Format

Send to:

Choose Destination

Download Assembly



X_maculatus-5.0-male

Organism name:
Xiphophorus maculatus (southern platyfish)
Infraspecific name:
Strain: JP 163 A
Sex:
male
BioSample:
SAMN08025980
BioProject:
PRJNA72525
Submitter:
The Genome Institute, Washington University at St. Louis
Date:
2017/12/07
Assembly level:
Chromosome
Genome representation:
full
RefSeq category:
representative genome
GenBank assembly accession:
GCA_002775205.2 (latest)
RefSeq assembly accession:
GCF_002775205.1 (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:
PGSD01
Assembly method:
HGAP4_SMRT_Link v. 5.0.19585
Genome coverage:
83x
Sequencing technology:
PacBio_Sequel

IDs: 1460771 [UID] 5715828 [GenBank] 5738908 [RefSeq]

See Genome Information for Xiphophorus maculatus

There are 2 assemblies for this organism

See more

History (Show revision history)

Comment

Xiphophorus maculatus 5.0 assembly.
 The platyfish DNA for single molecule real time (SMRT) sequencing is derived from a single male (Xiphophorus maculatus, Strain - JP 163 A) from the Xiphophorus Genetic Stock Center (Dr. Ron Walter, Director), Texas State ... University, San Marcos, Texas, USA. X. maculatus Jp 163 A are line bred (i.e., brother-sister matings) and this fish is from the 114th generation if line breeding. Sequences were generated on the Pacific Biosciences Sequel instrument (V2 chemistry) to approx. 83x genome coverage based on a genome size estimate of 700 Mb. All SMRT sequences were assembled with the HGAP4 algorithm (SMRT Link v5.0.1.9585) then error corrected using the Arrow error-correction module. Additional polishing of the assembly for residual indels was done by aligning 
50x coverage of Illumina data and the Pilon algorithm. Scaffolds were generated by alignment to a Bionano map created with the same DNA source using the Irys software. Finally, all scaffolds were ordered and oriented by alignment to the genetic linkage map using Chromonomer (http://catchenlab.life.illinois.edu/chromonomer/.cite). 
 Of the 704 Mb assembled genome (X_maculatus-5.0), the total assembly N50 contig and scaffold lengths are 9.2Mb (n=259) and 31.5Mb (n=103), respectively. 
 For questions regarding this X_maculatus-5.0 assembly please contact Dr. Wes Warren, McDonnell Genome Institute at Washington University School of Medicine, St. Louis, MO or Dr. Ron Walter, Texas State University, San Marcos, Texas, USA. 
 Data use:
 The X_maculatus-5.0 assembly sequence is made freely available to the community by McDonnell Genome Institute at Washington University School of Medicine, with the following understanding: 1. The data may be freely downloaded, used in analyses, and repackaged in databases. 2. Users are free to use the data in scientific papers analyzing these data if the providers of this data are properly cited. 3. Any redistribution of the data should carry this notice. 
 Xiphophorus maculatus Sequence and Assembly Credits:
 DNA source - Dr. Ron Walter, Texas State University, San Marcos, TX.
 Genome Sequence - The McDonnell Genome Institute, Washington University School of Medicine.
 Sequence Assembly and Chromosomal Sequence Construction - The McDonnell Genome Institute, Washington University School of Medicine
 Platyfish RNAseq data - Dr. Ron Walter, Texas State University, San Marcos, TX. 
 Funding for the sequence characterization of the platyfish genome is being provided by grants to Dr. Wesley Warren, McDonnell Genome Institute, Washington University Schoold of Medicine and Dr. Ron Walter through the National Institutes of Health (NIH) and Dr. Manfred Schartl at the Universitat Wurzburg, Germany.

