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Astyanax_mexicanus-1.0.2

Organism name:
Astyanax mexicanus (Mexican tetra)
Sex:
female
BioSample:
SAMN02981523
Submitter:
Aquatic Genome Models
Date:
2013/04/23
Assembly level:
Scaffold
Genome representation:
full
GenBank assembly accession:
GCA_000372685.1 (replaced)
RefSeq assembly accession:
GCF_000372685.1 (replaced)
RefSeq assembly and GenBank assembly identical:
yes
WGS Project:
APWO01
Assembly method:
AllPathsLG v. Jan-2013
Genome coverage:
70x
Sequencing technology:
Illumina

IDs: 606128 [UID] 606128 [GenBank] 964988 [RefSeq]

See Genome Information for Astyanax mexicanus

History (Show revision history)

Comment

Background: The Astyanax mexicanus DNA sample was obtained from Dr. William Jeffery, University of Maryland. This heart, liver and a part of gill was obtained from a 7year old adult female which was 2nd or 3rd generation from wild ... caught from PachUn cave near the Sierra de el Abra in northeastern Mexico. Genomic DNA was prepared by Dr. William Jeffery's lab, University of Maryland from this single individual. Total assembled sequence coverage of Illumina reads was 
70X (fragments, 3, and 8kb) using a genome size estimate of 1Gb. The combined sequence reads were assembled using the ALLPATHS software (Broad Institute). This draft assembly was referred to as Astyanax mexicanus 1.0.2. This version has been gap filled and cleaned of contaminating contigs. The assembly is made up of a total of 10,735 scaffolds with an N50 scaffold length of over 1491kb (N50 contig length was 14.7kb). The assembly spans 1.225 Gb.
 This work was supported by NIH grant R24 RR032658-01 to WCW, The Genome Institute at Washington University School of Medicine.
 For questions regarding this Astyanax mexicanus 1.0.2 assembly please contact Dr. Wesley Warren, Washington University School of Medicine (wwarren@genome.wustl.edu). Funding for the sequence characterization of the Astyanax mexicanus genome was provided by the Office of Director, National Institutes of Health (NIH).
The sequenced individual was the offspring of two wild-caught Pachon cavefish captured in 2001 and bred in 2004. The wild caught fis  more

Global statistics

Total sequence length1,191,242,572
Total assembly gap length226,994,370
Gaps between scaffolds0
Number of scaffolds10,735
Scaffold N501,775,308
Scaffold L50185
Number of contigs121,345
Contig N5014,739
Contig L5016,919
Total number of chromosomes and plasmids0

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
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
unplaced1,191,242,57210,735964,248,2021,775,308110,6100
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