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sAmbRad1.1.pri

Organism name:
Amblyraja radiata (thorny skate)
Isolate:
CabotCenter1
Sex:
male
BioSample:
SAMN09948523
BioProject:
PRJNA591369
Submitter:
Vertebrate Genomes Project
Date:
2020/02/21
Assembly type:
haploid (principal pseudohaplotype of diploid)
Release type:
minor
Assembly level:
Chromosome
Genome representation:
full
RefSeq category:
representative genome
GenBank assembly accession:
GCA_010909765.2 (latest)
RefSeq assembly accession:
GCF_010909765.2 (latest)
RefSeq assembly and GenBank assembly identical:
no (hide details)
  • Only in GenBank: chromosome MT
  • Data displayed for RefSeq version
WGS Project:
JAAGWR01
Assembly method:
Canu v. 1.7; purge_haplotigs v. bitbucket 7.10.2018; scaff10x v. 4.1.0; Bionano Solve DLS v. 3.3; Salsa HiC v. 2.2; Arrow smrtanalysis Pacbio polishing & gap filling v. 5.1.0.26412; longranger align v. 2.2.2; freebayes Illumina polishing v. 1.3.1; purge_dups v. ca23030ccf4254dfd2d3a5ea90d0eed41c24f88b; gEVAL manual curation v. 2020-01-13; VGP assembly pipeline v. 1.5
Expected final version:
no
Genome coverage:
128.24x
Sequencing technology:
PacBio Sequel; Illumina NovaSeq; Arima Genomics Hi-C; Bionano Genomics DLS
Linked assembly:
GCA_010909745.1 (alternate pseudohaplotype of diploid)

IDs: 9660461 [UID] 25854908 [GenBank] 25858558 [RefSeq]

See Genome Information for Amblyraja radiata

Pathogen Detection Resources

There are 2 assemblies for this organism

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History (Show revision history)

Comment

This assembly represents the principal haplotype of the diploid genome Amblyraja radiata and includes the chromosomes. The alternate haplotype sequences are in WGS project JAAGWS000000000
Chromosome 44 in assembly sAmbRad1.pri was reidentified as chromosome X in assembly sAmbRad1.1.pri in March 2021.

Global statistics

Total sequence length2,558,784,953
Total ungapped length2,367,812,701
Gaps between scaffolds0
Number of scaffolds957
Scaffold N5062,052,929
Scaffold L5013
Number of contigs4,672
Contig N501,462,921
Contig L50445
Total number of chromosomes and plasmids49
Number of component sequences (WGS or clone)957

Supplemental Content

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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_010909815.2)
Molecule nameGenBank sequenceRefSeq sequenceUnlocalized
sequences count
Chromosome 1CM021366.1=NC_045956.10
Chromosome 2CM021367.1=NC_045957.10
Chromosome 3CM021368.1=NC_045958.10
Chromosome 4CM021369.1=NC_045959.10
Chromosome 5CM021370.1=NC_045960.10
Chromosome 6CM021371.1=NC_045961.10
Chromosome 7CM021372.1=NC_045962.10
Chromosome 8CM021373.1=NC_045963.10
Chromosome 9CM021374.1=NC_045964.10
Chromosome 10CM021375.1=NC_045965.10
Chromosome 11CM021376.1=NC_045966.10
Chromosome 12CM021377.1=NC_045967.10
Chromosome 13CM021378.1=NC_045968.10
Chromosome 14CM021379.1=NC_045969.10
Chromosome 15CM021380.1=NC_045970.10
Chromosome 16CM021381.1=NC_045971.10
Chromosome 17CM021382.1=NC_045972.10
Chromosome 18CM021383.1=NC_045973.10
Chromosome 19CM021384.1=NC_045974.10
Chromosome 20CM021385.1=NC_045975.10
Chromosome 21CM021386.1=NC_045976.10
Chromosome 22CM021387.1=NC_045977.10
Chromosome 23CM021388.1=NC_045978.10
Chromosome 24CM021389.1=NC_045979.10
Chromosome 25CM021390.1=NC_045980.10
Chromosome 26CM021391.1=NC_045981.10
Chromosome 27CM021392.1=NC_045982.10
Chromosome 28CM021393.1=NC_045983.10
Chromosome 29CM021394.1=NC_045984.10
Chromosome 30CM021395.1=NC_045985.10
Chromosome 31CM021396.1=NC_045986.10
Chromosome 32CM021397.1=NC_045987.10
Chromosome 33CM021398.1=NC_045988.10
Chromosome 34CM021399.1=NC_045989.10
Chromosome 35CM021400.1=NC_045990.10
Chromosome 36CM021401.1=NC_045991.10
Chromosome 37CM021402.1=NC_045992.10
Chromosome 38CM021403.1=NC_045993.10
Chromosome 39CM021404.1=NC_045994.10
Chromosome 40CM021405.1=NC_045995.10
Chromosome 41CM021406.1=NC_045996.10
Chromosome 42CM021407.1=NC_045997.12
Chromosome 43CM021408.1=NC_045998.14
Chromosome 45CM021410.1=NC_046000.10
Chromosome 46CM021411.1=NC_046001.10
Chromosome 47CM021412.1=NC_046002.10
Chromosome 48CM021413.1=NC_046003.10
Chromosome 49CM021414.1=NC_046004.10
Chromosome XCM021409.1=NC_045999.10
unplacedn/an/an/a902

