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ASM15795v1

Organism name:
Subdoligranulum variabile DSM 15176
Infraspecific name:
Strain: DSM 15176
BioSample:
SAMN00008862
Submitter:
Washington University Genome Sequencing Center
Date:
2009/10/06
Assembly level:
Scaffold
Genome representation:
full
RefSeq category:
representative genome
GenBank assembly accession:
GCA_000157955.1 (latest)
RefSeq assembly accession:
GCF_000157955.1 (latest)
RefSeq assembly and GenBank assembly identical:
yes
WGS Project:
ACBY02

IDs: 186818 [UID] 186798 [GenBank] 186818 [RefSeq]

See Genome Information for Subdoligranulum variabile

History (Show revision history)

Comment

Subdoligranulum variabile (GenBank Accession Number for 16S rDNA gene: AJ518869) is a member of the division Firmicutes. In one comprehensive 16S rDNA sequence-based enumeration of the colonic microbiota of three healthy adult humans, it represents, on average, 0.532% of ... all 16S rDNA sequences and 1.048% of the sequences in its division (Eckburg et. al. (2005)). The sequenced strain was obtained from Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSMZ) (DSM 15176).

We have performed one round of automated sequence improvement (pre-finishing), along with manual improvement that includes breaking apart any mis-assembly, and making manual joins where possible. Manual edits also are made where the consensus appears to be incorrect. All low quality data on the ends of contigs is removed. Contigs are ordered and oriented where possible.

Coding sequences were predicted using GeneMark v3.3 and Glimmer2 v2.13. Intergenic regions not spanned by GeneMark and Glimmer2 were blasted against NCBI's non-redundant (NR) database and predictions generated based on protein alignments. tRNA genes were determined using tRNAscan-SE 1.23 and non-coding RNA genes by RNAmmer-1.2 and Rfam v8.0. Gene names are generated at the contig level and may not necessarily reflect any known order or orientation between contigs. 

This work was supported by the National Human Genome Research Institute and the NIH Roadmap Human Microbiome Project [http://nihroadmap.nih.gov/hmp/].

This is a reference genome for the Human Microbiome Project. This project is co-owned with the Human Microbiome Project DACC. 
Genome Coverage: 23.9x 
Sequencing Technology: 454

Annotation was added to the contigs in December 2009.
Product names were updated in August 2012  more

Global statistics

Total sequence length3,245,471
Total assembly gap length8,000
Gaps between scaffolds0
Number of scaffolds11
Scaffold N502,385,595
Scaffold L501
Number of contigs91
Contig N50166,480
Contig L506
Total number of chromosomes and plasmids0

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Global assembly definition

Download the full sequence report
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
unplaced3,245,471113,237,4712,385,595800