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CB4

Organism name:
Caenorhabditis briggsae (nematodes)
Infraspecific name:
Strain: AF16
BioSample:
SAMEA3138181
BioProject:
PRJNA10731
Submitter:
The C.briggsae Sequencing Consortium
Date:
2014/07/02
Assembly level:
Chromosome
Genome representation:
full
RefSeq category:
representative genome
GenBank assembly accession:
GCA_000004555.3 (latest)
RefSeq assembly accession:
n/a
RefSeq assembly and GenBank assembly identical:
n/a
WGS Project:
CAAC03
Genome coverage:
10x

IDs: 216471 [UID] 1356838 [GenBank]

See Genome Information for Caenorhabditis briggsae

History (Show revision history)

Comment

Details of C.briggsae assembly version CB4: 
To improve upon the C. briggsae nuclear genome assembly CB3, 167 AF16/HK104 advanced-intercross recombinant inbred lines were successfully genotyped at 1,032 single nucleotide polymorphism (SNP) markers. The resulting data were used to estimate ... high-density genetic maps. Sequences were assembled by combining the physical and genetic positions of the SNPs to inform the process of ordering and orienting the cb25 supercontigs into chromosome assemblies.
The total nuclear genome content decreased from cb25 to cb4 because of the removal of three supercontigs containing mitochondrial genome sequence (totaling 20.1 kbp).
The cb25.agp8 assembly was produced for the C. briggsae strain AF16 from 2.05 million whole genome shotgun (WGS) reads, of which 88.2% were in read pairs. The sequence reads were generated at Washington University School of Medicine's Genome Sequencing Center and the Sanger Institute (Hinxton, UK). The Phusion (Mullikin, J) assembler was used to assemble the WGS reads into contigs based on overlap information, and then into supercontigs using read pair information to cross gaps. These supercontigs were assembled into mapped ultracontigs based on FPC fingerprint mapping (generated at Washington University School of Medicine's Genome Sequencing Center), with material from previously finished clones used to bridge gaps.
Data generated by:
 Genome Sequencing Center
 Department of Genetics, Washington University 
 St. Louis , MO 63110, USA, and
 Wellcome Trust Sanger Institute, Hinxton,
 Cambridge CB10 1SA, United Kingdom
 email: stlouis@wormbase.org and hinxton@wormbase.org  more

Global statistics

Total sequence length108,384,165
Total ungapped length105,418,679
Gaps between scaffolds271
Number of scaffolds638
Scaffold N50727,881
Scaffold L5040
Number of contigs5,074
Contig N5045,098
Contig L50607
Total number of chromosomes and plasmids6
Number of component sequences (WGS or clone)5,493

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
Assembly Unit: Primary Assembly (GCA_000004565.3)
Molecule nameGenBank sequenceRefSeq sequenceUnlocalized
sequences count
Chromosome IFR847112.2n/an/a2
Chromosome IIFR847113.2n/an/a0
Chromosome IIIFR847114.2n/an/a3
Chromosome IVFR847118.2n/an/a1
Chromosome VFR847121.2n/an/a1
Chromosome XFR847123.2n/an/a1
unplacedn/an/an/a353

Assembly statistics

MoleculeSequence RoleTotal
Length
Scaffold
Count
Ungapped
Length
Scaffold
N50
Spanned
Gaps
Unspanned
Gaps
AllAssembled molecule108,384,165638105,418,679727,8814,436271
Chromosome IAllAssembled moleculeUnlocalized scaffolds15,499,55415,455,97943,5755048215,041,73514,999,08142,654536,425536,42523,652773771247470
Chromosome IIAssembled molecule16,627,1544616,060,964664,22374845
Chromosome IIIAllAssembled moleculeUnlocalized scaffolds14,683,99514,578,851105,1444542314,270,06314,171,21898,845707,618707,61836,434646644241410
Chromosome IVAllAssembled moleculeUnlocalized scaffolds17,510,55617,485,43925,1176160116,968,33016,944,71223,618606,282606,28225,117824822259590
Chromosome VAllAssembled moleculeUnlocalized scaffolds19,580,44919,495,15785,2925352119,099,85819,015,41884,440938,6521,058,55885,292744742251510
Chromosome XAllAssembled moleculeUnlocalized scaffolds21,569,24321,540,57028,6733029121,148,76021,120,08728,6731,191,9161,191,91628,673471471028280
unplacedAssembled molecule2,913,2143532,828,96913,4132300
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