Assembly statistics

MoleculeSequence RoleTotal
Length		Scaffold
Count		Ungapped
Length		Scaffold
N50		Spanned
Gaps		Unspanned
Gaps
AllAssembled molecule2,558,784,9539572,367,812,70162,052,9293,7150
Chromosome 1Assembled molecule193,168,3041187,775,042193,168,3042670
Chromosome 2Assembled molecule151,573,6991148,186,082151,573,6991830
Chromosome 3Assembled molecule131,315,1321125,204,339131,315,1321350
Chromosome 4Assembled molecule121,814,7361119,070,747121,814,7361620
Chromosome 5Assembled molecule115,635,2431113,507,128115,635,2431530
Chromosome 6Assembled molecule104,925,409198,282,510104,925,4091210
Chromosome 7Assembled molecule91,022,384187,766,68691,022,3841070
Chromosome 8Assembled molecule83,634,287181,582,24083,634,287870
Chromosome 9Assembled molecule75,329,052173,353,93975,329,052960
Chromosome 10Assembled molecule70,094,763167,775,44270,094,763760
Chromosome 11Assembled molecule66,065,264164,586,63666,065,264850
Chromosome 12Assembled molecule62,869,304161,500,59462,869,304680
Chromosome 13Assembled molecule62,052,929160,562,99062,052,929690
Chromosome 14Assembled molecule60,892,660159,661,34160,892,660740
Chromosome 15Assembled molecule59,888,763154,516,01759,888,763720
Chromosome 16Assembled molecule52,893,959141,198,35352,893,959950
Chromosome 17Assembled molecule50,970,858149,689,15750,970,858650
Chromosome 18Assembled molecule49,750,689149,246,60149,750,689500
Chromosome 19Assembled molecule47,691,316146,421,35247,691,316540
Chromosome 20Assembled molecule46,754,034145,958,66746,754,034570
Chromosome 21Assembled molecule43,974,050142,079,04343,974,050610
Chromosome 22Assembled molecule43,788,383141,834,87043,788,383510
Chromosome 23Assembled molecule42,150,951141,587,97242,150,951460
Chromosome 24Assembled molecule40,557,729139,580,15940,557,729620
Chromosome 25Assembled molecule38,239,757136,414,94238,239,757510
Chromosome 26Assembled molecule37,436,020136,931,19437,436,020380
Chromosome 27Assembled molecule36,920,888135,930,98836,920,888580
Chromosome 28Assembled molecule36,421,429135,546,45636,421,429490
Chromosome 29Assembled molecule34,661,412134,284,76034,661,412450
Chromosome 30Assembled molecule33,336,678122,179,69833,336,678920
Chromosome 31Assembled molecule32,228,550130,615,72632,228,550470
Chromosome 32Assembled molecule31,195,906130,735,14931,195,906430
Chromosome 33Assembled molecule30,292,166129,890,61330,292,166240
Chromosome 34Assembled molecule26,768,200126,130,66526,768,200180
Chromosome 35Assembled molecule23,999,460118,453,27723,999,460460
Chromosome 36Assembled molecule23,458,400111,162,98223,458,400610
Chromosome 37Assembled molecule22,547,758122,236,39422,547,758240
Chromosome 38Assembled molecule19,490,429116,144,14919,490,429510
Chromosome 39Assembled molecule18,403,737117,444,18918,403,737410
Chromosome 40Assembled molecule17,663,30217,161,38317,663,302350
Chromosome 41Assembled molecule16,656,569113,222,19916,656,569520
Chromosome 42AllAssembled moleculeUnlocalized scaffolds16,424,5258,043,3188,381,2073125,511,7001,462,5204,049,1804,448,7698,043,3184,448,76935926000
Chromosome 43AllAssembled moleculeUnlocalized scaffolds16,213,59813,435,8642,777,73451410,243,5118,563,2101,680,30113,435,86413,435,864580,91147398000
Chromosome 45Assembled molecule15,599,296110,109,34615,599,296470
Chromosome 46Assembled molecule8,673,53717,797,2988,673,537190
Chromosome 47Assembled molecule8,058,31212,208,6918,058,312180
Chromosome 48Assembled molecule6,924,34612,472,8426,924,346150
Chromosome 49Assembled molecule3,795,52713,391,5883,795,527160
Chromosome XAssembled molecule16,063,002115,587,56016,063,002410
unplacedAssembled molecule118,498,25190285,077,494390,5864060