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bPhaCar2.1

Organism name:
Phalacrocorax carbo (great cormorant)
BioSample:
SAMEA8228692
BioProject:
PRJEB71801
Submitter:
WELLCOME SANGER INSTITUTE
Date:
2024/02/09
Assembly type:
haploid (principal pseudohaplotype of diploid)
Assembly level:
Chromosome
Genome representation:
full
RefSeq category:
representative genome
GenBank assembly accession:
GCA_963921805.1 (latest)
RefSeq assembly accession:
GCF_963921805.1 (latest)
RefSeq assembly and GenBank assembly identical:
no (hide details)
  • Only in GenBank: chromosome MT
  • Data displayed for RefSeq version
WGS Project:
CAWUGV01
Assembly method:
various
Genome coverage:
40x
Sequencing technology:
PacBio,Arima2
Linked assembly:
GCA_963921815.1 (alternate pseudohaplotype of diploid)

IDs: 21309311 [UID] 53625498 [GenBank] 56119408 [RefSeq]

See Genome Information for Phalacrocorax carbo

Pathogen Detection Resources

There are 3 assemblies for this organism

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History (Show revision history)

Comment

The assembly bPhaCar2.1 is based on 40x 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. It was not possible to assemble the W chromosome in this assembly as although the sequence data is from a female the HiC data was from a male.  more

Global statistics

Total sequence length1,283,623,959
Total ungapped length1,283,525,359
Gaps between scaffolds0
Number of scaffolds350
Scaffold N5084,621,172
Scaffold L505
Number of contigs843
Contig N504,631,399
Contig L5084
Total number of chromosomes and plasmids36
Number of component sequences (WGS or clone)350

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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_963921804.1)
Molecule nameGenBank sequenceRefSeq sequenceUnlocalized
sequences count
Chromosome 1OY997601.1=NC_087513.10
Chromosome 2OY997602.1=NC_087514.10
Chromosome 3OY997603.1=NC_087515.10
Chromosome 4OY997605.1=NC_087516.10
Chromosome 5OY997606.1=NC_087517.10
Chromosome 6OY997607.1=NC_087518.10
Chromosome 7OY997608.1=NC_087519.10
Chromosome 8OY997609.1=NC_087520.10
Chromosome 9OY997610.1=NC_087521.10
Chromosome 10OY997611.1=NC_087522.10
Chromosome 11OY997612.1=NC_087523.10
Chromosome 12OY997613.1=NC_087524.10
Chromosome 13OY997615.1=NC_087525.10
Chromosome 14OY997616.1=NC_087526.10
Chromosome 15OY997617.1=NC_087527.10
Chromosome 16OY997618.1=NC_087528.10
Chromosome 17OY997619.1=NC_087529.10
Chromosome 18OY997620.1=NC_087530.10
Chromosome 19OY997621.1=NC_087531.10
Chromosome 20OY997622.1=NC_087532.10
Chromosome 21OY997623.1=NC_087533.10
Chromosome 22OY997624.1=NC_087534.10
Chromosome 23OY997625.1=NC_087535.10
Chromosome 24OY997626.1=NC_087536.10
Chromosome 25OY997627.1=NC_087537.10
Chromosome 26OY997628.1=NC_087538.10
Chromosome 27OY997629.1=NC_087539.10
Chromosome 28OY997630.1=NC_087540.10
Chromosome 29OY997631.1=NC_087541.15
Chromosome 30OY997632.1=NC_087542.13
Chromosome 31OY997633.1=NC_087543.14
Chromosome 32OY997634.1=NC_087544.10
Chromosome 33OY997635.1=NC_087545.10
Chromosome 34OY997636.1=NC_087546.10
Chromosome WOY997614.1=NC_087547.118
Chromosome ZOY997604.1=NC_087548.10
unplacedn/an/an/a284

Assembly statistics

MoleculeSequence RoleTotal
Length		Scaffold
Count		Ungapped
Length		Scaffold
N50		Spanned
Gaps		Unspanned
Gaps
AllAssembled molecule1,283,623,9593501,283,525,35984,621,1724930
Chromosome 1Assembled molecule218,912,2291218,895,829218,912,229820
Chromosome 2Assembled molecule168,492,1251168,478,125168,492,125700
Chromosome 3Assembled molecule129,753,6301129,743,830129,753,630490
Chromosome 4Assembled molecule84,621,172184,615,57284,621,172280
Chromosome 5Assembled molecule72,237,540172,233,74072,237,540190
Chromosome 6Assembled molecule63,774,815163,771,61563,774,815160
Chromosome 7Assembled molecule55,331,872155,327,67255,331,872210
Chromosome 8Assembled molecule46,689,938146,687,53846,689,938120
Chromosome 9Assembled molecule39,742,900139,741,10039,742,90090
Chromosome 10Assembled molecule26,938,933126,937,93326,938,93350
Chromosome 11Assembled molecule24,782,708124,781,10824,782,70880
Chromosome 12Assembled molecule23,960,227123,959,22723,960,22750
Chromosome 13Assembled molecule18,845,095118,844,09518,845,09550
Chromosome 14Assembled molecule18,068,808118,068,60818,068,80810
Chromosome 15Assembled molecule17,445,492117,444,69217,445,49240
Chromosome 16Assembled molecule15,300,844115,300,44415,300,84420
Chromosome 17Assembled molecule13,918,507113,918,10713,918,50720
Chromosome 18Assembled molecule13,167,548113,166,94813,167,54830
Chromosome 19Assembled molecule10,041,279110,039,87910,041,27970
Chromosome 20Assembled molecule9,979,39119,978,5919,979,39140
Chromosome 21Assembled molecule8,926,21518,925,6158,926,21530
Chromosome 22Assembled molecule8,777,38818,776,5888,777,38840
Chromosome 23Assembled molecule8,193,92718,193,3278,193,92730
Chromosome 24Assembled molecule8,090,66718,089,4678,090,66760
Chromosome 25Assembled molecule7,619,42817,618,8287,619,42830
Chromosome 26Assembled molecule5,560,76115,557,7615,560,761150
Chromosome 27Assembled molecule4,397,20814,396,4084,397,20840
Chromosome 28Assembled molecule3,969,74813,969,5483,969,74810
Chromosome 29AllAssembled moleculeUnlocalized scaffolds1,883,3111,555,303328,0086151,881,3111,553,503327,8081,555,3031,555,30367,6201091000
Chromosome 30AllAssembled moleculeUnlocalized scaffolds1,641,3321,526,071115,2614131,640,1321,524,871115,2611,526,0711,526,07132,976660000
Chromosome 31AllAssembled moleculeUnlocalized scaffolds1,488,980898,613590,3675141,487,980897,813590,167898,613898,613380,677541000
Chromosome 32Assembled molecule1,101,92611,101,1261,101,92640
Chromosome 33Assembled molecule996,0001996,000996,00000
Chromosome 34Assembled molecule960,7211958,921960,72190
Chromosome WAllAssembled moleculeUnlocalized scaffolds20,849,7875,556,83915,292,9481911820,849,7875,556,83915,292,9482,255,3385,556,8391,934,214000000
Chromosome ZAssembled molecule85,784,825185,772,22585,784,825630
unplacedAssembled molecule41,376,68228441,375,682539,01750