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mCalJa1.2.pat.X

Organism name:
Callithrix jacchus (white-tufted-ear marmoset)
Isolate:
mCalJac1
Sex:
male
BioSample:
SAMN12368443
BioProject:
PRJNA597600
Submitter:
Vertebrate Genomes Project
Date:
2021/04/28
Assembly level:
Chromosome
Genome representation:
full
RefSeq category:
representative genome
GenBank assembly accession:
GCA_011100555.2 (latest)
RefSeq assembly accession:
GCF_011100555.1 (latest)
RefSeq assembly and GenBank assembly identical:
no (hide details)
  • Only in GenBank: chromosome MT
  • Data displayed for RefSeq version
WGS Project:
JAALXP02
Assembly method:
TrioCanu v. 1.8; purge_dups v. 1.0.0; Scaff 10x v. 4.1.0; Bionano solve solve v. 3.2.1_04122018; Salsa2 HiC v. 2.2; Arrow polishing and gap filling v. smrtlink_6.0.0.47841; Longranger Align v. 2.2.2; Freebayes v. 1.3.1; gEVAL manual curation v. 2019-12-11; Zhang manual curation v. 2021-04-25; VGP assembly pipeline v. 1.6
Expected final version:
no
Genome coverage:
63.44x
Sequencing technology:
PacBio Sequel I CLR; Illumina NovaSeq; Arima Genomics Hi-C; Bionano Genomics DLS

IDs: 9936991 [UID] 26492428 [GenBank] 41093638 [RefSeq]

See Genome Information for Callithrix jacchus

Pathogen Detection Resources

There are 13 assemblies for this organism

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History (Show revision history)

Comment

Global statistics

Total sequence length2,874,864,526
Total ungapped length2,861,174,012
Gaps between scaffolds0
Number of scaffolds1,233
Scaffold N50136,971,485
Scaffold L509
Number of contigs2,398
Contig N5013,222,669
Contig L5060
Total number of chromosomes and plasmids24
Number of component sequences (WGS or clone)1,233

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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_011100565.1)
Molecule nameGenBank sequenceRefSeq sequenceUnlocalized
sequences count
Chromosome 1CM021915.1=NC_071442.10
Chromosome 2CM021916.1=NC_071443.10
Chromosome 3CM021917.1=NC_071444.10
Chromosome 4CM021918.1=NC_071445.10
Chromosome 5CM021919.1=NC_071446.10
Chromosome 6CM021920.1=NC_071447.10
Chromosome 7CM021921.1=NC_071448.10
Chromosome 8CM021922.1=NC_071449.10
Chromosome 9CM021923.1=NC_071450.10
Chromosome 10CM021924.1=NC_071451.10
Chromosome 11CM021925.1=NC_071452.10
Chromosome 12CM021926.1=NC_071453.10
Chromosome 13CM021927.1=NC_071454.10
Chromosome 14CM021928.1=NC_071455.10
Chromosome 15CM021929.1=NC_071456.10
Chromosome 16CM021930.1=NC_071457.10
Chromosome 17CM021931.1=NC_071458.10
Chromosome 18CM021932.1=NC_071459.10
Chromosome 19CM021933.1=NC_071460.10
Chromosome 20CM021934.1=NC_071461.10
Chromosome 21CM021935.1=NC_071462.10
Chromosome 22CM021936.1=NC_071463.10
Chromosome XCM021937.1=NC_071464.115
Chromosome YCM021938.2=NC_071465.186
unplacedn/an/an/a1,108

Assembly statistics

MoleculeSequence RoleTotal
Length		Scaffold
Count		Ungapped
Length		Scaffold
N50		Spanned
Gaps		Unspanned
Gaps
AllAssembled molecule2,874,864,5261,2332,861,174,012136,971,4851,1650
Chromosome 1Assembled molecule216,975,7691215,404,040216,975,769810
Chromosome 2Assembled molecule202,808,4611202,516,445202,808,461200
Chromosome 3Assembled molecule189,455,0761189,024,231189,455,076270
Chromosome 4Assembled molecule173,414,0571172,460,868173,414,057490
Chromosome 5Assembled molecule161,716,9021160,956,221161,716,902480
Chromosome 6Assembled molecule159,674,5591159,201,487159,674,559430
Chromosome 7Assembled molecule156,129,2521155,866,778156,129,252370
Chromosome 8Assembled molecule126,104,5921125,968,902126,104,592220
Chromosome 9Assembled molecule132,900,6401132,536,250132,900,640270
Chromosome 10Assembled molecule136,971,4851136,177,333136,971,485270
Chromosome 11Assembled molecule128,529,4011128,477,923128,529,40180
Chromosome 12Assembled molecule123,697,8271122,182,016123,697,827480
Chromosome 13Assembled molecule117,638,7871117,309,713117,638,787110
Chromosome 14Assembled molecule112,969,5291112,724,439112,969,529490
Chromosome 15Assembled molecule98,621,277198,018,30198,621,277180
Chromosome 16Assembled molecule98,110,366198,025,94598,110,366240
Chromosome 17Assembled molecule74,700,100174,452,82074,700,100110
Chromosome 18Assembled molecule47,063,576145,916,03247,063,576230
Chromosome 19Assembled molecule50,540,917150,323,25250,540,917200
Chromosome 20Assembled molecule44,412,365144,373,88344,412,365110
Chromosome 21Assembled molecule50,614,742150,543,75450,614,742250
Chromosome 22Assembled molecule49,900,457149,679,83649,900,457320
Chromosome XAllAssembled moleculeUnlocalized scaffolds147,394,785146,897,247497,53816115145,176,371144,678,833497,538146,897,247146,897,24733,8971711710000
Chromosome YAllAssembled moleculeUnlocalized scaffolds13,847,7434,974,7738,872,9708718613,529,0664,703,6908,825,3761,024,4964,974,773128,013903654000
unplacedAssembled molecule60,671,8611,10860,328,10659,8442430