010000162.1 <> na Primary Assembly 30069 na Scaffold_409 unplaced-scaffold na na JBDMBA010000163.1 <> na Primary Assembly 29447 na Scaffold_1039 unplaced-scaffold na na JBDMBA010000164.1 <> na Primary Assembly 29280 na Scaffold_410 unplaced-scaffold na na JBDMBA010000165.1 <> na Primary Assembly 28711 na Scaffold_1041 unplaced-scaffold na na JBDMBA010000166.1 <> na Primary Assembly 28572 na Scaffold_411 unplaced-scaffold na na JBDMBA010000167.1 <> na Primary Assembly 28484 na Scaffold_412 unplaced-scaffold na na JBDMBA010000168.1 <> na Primary Assembly 28451 na Scaffold_1044 unplaced-scaffold na na JBDMBA010000169.1 <> na Primary Assembly 27887 na Scaffold_1045 unplaced-scaffold na na JBDMBA010000170.1 <> na Primary Assembly 27707 na Scaffold_413 unplaced-scaffold na na JBDMBA010000171.1 <> na Primary Assembly 27539 na Scaffold_1047 unplaced-scaffold na na JBDMBA010000172.1 <> na Primary Assembly 27513 na Scaffold_1048 unplaced-scaffold na na JBDMBA010000173.1 <> na Primary Assembly 27471 na Scaffold_414 unplaced-scaffold na na JBDMBA010000174.1 <> na Primary Assembly 27198 na Scaffold_1050 unplaced-scaffold na na JBDMBA010000175.1 <> na Primary Assembly 26789 na Scaffold_415 unplaced-scaffold na na JBDMBA010000176.1 <> na Primary Assembly 25917 na Scaffold_1052 unplaced-scaffold na na JBDMBA010000177.1 <> na Primary Assembly 25660 na Scaffold_416 unplaced-scaffold na na JBDMBA010000178.1 <> na Primary Assembly 25183 na Scaffold_1054 unplaced-scaffold na na JBDMBA010000179.1 <> na Primary Assembly 24768 na Scaffold_1055 unplaced-scaffold na na JBDMBA010000180.1 <> na Primary Assembly 24050 na Scaffold_417 unplaced-scaffold na na JBDMBA010000181.1 <> na Primary Assembly 23991 na Scaffold_1057 unplaced-scaffold na na JBDMBA010000182.1 <> na Primary Assembly 23787 na Scaffold_418 unplaced-scaffold na na JBDMBA010000183.1 <> na Primary Assembly 23326 na Scaffold_1059 unplaced-scaffold na na JBDMBA010000184.1 <> na Primary Assembly 23063 na Scaffold_1060 unplaced-scaffold na na JBDMBA010000185.1 <> na Primary Assembly 22866 na Scaffold_419 unplaced-scaffold na na JBDMBA010000186.1 <> na Primary Assembly 22638 na Scaffold_1062 unplaced-scaffold na na JBDMBA010000187.1 <> na Primary Assembly 22327 na Scaffold_420 unplaced-scaffold na na JBDMBA010000188.1 <> na Primary Assembly 20140 na Scaffold_1064 unplaced-scaffold na na JBDMBA010000189.1 <> na Primary Assembly 19470 na Scaffold_1065 unplaced-scaffold na na JBDMBA010000190.1 <> na Primary Assembly 19001 na Scaffold_421 unplaced-scaffold na na JBDMBA010000191.1 <> na Primary Assembly 17297 na