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dyak_caf1

Organism name:
Drosophila yakuba (flies)
Infraspecific name:
Strain: Tai18E2
BioSample:
SAMN02952910
BioProject:
PRJNA12366
Submitter:
FlyBase
Date:
2006/06/27
Assembly level:
Chromosome
Genome representation:
full
RefSeq category:
representative genome
GenBank assembly accession:
GCA_000005975.1 (latest)
RefSeq assembly accession:
GCF_000005975.2 (latest)
RefSeq assembly and GenBank assembly identical:
no (hide details)
  • Only in RefSeq: chromosome MT (in non-nuclear assembly-unit)
  • Data displayed for RefSeq version
WGS Project:
AAEU02
Genome coverage:
9.1x

IDs: 368388 [UID] 281108 [GenBank] 368388 [RefSeq]

See Genome Information for Drosophila yakuba

History (Show revision history)

Comment

This is the CAF1 assembly of the Drosophila yakuba genome. It has 9.1x coverage. The D. yakuba chromosomes were created by using the Drosophila melanogaster genome as a reference, as described in PMID: 17994087. However, inversions were introduced to ... remain consistent with the D. yakuba assembly scaffolds. Inversions were only introduced between contigs and not within contigs. The resulting assembly is consistent with polytene chromosome banding data. Subsequently, major breakpoints in the D. yakuba chromosomal assembly relative to D. melanogaster were all validated (PMID: 17550304).
This line is derived from a single inseminated female collected by D. Lachaise in 1983 from the wild population in the Tai rainforest, on the border between Liberia and Ivory Coast. The isofemale line, Tai18 came to J. Coyne's laboratory where it was inbred (sib-pair mating) for 7 generations in 2001 yielding Tai182E. A. Llopart established the homokaryotypic (2Rn) subline, Tai18E2 from a pair mating.
Annotation was updated in November 2015.  more

Global statistics

Total sequence length165,709,965
Total ungapped length162,597,976
Gaps between scaffolds0
Number of scaffolds8,123
Scaffold N5021,770,863
Scaffold L504
Number of contigs13,441
Contig N50115,562
Contig L50275
Total number of chromosomes and plasmids8
Number of component sequences (WGS or clone)13,440

Supplemental Content

PubMed articles for this assembly

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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 (GCF_000005985.1)
Molecule nameGenBank sequenceRefSeq sequenceUnlocalized
sequences count
Chromosome XCM000162.2=NC_011091.159
Chromosome 2LCM000157.2=NT_167062.142
Chromosome 2RCM000158.2=NT_167063.114
Chromosome 3LCM000159.2=NT_167064.1353
Chromosome 3RCM000160.2=NT_167065.1579
Chromosome 4CM000161.2=NC_011090.11
Chromosome Yn/an/an/a1
unplacedn/an/an/a7,067

Assembly statistics

MoleculeSequence RoleTotal
Length
Scaffold
Count
Ungapped
Length
Scaffold
N50
Spanned
Gaps
Unspanned
Gaps
AllAssembled molecule165,693,9468,122162,581,95721,770,8635,3180
Chromosome XAllAssembled moleculeUnlocalized scaffolds23,688,92121,770,8631,918,0586015923,367,41321,537,7301,829,68321,770,86321,770,863156,996715569146000
Chromosome 2LAllAssembled moleculeUnlocalized scaffolds26,347,87722,324,4524,023,4254314226,108,49122,210,0253,898,46622,324,45222,324,452744,880424221203000
Chromosome 2RAllAssembled moleculeUnlocalized scaffolds21,193,45521,139,21754,2381511421,098,00221,046,83451,16821,139,21721,139,2178,7491951905000
Chromosome 3LAllAssembled moleculeUnlocalized scaffolds28,643,27024,197,6274,445,643354135328,241,52823,932,1234,309,40524,197,62724,197,62729,684791550241000
Chromosome 3RAllAssembled moleculeUnlocalized scaffolds31,531,56928,832,1122,699,457580157931,177,37628,614,6352,562,74128,832,11228,832,1128,932768602166000
Chromosome 4AllAssembled moleculeUnlocalized scaffolds1,406,1741,374,47431,7002111,391,5231,363,84227,6811,374,4741,374,47431,70051465000
Chromosome YAllAssembled moleculeUnlocalized scaffolds114,1510114,15110196,251096,251114,1510114,15117017000
unplacedAssembled molecule32,768,5297,06731,101,37322,8402,3570
MoleculeTotal
Length
Mitochondrion MT16,019
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