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Musca_domestica-2.0.2

Organism name:
Musca domestica (house fly)
Infraspecific name:
Strain: aabys
BioSample:
SAMN02953849
BioProject:
PRJNA176013
Submitter:
Glossina Genomes Consortium
Date:
2013/04/22
Assembly level:
Scaffold
Genome representation:
full
RefSeq category:
representative genome
GenBank assembly accession:
GCA_000371365.1 (latest)
RefSeq assembly accession:
GCF_000371365.1 (latest)
RefSeq assembly and GenBank assembly identical:
yes
WGS Project:
AQPM01
Assembly method:
AllPathsLG v. September 2012
Genome coverage:
76x
Sequencing technology:
Illumina

IDs: 643478 [UID] 643478 [GenBank] 717948 [RefSeq]

See Genome Information for Musca domestica

There are 2 assemblies for this organism

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History (Show revision history)

Comment

2.0.2 Assembly of Musca domestica
 A total of 6 female individual DNA isolates were provided in TE buffer for house fly Musca domestica courtesy of Dr. Jeffery Scott. The sequencing plan followed the recommendations provided in the ALLPATHS-LG assembler ... manual. This model requires 45x sequence coverage each of short inserts (overlapping paired reads 
180bp length) and 3kb paired end (PE) reads as well as 5x coverage of 8kb PE reads. For fragments we used DNA sample MDAB-9-14174 and for all jumping libraries (3 and 8kb) we used a pool of these DNA samples MDAB-group40-40, MDAB-group43-43, MDAB-group44-44, MDAB-group47-47 and MDAB-group48-48. We achieved 35x, 27x and 2x sequence coverage for short inserts, 3 and 8kb reads, respectively. PyGap, a post-assembly gap closing program, was run to improve contiguity. The assembly was also screened for contamination, which consisted mostly of human and bacterial contaminants. Trimmed vector in the form of X's and ambiguous bases as N's in the sequence were removed. NCBI requires that all contigs 200bp and smaller be removed. Removing these contigs was the final step in preparation for submitting the 2.0.2 assembly to NCBI.

 Various assembly metrics are summarized here:
 *** Contiguity: Contig *** Total contig number: 104054 Total contig bases: 691739271 bp (genome size, minus gaps) Average contig length: 6648 bp Maximum contig length: 300103 bp N50 contig length: 11807 bp N50 contig number: 14930
 *** Contiguity: Supercontig *** Total supercontig number: 20487 Average supercontig length: 33765 bp Maximum supercontig length: 2295392 bp N50 supercontig length: 213348 bp N50 supercontig number: 786
 ***Scaffold/Supercontigs Distribution*** Scaffolds > 1M: 35 Scaffold 250K--1M: 604 Scaffold 100K--250K: 1082 Scaffold 10--100K: 4640 Scaffold 5--10K: 2584 Scaffold 2--5K: 6000 Scaffold 0--2K: 5542  more

Global statistics

Total sequence length750,403,944
Total assembly gap length58,664,749
Gaps between scaffolds0
Number of scaffolds20,487
Scaffold N50226,573
Scaffold L50809
Number of contigs104,054
Contig N5011,807
Contig L5014,933
Total number of chromosomes and plasmids0
Number of component sequences (WGS or clone)104,054

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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
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
unplaced750,403,94420,487691,739,195226,57383,5670
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