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icHalSede1.1

Organism name:
Halyzia sedecimguttata (orange ladybird)
BioSample:
SAMEA8563708
BioProject:
PRJEB52234
Submitter:
WELLCOME SANGER INSTITUTE
Date:
2022/05/03
Assembly type:
haploid (principal pseudohaplotype of diploid)
Assembly level:
Chromosome
Genome representation:
full
GenBank assembly accession:
GCA_937662695.1 (replaced)
RefSeq assembly accession:
n/a
RefSeq assembly and GenBank assembly identical:
n/a
WGS Project:
CALNDA01
Genome coverage:
55x
Linked assembly:
GCA_937616445.1 (alternate pseudohaplotype of diploid)

IDs: 12882251 [UID] 33654078 [GenBank]

See Genome Information for Halyzia sedecimguttata

Pathogen Detection Resources

There are 2 assemblies for this organism

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History (Show revision history)

Comment

The assembly icHalSede1.1 is based on 55x PacBio data, 10X Genomics Chromium data, and Arima 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, short-read polishing using FreeBayes-called variants from 10X Genomics Chromium reads aligned with LongRanger, and Hi-C based scaffolding with YaHS. The mitochondrial genome was assembled using MitoHiFi. Finally, the 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. Heterozygous inversion at 
110Mb on chromosome 2, and 
61Mb on chromosome 5.  more

Global statistics

Total sequence length911,597,312
Total ungapped length911,553,705
Gaps between scaffolds0
Number of scaffolds39
Scaffold N50110,337,179
Scaffold L504
Number of contigs257
Contig N5013,814,148
Contig L5020
Total number of chromosomes and plasmids11
Number of component sequences (WGS or clone)39

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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_937662694.1)
Molecule nameGenBank sequenceRefSeq sequenceUnlocalized
sequences count
Chromosome 1OW569411.1n/an/a0
Chromosome 2OW569412.1n/an/a0
Chromosome 3OW569413.1n/an/a0
Chromosome 4OW569414.1n/an/a0
Chromosome 5OW569415.1n/an/a0
Chromosome 6OW569416.1n/an/a0
Chromosome 7OW569417.1n/an/a0
Chromosome 8OW569418.1n/an/a0
Chromosome 9OW569419.1n/an/a0
Chromosome XOW569420.1n/an/a5
unplacedn/an/an/a23

Assembly statistics

MoleculeSequence RoleTotal
Length		Scaffold
Count		Ungapped
Length		Scaffold
N50		Spanned
Gaps		Unspanned
Gaps
AllAssembled molecule911,579,81338911,536,206110,337,1792180
Chromosome 1Assembled molecule148,629,8271148,621,020148,629,827440
Chromosome 2Assembled molecule121,065,1331121,058,733121,065,133320
Chromosome 3Assembled molecule112,472,8631112,468,663112,472,863210
Chromosome 4Assembled molecule110,337,1791110,334,179110,337,179150
Chromosome 5Assembled molecule94,329,082194,326,08294,329,082150
Chromosome 6Assembled molecule88,423,013188,418,41388,423,013230
Chromosome 7Assembled molecule78,945,363178,942,56378,945,363140
Chromosome 8Assembled molecule68,497,186168,494,78668,497,186120
Chromosome 9Assembled molecule48,677,697148,671,89748,677,697290
Chromosome XAllAssembled moleculeUnlocalized scaffolds36,282,42829,713,4516,568,97761536,280,22829,711,4516,568,77729,713,45129,713,4511,364,82311101000
unplacedAssembled molecule3,920,042233,919,6422,651,80120
MoleculeTotal
Length		Scaffold
Count		Ungapped
Length		Scaffold
N50		Spanned
Gaps		Unspanned
Gaps
Mitochondrion MT17,499117,49917,49900