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fTakRub1.2

Organism name:
Takifugu rubripes (torafugu)
BioSample:
SAMEA104384834
BioProject:
PRJEB31988
Submitter:
SC
Date:
2019/06/05
Assembly type:
haploid (principal pseudohaplotype of diploid)
Assembly level:
Chromosome
Genome representation:
full
GenBank assembly accession:
GCA_901000725.2 (replaced)
RefSeq assembly accession:
GCF_901000725.2 (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:
CAAJGN02
Genome coverage:
83x
Linked assembly:
GCA_901000745.3 (alternate pseudohaplotype of diploid)

IDs: 3430901 [UID] 11185868 [GenBank] 11364278 [RefSeq]

See Genome Information for Takifugu rubripes

There are 3 assemblies for this organism

See more

History (Show revision history)

Comment

The assembly fTakRub1.1 is based on 
83x PacBio Sequel data, 
70x coverage Illumina HiSeqX data from a 10X Genomics Chromium library generated at the Wellcome Sanger Institute as well as BioNano Saphyr DLE data generated at the Rockefeller University ... Vertebrate Genome Laboratory and 
51x coverage HiSeqX data from a Hi-C library prepared by Arima Genomics. An initial PacBio assembly was made using Falcon-unzip, and retained haplotigs were identified using purge_haplotigs. The primary contigs were then scaffolded using the 10X data with scaff10x, then scaffolded further with BioNano hybrid scaffolding and scaffolded further still using the Hi-C data with SALSA2. Polishing and gap-filling of both the primary scaffolds and haplotigs was performed using the PacBio reads and Arrow, followed by two rounds of Illumina polishing using the 10X data and freebayes. Finally, the assembly was manually improved using gEVAL to correct mis-joins and improve concordance with the BioNano and Hi-C data. Chromosome-scale scaffolds are named by synteny to the GCA_000180615.2 assembly of Takifugu rubripes.  more

Global statistics

Total sequence length384,126,662
Total ungapped length380,438,133
Gaps between scaffolds0
Number of scaffolds128
Scaffold N5016,705,553
Scaffold L5010
Number of contigs530
Contig N503,136,617
Contig L5035
Total number of chromosomes and plasmids23
Number of component sequences (WGS or clone)128

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
non-nuclear
Assembly Unit: Primary Assembly (GCF_901000724.2)
Molecule nameGenBank sequenceRefSeq sequenceUnlocalized
sequences count
Chromosome 1LR584231.2=NC_042285.10
Chromosome 2LR584245.2=NC_042286.10
Chromosome 3LR584237.1=NC_042287.10
Chromosome 4LR584242.2=NC_042288.10
Chromosome 5LR584247.1=NC_042289.10
Chromosome 6LR584250.1=NC_042290.10
Chromosome 7LR584238.1=NC_042291.10
Chromosome 8LR584234.2=NC_042292.10
Chromosome 9LR584246.2=NC_042293.10
Chromosome 10LR584251.2=NC_042294.10
Chromosome 11LR584241.1=NC_042295.10
Chromosome 12LR584248.2=NC_042296.10
Chromosome 13LR584232.1=NC_042297.10
Chromosome 14LR584244.1=NC_042298.10
Chromosome 15LR584240.2=NC_042299.10
Chromosome 16LR584249.2=NC_042300.10
Chromosome 17LR584239.2=NC_042301.10
Chromosome 18LR584252.2=NC_042302.10
Chromosome 19LR584235.1=NC_042303.10
Chromosome 20LR584236.2=NC_042304.10
Chromosome 21LR584233.2=NC_042305.10
Chromosome 22LR584243.1=NC_042306.10
unplacedn/an/an/a105

Assembly statistics

MoleculeTotal
Length
Scaffold
Count
Ungapped
Length
Scaffold
N50
Spanned
Gaps
Unspanned
Gaps
All384,110,215127380,421,68616,705,5534020
Chromosome 129,232,231128,970,41829,232,231200
Chromosome 215,686,389115,568,97915,686,389140
Chromosome 317,484,280117,225,93817,484,280190
Chromosome 416,363,587116,202,03616,363,587140
Chromosome 514,586,308114,398,33514,586,308140
Chromosome 612,913,240112,823,58112,913,240170
Chromosome 717,515,293117,512,78917,515,293240
Chromosome 819,721,368119,693,50019,721,368160
Chromosome 915,473,624115,336,98215,473,62460
Chromosome 1012,556,898112,556,08512,556,89890
Chromosome 1116,367,601116,351,49316,367,601160
Chromosome 1213,571,579113,570,42713,571,579150
Chromosome 1321,507,415121,410,04221,507,415250
Chromosome 1416,036,328116,022,07716,036,328120
Chromosome 1516,705,553116,611,05616,705,553270
Chromosome 1613,527,504113,470,22113,527,504150
Chromosome 1716,842,301116,804,30016,842,301170
Chromosome 1810,237,708110,237,29510,237,70850
Chromosome 1919,418,397118,982,01719,418,397190
Chromosome 2018,239,318117,997,25618,239,318130
Chromosome 2120,050,447119,153,41720,050,447260
Chromosome 2216,056,980115,896,39516,056,980130
unplaced14,015,86610513,627,047255,904460
MoleculeTotal
Length
Mitochondrion MT16,447
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