 ASSEMBLY STATS:
 SCAFFOLDS
 COUNT 103 
 LENGTH 704,304,639 bp 
 AVG 6,837,909 bp 
 N50 31,535,491 bp
 LARGEST 35,293,739 bp 
 Scaffolds > 1M: 24 ( 699,980,690 bp ) 99.4%
 Scaffolds 250K--1M: 1 ( 269,636 bp ) 0.04%
 Scaffolds 100K--250K: 14 ( 1,854,102 bp ) 0.26%
 Scaffolds 10K--100K: 52 ( 2,150,311 bp ) 0.31%
 Scaffolds 5K--10K: 5 ( 37,383 bp ) 0.005%
 Scaffolds 2K--5K: 3 ( 9,783 bp ) 0.001%
 Scaffolds 0--2K: 4 ( 2,734 bp ) 0.0004%
 CONTIGS
 COUNT 259 
 LENGTH 700,976,734 bp 
 AVG 2,706,473 bp 
 N50 9,181,372 bp
 LARGEST 26,812,185 bp 
 Contigs > 1M: 115 ( 664,204,175 bp ) 94.8%
 Contigs 250K--1M: 54 ( 30,725,410 bp ) 4.4%
 Contigs 100K--250K: 26 ( 3,846,938 bp ) 0.55%
 Contigs 10K--100K: 52 ( 2,150,311 bp ) 0.31%
 Contigs 5K--10K: 5 ( 37,383 bp ) 0.005%
 Contigs 2K--5K: 3 ( 9,783 bp ) 0.001%
 Contigs 0--2K: 4 ( 2,734 bp ) 0.0004%  more

Global statistics

Total sequence length704,321,165
Total ungapped length700,993,260
Gaps between scaffolds0
Number of scaffolds102
Scaffold N5031,535,491
Scaffold L5011
Number of contigs258
Contig N509,181,372
Contig L5025
Total number of chromosomes and plasmids25
Number of component sequences (WGS or clone)102

Supplemental Content

PubMed articles for this assembly

Recent activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...

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
Assembly Unit: Primary Assembly (GCF_002775215.1)
Molecule nameGenBank sequenceRefSeq sequenceUnlocalized
sequences count
Chromosome 1CM008938.1=NC_036443.10
Chromosome 2CM008939.1=NC_036444.10
Chromosome 3CM008940.1=NC_036445.10
Chromosome 4CM008941.1=NC_036446.10
Chromosome 5CM008942.1=NC_036447.10
Chromosome 6CM008943.1=NC_036448.10
Chromosome 7CM008944.1=NC_036449.10
Chromosome 8CM008945.1=NC_036450.10
Chromosome 9CM008946.1=NC_036451.10
Chromosome 10CM008947.1=NC_036452.10
Chromosome 11CM008948.1=NC_036453.10
Chromosome 12CM008949.1=NC_036454.10
Chromosome 13CM008950.1=NC_036455.10
Chromosome 14CM008951.1=NC_036456.10
Chromosome 15CM008952.1=NC_036457.10
Chromosome 16CM008953.1=NC_036458.10
Chromosome 17CM008954.1=NC_036459.10
Chromosome 18CM008955.1=NC_036460.10
Chromosome 19CM008956.1=NC_036461.10
Chromosome 20CM008957.1=NC_036462.10
Chromosome 21CM008958.1=NC_036463.10
Chromosome 22CM008959.1=NC_036464.10
Chromosome 23CM008960.1=NC_036465.10
Chromosome 24CM008961.1=NC_036466.10
unplacedn/an/an/a77

Assembly statistics

MoleculeTotal
Length
Scaffold
Count
Ungapped
Length
Scaffold
N50
Spanned
Gaps
Unspanned
Gaps
All704,304,519101700,976,61431,535,4911560
Chromosome 132,265,191132,177,59832,265,19140
Chromosome 231,535,491131,435,63731,535,49160
Chromosome 333,395,476133,194,20133,395,476100
Chromosome 435,293,739135,136,16235,293,73970
Chromosome 533,362,219133,354,06033,362,21920
Chromosome 630,192,296130,078,72230,192,29660
Chromosome 731,701,063131,533,74931,701,06370
Chromosome 827,836,836127,510,82527,836,83690
Chromosome 931,544,005131,485,53631,544,00560
Chromosome 1025,258,764125,208,25525,258,76450
Chromosome 1132,424,306132,422,11032,424,30660
Chromosome 1230,270,779130,248,08130,270,77950
Chromosome 1328,669,031127,886,82728,669,03190
Chromosome 1427,921,107127,885,33227,921,10780
Chromosome 1524,466,587124,272,41424,466,58780
Chromosome 1625,766,145125,688,11825,766,14550
Chromosome 1720,566,889120,334,52620,566,889120
Chromosome 1833,421,192133,352,43733,421,19260
Chromosome 1927,874,734127,818,30827,874,73490
Chromosome 2032,926,076132,659,24832,926,07640
Chromosome 2126,619,551126,586,12226,619,55190
Chromosome 2229,576,354129,554,67129,576,35450
Chromosome 2332,170,657131,946,10832,170,65770
Chromosome 2414,922,202114,883,73814,922,20210
unplaced4,323,829774,323,82999,80000
MoleculeTotal
Length
Mitochondrion MT16,646
Support Center