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fAloSap1.pri

Organism name:
Alosa sapidissima (American shad)
Isolate:
fAloSap1
Sex:
male
BioSample:
SAMN18857608
BioProject:
PRJNA728145
Submitter:
Vertebrate Genomes Project
Date:
2021/05/25
Assembly type:
haploid (principal pseudohaplotype of diploid)
Assembly level:
Chromosome
Genome representation:
full
RefSeq category:
representative genome
GenBank assembly accession:
GCA_018492685.1 (latest)
RefSeq assembly accession:
GCF_018492685.1 (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:
JAHDTN01
Assembly method:
Hifisam v. 0.14; Purge_dups v. 1.0.1; Salsa v. 2.2; Scaff10X v. 3.2.1; Bionano Solve v. 3.6.1; VGP pipeline v. 2.0; gEVAL manual curation v. 2021-04-21
Expected final version:
no
Genome coverage:
33.0x
Sequencing technology:
PacBio Sequel II HiFi; 10X Genomics linked reads; Bionano Genomics DLS; Arima Genomics Hi-C
Linked assembly:
GCA_018492705.1 (alternate pseudohaplotype of diploid)

IDs: 10117431 [UID] 26892258 [GenBank] 27280478 [RefSeq]

See Genome Information for Alosa sapidissima

There are 3 assemblies for this organism

See more

History (Show revision history)

Comment

Global statistics

Total sequence length903,581,644
Total ungapped length898,585,832
Gaps between scaffolds0
Number of scaffolds74
Scaffold N5038,440,066
Scaffold L5011
Number of contigs1,713
Contig N501,565,278
Contig L50165
Total number of chromosomes and plasmids25
Number of component sequences (WGS or clone)74

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_018492695.1)
Molecule nameGenBank sequenceRefSeq sequenceUnlocalized
sequences count
Chromosome 1CM031716.1=NC_055957.10
Chromosome 2CM031717.1=NC_055958.10
Chromosome 3CM031718.1=NC_055959.10
Chromosome 4CM031719.1=NC_055960.10
Chromosome 5CM031720.1=NC_055961.10
Chromosome 6CM031721.1=NC_055962.11
Chromosome 7CM031722.1=NC_055963.10
Chromosome 8CM031723.1=NC_055964.10
Chromosome 9CM031724.1=NC_055965.10
Chromosome 10CM031725.1=NC_055966.10
Chromosome 11CM031726.1=NC_055967.10
Chromosome 12CM031727.1=NC_055968.10
Chromosome 13CM031728.1=NC_055969.10
Chromosome 14CM031729.1=NC_055970.10
Chromosome 15CM031730.1=NC_055971.10
Chromosome 16CM031731.1=NC_055972.10
Chromosome 17CM031732.1=NC_055973.10
Chromosome 18CM031733.1=NC_055974.10
Chromosome 19CM031734.1=NC_055975.11
Chromosome 20CM031735.1=NC_055976.10
Chromosome 21CM031736.1=NC_055977.10
Chromosome 22CM031737.1=NC_055978.10
Chromosome 23CM031738.1=NC_055979.10
Chromosome 24CM031739.1=NC_055980.12
unplacedn/an/an/a45

Assembly statistics

MoleculeSequence RoleTotal
Length
Scaffold
Count
Ungapped
Length
Scaffold
N50
Spanned
Gaps
Unspanned
Gaps
AllAssembled molecule903,564,94773898,569,13538,440,0661,6390
Chromosome 1Assembled molecule56,504,578156,319,68956,504,578600
Chromosome 2Assembled molecule44,392,265144,105,49944,392,265840
Chromosome 3Assembled molecule41,744,500141,503,79141,744,500430
Chromosome 4Assembled molecule40,364,483140,209,71440,364,483520
Chromosome 5Assembled molecule40,211,269140,080,04740,211,269590
Chromosome 6AllAssembled moleculeUnlocalized scaffolds39,837,10339,814,91122,19221139,480,53339,458,34122,19239,814,91139,814,91122,19261610000
Chromosome 7Assembled molecule39,350,476139,238,83739,350,476730
Chromosome 8Assembled molecule38,912,301138,705,16538,912,301670
Chromosome 9Assembled molecule38,593,806138,328,06238,593,806800
Chromosome 10Assembled molecule38,583,819138,487,40738,583,819670
Chromosome 11Assembled molecule38,440,066138,240,04938,440,066550
Chromosome 12Assembled molecule38,278,902137,934,97938,278,902660
Chromosome 13Assembled molecule37,159,020137,042,71937,159,020500
Chromosome 14Assembled molecule36,832,652136,718,00136,832,652520
Chromosome 15Assembled molecule35,536,770135,354,78435,536,770850
Chromosome 16Assembled molecule35,201,806135,038,09935,201,806770
Chromosome 17Assembled molecule34,941,941134,481,26934,941,941410
Chromosome 18Assembled molecule32,793,614132,500,72432,793,614910
Chromosome 19AllAssembled moleculeUnlocalized scaffolds32,502,17032,206,363295,80721132,422,12232,126,315295,80732,206,36332,206,363295,80761610000
Chromosome 20Assembled molecule32,252,668132,050,74232,252,668830
Chromosome 21Assembled molecule32,081,259131,847,47232,081,259900
Chromosome 22Assembled molecule31,742,902131,481,84831,742,902810
Chromosome 23Assembled molecule31,227,213131,005,89231,227,213710
Chromosome 24AllAssembled moleculeUnlocalized scaffolds30,893,97530,811,94382,03231230,806,80230,725,27081,53230,811,94330,811,94349,70289881000
unplacedAssembled molecule5,185,389455,184,889233,92610
MoleculeTotal
Length
Mitochondrion MT16,697
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