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fScoJap1.pri

Organism name:
Scomber japonicus (chub mackerel)
Infraspecific name:
Specimen-voucher: 20180430
Isolate:
fScoJap1
Sex:
male
BioSample:
SAMN32224830
BioProject:
PRJNA912108
Submitter:
Vertebrate Genomes Project
Date:
2022/12/28
Assembly type:
haploid (principal pseudohaplotype of diploid)
Assembly level:
Chromosome
Genome representation:
full
RefSeq category:
representative genome
GenBank assembly accession:
GCA_027409825.1 (latest)
RefSeq assembly accession:
GCF_027409825.1 (latest)
RefSeq assembly and GenBank assembly identical:
no (hide details)
  • Only in GenBank: chromosome MT
  • Data displayed for RefSeq version
WGS Project:
JAPYKA01
Assembly method:
HiFiasm v. 0.15.4-r343; purge_dups v. 1.2.5; salsa v. 2.3; VGP pipeline v. 2.0; gEVAL manual curation v. 2022-02-03
Expected final version:
no
Genome coverage:
49.19x
Sequencing technology:
PacBio Sequel II HiFi; Arima Hi-C v2
Linked assembly:
GCA_027409835.1 (alternate pseudohaplotype of diploid)

IDs: 15196031 [UID] 39150458 [GenBank] 39980498 [RefSeq]

See Genome Information for Scomber japonicus

Pathogen Detection Resources

There are 2 assemblies for this organism

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History (Show revision history)

Comment

Global statistics

Total sequence length828,681,152
Total ungapped length828,034,052
Gaps between scaffolds0
Number of scaffolds360
Scaffold N5034,636,535
Scaffold L5011
Number of contigs1,932
Contig N504,898,551
Contig L5046
Total number of chromosomes and plasmids24
Number of component sequences (WGS or clone)360

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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
Assembly Unit: Primary Assembly (GCF_027409885.1)
Molecule nameGenBank sequenceRefSeq sequenceUnlocalized
sequences count
Chromosome 1CM050003.1=NC_070578.10
Chromosome 2CM050004.1=NC_070579.10
Chromosome 3CM050005.1=NC_070580.10
Chromosome 4CM050006.1=NC_070581.10
Chromosome 5CM050007.1=NC_070582.16
Chromosome 6CM050008.1=NC_070583.10
Chromosome 7CM050009.1=NC_070584.10
Chromosome 8CM050010.1=NC_070585.15
Chromosome 9CM050011.1=NC_070586.10
Chromosome 10CM050012.1=NC_070587.11
Chromosome 11CM050013.1=NC_070588.10
Chromosome 12CM050014.1=NC_070589.10
Chromosome 13CM050015.1=NC_070590.10
Chromosome 14CM050016.1=NC_070591.12
Chromosome 15CM050017.1=NC_070592.11
Chromosome 16CM050018.1=NC_070593.10
Chromosome 17CM050019.1=NC_070594.10
Chromosome 18CM050020.1=NC_070595.10
Chromosome 19CM050021.1=NC_070596.10
Chromosome 20CM050022.1=NC_070597.10
Chromosome 21CM050023.1=NC_070598.10
Chromosome 22CM050024.1=NC_070599.10
Chromosome 23CM050025.1=NC_070600.12
Chromosome 24CM050026.1=NC_070601.10
unplacedn/an/an/a319

Assembly statistics

MoleculeSequence RoleTotal
Length		Scaffold
Count		Ungapped
Length		Scaffold
N50		Spanned
Gaps		Unspanned
Gaps
AllAssembled molecule828,681,152360828,034,05234,636,5351,5720
Chromosome 1Assembled molecule44,105,842144,071,44244,105,842820
Chromosome 2Assembled molecule42,190,636142,172,33642,190,636480
Chromosome 3Assembled molecule39,922,077139,896,07739,922,077670
Chromosome 4Assembled molecule36,314,758136,281,25836,314,758820
Chromosome 5AllAssembled moleculeUnlocalized scaffolds36,978,01236,702,885275,12771636,951,11236,676,485274,62736,702,88536,702,88546,08567661000
Chromosome 6Assembled molecule40,183,386140,148,18640,183,386800
Chromosome 7Assembled molecule37,153,179137,125,17937,153,179710
Chromosome 8AllAssembled moleculeUnlocalized scaffolds34,955,95834,636,535319,42361534,933,65834,615,235318,42334,636,53534,636,53567,03753512000
Chromosome 9Assembled molecule40,751,155140,718,75540,751,155780
Chromosome 10AllAssembled moleculeUnlocalized scaffolds36,978,64636,931,70446,94221136,961,04636,914,60446,44236,931,70436,931,70446,94249481000
Chromosome 11Assembled molecule34,100,855134,082,25534,100,855480
Chromosome 12Assembled molecule36,016,775135,985,27536,016,775780
Chromosome 13Assembled molecule32,593,298132,572,99832,593,298550
Chromosome 14AllAssembled moleculeUnlocalized scaffolds34,260,65734,185,79274,86531234,231,65734,156,79274,86534,185,79234,185,79248,73067670000
Chromosome 15AllAssembled moleculeUnlocalized scaffolds30,747,85430,702,76645,08821130,713,75430,669,16644,58830,702,76630,702,76645,08879781000
Chromosome 16Assembled molecule32,095,705132,069,10532,095,705670
Chromosome 17Assembled molecule32,576,629132,548,12932,576,629690
Chromosome 18Assembled molecule31,458,150131,438,65031,458,150480
Chromosome 19Assembled molecule33,498,519133,470,41933,498,519670
Chromosome 20Assembled molecule29,648,155129,618,55529,648,155730
Chromosome 21Assembled molecule28,928,886128,902,78628,928,886630
Chromosome 22Assembled molecule29,061,689129,036,68929,061,689560
Chromosome 23AllAssembled moleculeUnlocalized scaffolds26,646,38726,575,81370,57431226,613,58726,543,01370,57426,575,81326,575,81340,10071710000
Chromosome 24Assembled molecule18,708,008118,687,70818,708,008490
unplacedAssembled molecule8,805,9363198,803,43628,46950