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G_variegatus-3.0.2

Organism name:
Galeopterus variegatus (Sunda flying lemur)
Sex:
male
BioSample:
SAMN01758971
BioProject:
PRJNA20511
Submitter:
Washington University (WashU)
Date:
2014/06/05
Synonyms:
galVar1
Assembly level:
Scaffold
Genome representation:
full
RefSeq category:
representative genome
GenBank assembly accession:
GCA_000696425.1 (latest)
RefSeq assembly accession:
GCF_000696425.1 (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:
JMZW01
Assembly method:
SOAPdenovo2 v. April 2014
Genome coverage:
55x
Sequencing technology:
Illumina

IDs: 182621 [UID] 1104068 [GenBank] 1174948 [RefSeq]

See Genome Information for Galeopterus variegatus

There are 2 assemblies for this organism

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History (Show revision history)

Comment

The DNA used for sequencing the Malayan flying lemur, Galeopterus variegatus, was derived from a single male animal collected in West Java by Minoru Baba (Kitakyushu Museum of Natural History and Human History,Japan) under Indonesian Institute of Sciences Research ... Permits 6541/I/KS/1999, 3452/SU/KS/2002, and 3380/SU/KS/2003. Ethanol preserved tissue was used to extract genomic DNA in the lab of William Murphy by Victor Mason (Texas A&M University).
 Total input sequence coverage of Illumina reads was 60X (45X 230-330 short inserts, 15X 3kbs, and 5X 8kbs) using a genome size estimate of 3.0Gb. The assembled sequence coverage was 55X. The combined sequence reads were assembled using the SOAPdenovo2 software (BGI). The assembly was improved using an unpublished program designed to close gaps, and SSPACE (Boetzer 2010). This draft assembly was referred to as Galeopterus variegatus 3.0.2. This version has been gap filled, error-corrected with approx. 12X Illumina reads, and cleaned of contaminating contigs. The assembly is made up of a total of 179,513 scaffolds with an N50 scaffold length of 249kb (N50 contig length was 20.8kb). The assembly spans over 2.9Gb.
 This work was funded by NIH grant HG003079 to RKW, The Genome Institute at Washington University School of Medicine.
 For questions regarding this Galeopterus variegatus 3.0.2 assembly please contact Wes Warren, Washington University School of Medicine (wwarren@genome.wustl.edu). Funding for the sequence characterization of the Galeopterus variegatus genome was provided by the Office of Director, National Institutes of Health (NIH). ***************************************************************************
 Sequence and Assembly Credits:
 Sequencing DNA source credit: - William Murphy
 DNA source can be obtained from:
 William Murphy, VIBS Texas A&M University 4458 TAMU College Station, TX 77843-4458
 Genome Sequence - The Genome Institute, Washington University School of Medicine
 Sequence Assembly - The Genome Institute, Washington University School of Medicine
 Citation upon use of this assembly in a manuscript:
 It is requested that users of this Galeopterus variegatus 3.0.2 sequence assembly acknowledge Richard K. Wilson and The Genome Institute, Washington University School of Medicine in any publications that result from use of this sequence assembly. *******************************************************************
 Assembly Stats:
 *** Contiguity: Contig *** Total contig number: 511879 Total contig bases: 2802903715 bp Average contig length: 5476 bp Maximum contig length: 521467 bp N50 contig length: 20753 bp N50 contig number: 33045
 *** Contiguity: Supercontig *** Total supercontig number: 179513 Average supercontig length: 15614 bp Maximum supercontig length: 3249419 bp N50 supercontig length: 249067 bp N50 supercontig number: 3001
 *** Scaffold Distribution *** Scaffolds > 1M: 137 Scaffold 250K--1M: 2843 Scaffold 100K--250K: 4525 Scaffold 10--100K: 12393 Scaffold 5--10K: 6621 Scaffold 2--5K: 17944 Scaffold 0--2K: 135050  more

Global statistics

Total sequence length3,187,660,572
Total ungapped length2,802,917,674
Gaps between scaffolds0
Number of scaffolds179,514
Scaffold N50245,189
Scaffold L503,423
Number of contigs511,878
Contig N5020,752
Contig L5033,050
Total number of chromosomes and plasmids1
Number of component sequences (WGS or clone)511,878

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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
The primary assembly unit does not have any assembled chromosomes or linkage groups.
Please download the full sequence report for information on the scaffolds.

Assembly statistics

MoleculeTotal
Length
Scaffold
Count
Ungapped
Length
Scaffold
N50
Spanned
Gaps
Unspanned
Gaps
unplaced3,187,643,824179,5132,802,900,926245,189332,3640
MoleculeTotal
Length
Mitochondrion MT16,748
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