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bCucCan1.pri

Organism name:
Cuculus canorus (common cuckoo)
Isolate:
bCucCan1
Sex:
female
BioSample:
SAMN12629508
BioProject:
PRJNA562015
Submitter:
Vertebrate Genomes Project
Date:
2021/04/15
Assembly type:
haploid (principal pseudohaplotype of diploid)
Assembly level:
Chromosome
Genome representation:
full
RefSeq category:
representative genome
GenBank assembly accession:
GCA_017976375.1 (latest)
RefSeq assembly accession:
GCF_017976375.1 (latest)
RefSeq assembly and GenBank assembly identical:
no (hide details)
  • Only in GenBank: chromosome MT
  • Data displayed for RefSeq version
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
Linked assembly:
GCA_017976305.1 (alternate pseudohaplotype of diploid)

IDs: 9844631 [UID] 26270308 [GenBank] 41093498 [RefSeq]

See Genome Information for Cuculus canorus

Pathogen Detection Resources

There are 3 assemblies for this organism

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History (Show revision history)

Comment

Global statistics

Total sequence length1,180,136,575
Total ungapped length1,175,214,260
Gaps between scaffolds0
Number of scaffolds150
Scaffold N5078,325,852
Scaffold L505
Number of contigs446
Contig N5020,797,936
Contig L5017
Total number of chromosomes and plasmids41
Number of component sequences (WGS or clone)150

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Assembly Information

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Global assembly definition

Download the full sequence report
Click on the table row to see sequence details in the table to the right
Assembly Unit Name
Primary Assembly
Assembly Unit: Primary Assembly (GCF_017976385.1)
Molecule nameGenBank sequenceRefSeq sequenceUnlocalized
sequences count
Chromosome 1CM030637.1=NC_071401.10
Chromosome 2CM030638.1=NC_071402.11
Chromosome 3CM030639.1=NC_071403.10
Chromosome 4CM030640.1=NC_071404.10
Chromosome 5CM030641.1=NC_071405.10
Chromosome 6CM030642.1=NC_071406.10
Chromosome 7CM030643.1=NC_071407.10
Chromosome 8CM030644.1=NC_071408.10
Chromosome 9CM030645.1=NC_071409.10
Chromosome 10CM030646.1=NC_071410.10
Chromosome 11CM030647.1=NC_071411.10
Chromosome 12CM030648.1=NC_071412.10
Chromosome 13CM030649.1=NC_071413.10
Chromosome 14CM030650.1=NC_071414.10
Chromosome 15CM030651.1=NC_071415.10
Chromosome 16CM030652.1=NC_071416.10
Chromosome 17CM030653.1=NC_071417.10
Chromosome 18CM030654.1=NC_071418.10
Chromosome 19CM030655.1=NC_071419.10
Chromosome 20CM030656.1=NC_071420.10
Chromosome 21CM030657.1=NC_071421.10
Chromosome 22CM030658.1=NC_071422.10
Chromosome 23CM030659.1=NC_071423.10
Chromosome 24CM030660.1=NC_071424.10
Chromosome 25CM030661.1=NC_071425.10
Chromosome 26CM030662.1=NC_071426.10
Chromosome 27CM030663.1=NC_071427.10
Chromosome 28CM030664.1=NC_071428.10
Chromosome 29CM030665.1=NC_071429.10
Chromosome 30CM030666.1=NC_071430.10
Chromosome 31CM030667.1=NC_071431.10
Chromosome 32CM030668.1=NC_071432.10
Chromosome 33CM030669.1=NC_071433.10
Chromosome 34CM030670.1=NC_071434.10
Chromosome 35CM030671.1=NC_071435.10
Chromosome 36CM030672.1=NC_071436.10
Chromosome 37CM030673.1=NC_071437.10
Chromosome 38CM030674.1=NC_071438.10
Chromosome 39CM030675.1=NC_071439.10
Chromosome WCM030676.1=NC_071440.10
Chromosome ZCM030677.1=NC_071441.10
unplacedn/an/an/a108

Assembly statistics

MoleculeSequence RoleTotal
Length		Scaffold
Count		Ungapped
Length		Scaffold
N50		Spanned
Gaps		Unspanned
Gaps
AllAssembled molecule1,180,136,5751501,175,214,26078,325,8522960
Chromosome 1Assembled molecule209,323,8291208,982,982209,323,829220
Chromosome 2AllAssembled moleculeUnlocalized scaffolds162,237,706162,173,29864,408211162,019,753161,955,84563,908162,173,298162,173,29864,40827261000
Chromosome 3Assembled molecule122,852,5021121,905,932122,852,50270
Chromosome 4Assembled molecule79,991,235179,990,43579,991,23540
Chromosome 5Assembled molecule69,231,175168,955,75469,231,17540
Chromosome 6Assembled molecule43,035,276142,872,40843,035,27650
Chromosome 7Assembled molecule39,352,363139,352,16339,352,36320
Chromosome 8Assembled molecule34,799,447134,777,72634,799,44710
Chromosome 9Assembled molecule28,160,375127,965,75028,160,37520
Chromosome 10Assembled molecule23,373,056122,900,06323,373,05680
Chromosome 11Assembled molecule22,916,006122,915,40622,916,00630
Chromosome 12Assembled molecule22,578,743122,578,54322,578,74310
Chromosome 13Assembled molecule21,767,650121,767,65021,767,65000
Chromosome 14Assembled molecule20,807,676120,807,57620,807,67610
Chromosome 15Assembled molecule18,412,470118,268,90918,412,47020
Chromosome 16Assembled molecule18,083,484117,585,24918,083,48480
Chromosome 17Assembled molecule15,626,348115,626,34815,626,34800
Chromosome 18Assembled molecule13,571,377113,570,77713,571,37720
Chromosome 19Assembled molecule12,779,522112,779,22212,779,52220
Chromosome 20Assembled molecule12,566,544112,566,54412,566,54400
Chromosome 21Assembled molecule9,296,79419,296,2949,296,79410
Chromosome 22Assembled molecule9,131,76118,817,4419,131,76120
Chromosome 23Assembled molecule8,474,50618,474,5068,474,50600
Chromosome 24Assembled molecule8,007,97218,007,5728,007,97220
Chromosome 25Assembled molecule7,729,15217,670,1887,729,15230
Chromosome 26Assembled molecule7,209,17017,132,3537,209,17070
Chromosome 27Assembled molecule7,090,99417,090,4817,090,99450
Chromosome 28Assembled molecule3,982,92313,982,7233,982,92320
Chromosome 29Assembled molecule3,644,48113,643,1813,644,48160
Chromosome 30Assembled molecule1,819,00211,818,6021,819,00230
Chromosome 31Assembled molecule1,761,59511,759,9951,761,59560
Chromosome 32Assembled molecule1,577,80411,574,2041,577,804120
Chromosome 33Assembled molecule1,484,75711,481,2141,484,757110
Chromosome 34Assembled molecule1,409,89011,408,1901,409,89080
Chromosome 35Assembled molecule1,344,32111,343,9211,344,32130
Chromosome 36Assembled molecule1,248,07211,247,1721,248,07240
Chromosome 37Assembled molecule1,235,81811,235,0181,235,81830
Chromosome 38Assembled molecule1,056,87211,056,5721,056,87220
Chromosome 39Assembled molecule1,003,58511,003,3851,003,58510
Chromosome WAssembled molecule22,312,972121,337,35322,312,972180
Chromosome ZAssembled molecule78,325,852178,154,68478,325,852200
unplacedAssembled molecule9,521,4981089,490,021295,228760