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fGobNig1.1

Organism name:
Gobius niger (black goby)
BioSample:
SAMEA13854149
BioProject:
PRJEB62588
Submitter:
WELLCOME SANGER INSTITUTE
Date:
2023/05/27
Assembly type:
haploid (principal pseudohaplotype of diploid)
Assembly level:
Chromosome
Genome representation:
full
RefSeq category:
representative genome
GenBank assembly accession:
GCA_951799975.1 (latest)
RefSeq assembly accession:
n/a
RefSeq assembly and GenBank assembly identical:
n/a
WGS Project:
CATOHO01
Assembly method:
various
Genome coverage:
30x
Sequencing technology:
PacBio,Arima2
Linked assembly:
GCA_951799965.1 (alternate pseudohaplotype of diploid)

IDs: 16778101 [UID] 43120798 [GenBank]

Pathogen Detection Resources

There are 2 assemblies for this organism

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History (Show revision history)

Comment

The assembly fGobNig1.1 is based on 30x PacBio data and Arima2 Hi-C data generated by the Darwin Tree of Life Project
(https://www.darwintreeoflife.org/). The assembly process included the following sequence of steps: initial PacBio assembly generation with Hifiasm, retained haplotig separation ... with purge_dups, and Hi-C based scaffolding with YaHS. The mitochondrial genome was assembled using MitoHiFi. Finally, the primary assembly was analysed and manually improved using rapid curation. Chromosome-scale scaffolds confirmed by the Hi-C data have been named in order of size.  more

Global statistics

Total sequence length870,572,126
Total ungapped length870,444,926
Gaps between scaffolds0
Number of scaffolds298
Scaffold N5036,708,673
Scaffold L5010
Number of contigs934
Contig N503,365,000
Contig L5081
Total number of chromosomes and plasmids25
Number of component sequences (WGS or clone)298

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Assembly Information

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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 (GCA_951799974.1)
Molecule nameGenBank sequenceRefSeq sequenceUnlocalized
sequences count
Chromosome 1OX637595.1n/an/a1
Chromosome 2OX637596.1n/an/a0
Chromosome 3OX637597.1n/an/a0
Chromosome 4OX637598.1n/an/a0
Chromosome 5OX637599.1n/an/a0
Chromosome 6OX637600.1n/an/a0
Chromosome 7OX637601.1n/an/a0
Chromosome 8OX637602.1n/an/a0
Chromosome 9OX637603.1n/an/a0
Chromosome 10OX637604.1n/an/a3
Chromosome 11OX637605.1n/an/a0
Chromosome 12OX637606.1n/an/a0
Chromosome 13OX637607.1n/an/a0
Chromosome 14OX637608.1n/an/a0
Chromosome 15OX637609.1n/an/a0
Chromosome 16OX637610.1n/an/a0
Chromosome 17OX637611.1n/an/a0
Chromosome 18OX637612.1n/an/a0
Chromosome 19OX637613.1n/an/a0
Chromosome 20OX637614.1n/an/a0
Chromosome 21OX637615.1n/an/a0
Chromosome 22OX637616.1n/an/a0
Chromosome 23OX637617.1n/an/a0
Chromosome 24OX637618.1n/an/a0
unplacedn/an/an/a269

Assembly statistics

MoleculeSequence RoleTotal
Length		Scaffold
Count		Ungapped
Length		Scaffold
N50		Spanned
Gaps		Unspanned
Gaps
AllAssembled molecule870,555,617297870,428,41736,708,6736360
Chromosome 1AllAssembled moleculeUnlocalized scaffolds76,730,80976,501,732229,07721176,719,80976,490,732229,07776,501,73276,501,732229,07755550000
Chromosome 2Assembled molecule47,756,716147,752,11647,756,716230
Chromosome 3Assembled molecule45,501,362145,496,96245,501,362220
Chromosome 4Assembled molecule42,849,440142,844,24042,849,440260
Chromosome 5Assembled molecule41,377,418141,371,41841,377,418300
Chromosome 6Assembled molecule40,904,900140,900,30040,904,900230
Chromosome 7Assembled molecule39,693,504139,687,90439,693,504280
Chromosome 8Assembled molecule38,465,593138,460,99338,465,593230
Chromosome 9Assembled molecule38,085,758138,079,35838,085,758320
Chromosome 10AllAssembled moleculeUnlocalized scaffolds37,877,96636,708,6731,169,29341337,872,76636,703,4731,169,29336,708,67336,708,673343,19226260000
Chromosome 11Assembled molecule35,417,365135,413,76535,417,365180
Chromosome 12Assembled molecule34,936,855134,930,45534,936,855320
Chromosome 13Assembled molecule33,768,751133,765,35133,768,751170
Chromosome 14Assembled molecule33,320,335133,315,53533,320,335240
Chromosome 15Assembled molecule31,913,492131,909,69231,913,492190
Chromosome 16Assembled molecule31,560,118131,554,71831,560,118270
Chromosome 17Assembled molecule30,238,673130,235,87330,238,673140
Chromosome 18Assembled molecule29,979,909129,975,70929,979,909210
Chromosome 19Assembled molecule29,794,981129,789,38129,794,981280
Chromosome 20Assembled molecule29,080,386129,078,78629,080,38680
Chromosome 21Assembled molecule28,533,545128,528,34528,533,545260
Chromosome 22Assembled molecule23,452,847123,440,44723,452,847620
Chromosome 23Assembled molecule17,228,438117,225,43817,228,438150
Chromosome 24Assembled molecule16,849,351116,844,95116,849,351220
unplacedAssembled molecule15,237,10526915,234,105123,445150
MoleculeTotal
Length		Scaffold
Count		Ungapped
Length		Scaffold
N50		Spanned
Gaps		Unspanned
Gaps
Mitochondrion MT16,509116,50916,50900