U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Download Assembly



bCinCin1.1

Organism name:
Cinclus cinclus (white-throated dipper)
BioSample:
SAMEA9679959
BioProject:
PRJEB68422
Submitter:
WELLCOME SANGER INSTITUTE
Date:
2023/12/11
Assembly type:
haploid (principal pseudohaplotype of diploid)
Assembly level:
Chromosome
Genome representation:
full
RefSeq category:
representative genome
GenBank assembly accession:
GCA_963662255.1 (latest)
RefSeq assembly accession:
GCF_963662255.1 (latest)
RefSeq assembly and GenBank assembly identical:
no (hide details)
  • Only in GenBank: chromosome MT
  • Data displayed for RefSeq version
WGS Project:
CAVLEW01
Assembly method:
various
Genome coverage:
41x
Sequencing technology:
PacBio,Arima2
Linked assembly:
GCA_963662415.1 (alternate pseudohaplotype of diploid)

IDs: 20123391 [UID] 50977688 [GenBank] 52797478 [RefSeq]

See Genome Information for Cinclus cinclus

Pathogen Detection Resources

There are 2 assemblies for this organism

See more

History (Show revision history)

Comment

The assembly bCinCin1.1 is based on 41x PacBio data and Arima2 Hi-C data generated by the Darwin Tree of Life Project
(https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation ... with purge_dups, and Hi-C based scaffolding with YaHS. The mitochondrial genome was assembled using MitoHiFi. Finally, the primary assembly was analysed and manually improved using gEVAL. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size. Z chromosome identifed based on synteny with Taeniopygia guttata (GCA_003957565.4).  more

Global statistics

Total sequence length1,170,837,027
Total ungapped length1,170,705,427
Gaps between scaffolds0
Number of scaffolds277
Scaffold N5074,357,285
Scaffold L506
Number of contigs935
Contig N503,563,180
Contig L50103
Total number of chromosomes and plasmids39
Number of component sequences (WGS or clone)277

Supplemental Content

Access the data

Assembly Information

Related Information

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...

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_963662254.1)
Molecule nameGenBank sequenceRefSeq sequenceUnlocalized
sequences count
Chromosome 1OY759677.1=NC_085046.13
Chromosome 2OY759678.1=NC_085047.10
Chromosome 3OY759679.1=NC_085048.10
Chromosome 4OY759681.1=NC_085049.10
Chromosome 5OY759682.1=NC_085050.10
Chromosome 6OY759683.1=NC_085051.10
Chromosome 7OY759684.1=NC_085052.10
Chromosome 8OY759685.1=NC_085053.10
Chromosome 9OY759686.1=NC_085054.10
Chromosome 10OY759687.1=NC_085055.10
Chromosome 11OY759688.1=NC_085056.10
Chromosome 12OY759689.1=NC_085057.10
Chromosome 13OY759690.1=NC_085058.10
Chromosome 14OY759691.1=NC_085059.10
Chromosome 15OY759692.1=NC_085060.10
Chromosome 16OY759693.1=NC_085061.10
Chromosome 17OY759694.1=NC_085062.10
Chromosome 18OY759695.1=NC_085063.10
Chromosome 19OY759696.1=NC_085064.10
Chromosome 20OY759697.1=NC_085065.10
Chromosome 21OY759698.1=NC_085066.10
Chromosome 22OY759699.1=NC_085067.10
Chromosome 23OY759700.1=NC_085068.10
Chromosome 24OY759701.1=NC_085069.10
Chromosome 25OY759702.1=NC_085070.10
Chromosome 26OY759703.1=NC_085071.10
Chromosome 27OY759704.1=NC_085072.10
Chromosome 28OY759705.1=NC_085073.10
Chromosome 29OY759706.1=NC_085074.10
Chromosome 30OY759707.1=NC_085075.10
Chromosome 31OY759708.1=NC_085076.10
Chromosome 32OY759709.1=NC_085077.10
Chromosome 33OY759710.1=NC_085078.10
Chromosome 34OY759711.1=NC_085079.10
Chromosome 35OY759712.1=NC_085080.10
Chromosome 36OY759713.1=NC_085081.10
Chromosome 37OY759714.1=NC_085082.10
Chromosome 38OY759715.1=NC_085083.10
Chromosome ZOY759680.1=NC_085084.11
unplacedn/an/an/a234

