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daEupConf1.1

Organism name:
Euphrasia confusa (eudicots)
BioSample:
SAMEA7515968
BioProject:
PRJEB63234
Submitter:
WELLCOME SANGER INSTITUTE
Date:
2023/07/15
Assembly type:
haploid (principal pseudohaplotype of diploid)
Assembly level:
Chromosome
Genome representation:
full
RefSeq category:
representative genome
GenBank assembly accession:
GCA_954870475.1 (latest)
RefSeq assembly accession:
n/a
RefSeq assembly and GenBank assembly identical:
n/a
WGS Project:
CATPAB01
Assembly method:
various
Genome coverage:
42x
Sequencing technology:
PacBio,Arima2
Linked assembly:
GCA_954870545.1 (alternate pseudohaplotype of diploid)

IDs: 17612341 [UID] 45145788 [GenBank]

See Genome Information for Euphrasia confusa

Pathogen Detection Resources

There are 2 assemblies for this organism

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History (Show revision history)

Comment

The assembly daEupConf1.1 is based on 42x 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, and Hi-C based ... scaffolding with YaHS. The mitochondrial and chloroplast genomes were assembled using OATK. Finally, the primary assembly was analysed and manually improved using rapid curation. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size.  more

Global statistics

Total sequence length977,066,659
Total ungapped length977,026,259
Gaps between scaffolds0
Number of scaffolds451
Scaffold N5041,336,645
Scaffold L5010
Number of contigs643
Contig N508,255,681
Contig L5041
Total number of chromosomes and plasmids25
Number of component sequences (WGS or clone)451

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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
non-nuclear
Assembly Unit: Primary Assembly (GCA_954870474.1)
Molecule nameGenBank sequenceRefSeq sequenceUnlocalized
sequences count
Chromosome 1OX940949.1n/an/a0
Chromosome 2OX940950.1n/an/a0
Chromosome 3OX940951.1n/an/a0
Chromosome 4OX940952.1n/an/a0
Chromosome 5OX940953.1n/an/a0
Chromosome 6OX940954.1n/an/a0
Chromosome 7OX940955.1n/an/a0
Chromosome 8OX940956.1n/an/a0
Chromosome 9OX940957.1n/an/a0
Chromosome 10OX940958.1n/an/a0
Chromosome 11OX940959.1n/an/a1
Chromosome 12OX940960.1n/an/a0
Chromosome 13OX940961.1n/an/a0
Chromosome 14OX940962.1n/an/a0
Chromosome 15OX940963.1n/an/a4
Chromosome 16OX940964.1n/an/a1
Chromosome 17OX940965.1n/an/a0
Chromosome 18OX940966.1n/an/a0
Chromosome 19OX940967.1n/an/a0
Chromosome 20OX940968.1n/an/a5
Chromosome 21OX940969.1n/an/a4
Chromosome 22OX940970.1n/an/a0
unplacedn/an/an/a411

Assembly statistics

MoleculeSequence RoleTotal
Length		Scaffold
Count		Ungapped
Length		Scaffold
N50		Spanned
Gaps		Unspanned
Gaps
AllAssembled molecule976,479,663448976,439,26341,336,6451920
Chromosome 1Assembled molecule66,608,978166,605,77866,608,978150
Chromosome 2Assembled molecule60,051,239160,049,43960,051,23990
Chromosome 3Assembled molecule56,408,396156,405,79656,408,396120
Chromosome 4Assembled molecule48,524,651148,521,45148,524,651160
Chromosome 5Assembled molecule48,373,420148,372,62048,373,42040
Chromosome 6Assembled molecule45,965,543145,962,74345,965,543130
Chromosome 7Assembled molecule44,868,400144,866,80044,868,40060
Chromosome 8Assembled molecule44,504,029144,502,02944,504,029100
Chromosome 9Assembled molecule42,212,847142,211,44742,212,84770
Chromosome 10Assembled molecule41,336,645141,334,84541,336,64590
Chromosome 11AllAssembled moleculeUnlocalized scaffolds41,246,85539,672,8551,574,00021141,245,45539,671,4551,574,00039,672,85539,672,8551,574,000770000
Chromosome 12Assembled molecule40,861,923140,859,72340,861,923100
Chromosome 13Assembled molecule39,772,078139,771,07839,772,07850
Chromosome 14Assembled molecule38,891,869138,888,66938,891,869150
Chromosome 15AllAssembled moleculeUnlocalized scaffolds38,636,55735,112,1033,524,45451438,634,95735,110,5033,524,45435,112,10335,112,103921,000770000
Chromosome 16AllAssembled moleculeUnlocalized scaffolds36,816,23536,341,755474,48021136,814,63536,340,155474,48036,341,75536,341,755474,480770000
Chromosome 17Assembled molecule36,615,266136,613,06636,615,266100
Chromosome 18Assembled molecule33,367,751133,366,15133,367,75180
Chromosome 19Assembled molecule32,831,144132,829,94432,831,14460
Chromosome 20AllAssembled moleculeUnlocalized scaffolds31,498,91329,761,9131,737,00061531,497,91329,760,9131,737,00029,761,91329,761,913344,000550000
Chromosome 21AllAssembled moleculeUnlocalized scaffolds30,537,48729,189,8811,347,60651430,536,28729,188,6811,347,60629,189,88129,189,881342,043660000
Chromosome 22Assembled molecule29,845,050129,844,25029,845,05040
unplacedAssembled molecule46,704,38741146,704,187255,00010
MoleculeTotal
Length		Scaffold
Count		Ungapped
Length		Scaffold
N50		Spanned
Gaps		Unspanned
Gaps
All586,9963586,996329,69200
Mitochondrion MT1329,6921329,692329,69200
Mitochondrion MT2112,3291112,329112,32900
Chloroplast Pltd144,9751144,975144,97500