Assembly statistics

MoleculeSequence RoleTotal
Length		Scaffold
Count		Ungapped
Length		Scaffold
N50		Spanned
Gaps		Unspanned
Gaps
AllAssembled molecule1,170,837,0272771,170,705,42774,357,2856580
Chromosome 1AllAssembled moleculeUnlocalized scaffolds152,574,333152,364,536209,797413152,561,133152,351,336209,797152,364,536152,364,53662,33866660000
Chromosome 2Assembled molecule117,953,1031117,943,303117,953,103490
Chromosome 3Assembled molecule117,726,6421117,713,242117,726,642670
Chromosome 4Assembled molecule74,413,991174,406,79174,413,991360
Chromosome 5Assembled molecule74,357,285174,352,08574,357,285260
Chromosome 6Assembled molecule62,870,128162,866,52862,870,128180
Chromosome 7Assembled molecule38,628,102138,625,70238,628,102120
Chromosome 8Assembled molecule30,975,208130,972,60830,975,208130
Chromosome 9Assembled molecule29,524,111129,521,51129,524,111130
Chromosome 10Assembled molecule27,245,051127,243,45127,245,05180
Chromosome 11Assembled molecule25,571,644125,570,04425,571,64480
Chromosome 12Assembled molecule22,056,645122,053,64522,056,645150
Chromosome 13Assembled molecule21,998,194121,996,39421,998,19490
Chromosome 14Assembled molecule21,630,564121,627,36421,630,564160
Chromosome 15Assembled molecule21,027,773121,025,97321,027,77390
Chromosome 16Assembled molecule17,499,973117,499,37317,499,97330
Chromosome 17Assembled molecule15,980,085115,979,08515,980,08550
Chromosome 18Assembled molecule15,801,390115,798,99015,801,390120
Chromosome 19Assembled molecule12,779,978112,778,97812,779,97850
Chromosome 20Assembled molecule12,672,844112,671,24412,672,84480
Chromosome 21Assembled molecule11,600,337111,598,93711,600,33770
Chromosome 22Assembled molecule11,484,647111,484,04711,484,64730
Chromosome 23Assembled molecule9,728,71519,726,9159,728,71590
Chromosome 24Assembled molecule8,453,29318,452,0938,453,29360
Chromosome 25Assembled molecule8,395,46218,394,4628,395,46250
Chromosome 26Assembled molecule8,299,35518,298,1558,299,35560
Chromosome 27Assembled molecule7,978,77017,978,1707,978,77030
Chromosome 28Assembled molecule7,297,47017,296,4707,297,47050
Chromosome 29Assembled molecule5,328,29615,326,8965,328,29670
Chromosome 30Assembled molecule4,618,59514,616,7954,618,59590
Chromosome 31Assembled molecule4,099,61214,097,0124,099,612130
Chromosome 32Assembled molecule3,794,65813,790,8583,794,658190
Chromosome 33Assembled molecule3,344,34213,340,9423,344,342170
Chromosome 34Assembled molecule1,580,41011,577,4101,580,410150
Chromosome 35Assembled molecule1,346,32111,344,1211,346,321110
Chromosome 36Assembled molecule1,304,97911,300,3791,304,979230
Chromosome 37Assembled molecule1,135,37311,131,9731,135,373170
Chromosome 38Assembled molecule742,9561740,756742,956110
Chromosome ZAllAssembled moleculeUnlocalized scaffolds85,428,01485,376,93751,07721185,413,41485,362,33751,07785,376,93785,376,93751,07773730000
unplacedAssembled molecule71,588,37823471,588,178780,00010