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Callithrix jacchus-3.2

Organism name:
Callithrix jacchus (white-tufted-ear marmoset)
BioSample:
SAMN02981242
BioProject:
PRJNA20401
Submitter:
Washington University (WashU)
Date:
2010/01/22
Synonyms:
calJac3
Assembly level:
Chromosome
Genome representation:
full
Excluded from RefSeq:
  • superseded by newer assembly for species
GenBank assembly accession:
GCA_000004665.1 (latest)
RefSeq assembly accession:
GCF_000004665.1 (suppressed) see latest RefSeq assembly for this species
RefSeq assembly and GenBank assembly identical:
yes
WGS Project:
ACFV01
Assembly method:
PCAP v. 2009
Genome coverage:
6.6x
Sequencing technology:
ABI 3730

IDs: 6608 [UID] 5898 [GenBank] 6608 [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

The marmoset (Callithrix jacchus) genome was sequenced to 6X coverage in collaboration with the Baylor University College of Medicine Human Genome Sequencing Center (BCM-HGSC). The assembly consists of whole genome shotgun plasmid, fosmid and BAC end sequences. The DNA ... source used for the plasmid and fosmid libraries (female, animal id# 186/17066) was kindly provided by Dr. Suzette Tardif, Southwestern National Primate Research Center (San Antonio, Texas). The DNA source for the CHORI-259 BAC library was male and the full brother of the female used for whole genome shotgun sequencing (# 186/17066). The combined sequence reads were assembled using the PCAP software (Genome Res. 13(9):2164-70 2003) and filtered for all known non-marmoset sequence contaminants. This assembly is referred to as Callithrix jacchus-3.2. For questions regarding this marmoset assembly please visit our marmoset genome web page and contact the designated person for marmoset. Funding for the sequence characterization of the marmoset genome was provided by the National Human Genome Research Institute (NHGRI), National Institutes of Health (NIH).  more

Global statistics

Total sequence length2,914,958,544
Total ungapped length2,752,505,800
Gaps between scaffolds2,242
Number of scaffolds16,399
Scaffold N505,167,444
Scaffold L50148
Number of contigs201,371
Contig N5029,273
Contig L5026,764
Total number of chromosomes and plasmids24
Number of component sequences (WGS or clone)201,514

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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 (GCA_000004685.1)
Molecule nameGenBank sequenceRefSeq sequenceUnlocalized
sequences count
Chromosome 1CM000856.1=NC_013896.1272
Chromosome 2CM000857.1=NC_013897.1160
Chromosome 3CM000858.1=NC_013898.1109
Chromosome 4CM000859.1=NC_013899.1153
Chromosome 5CM000860.1=NC_013900.1148
Chromosome 6CM000861.1=NC_013901.1155
Chromosome 7CM000862.1=NC_013902.1107
Chromosome 8CM000863.1=NC_013903.182
Chromosome 9CM000864.1=NC_013904.1138
Chromosome 10CM000865.1=NC_013905.1106
Chromosome 11CM000866.1=NC_013906.1114
Chromosome 12CM000867.1=NC_013907.187
Chromosome 13CM000868.1=NC_013908.176
Chromosome 14CM000869.1=NC_013909.198
Chromosome 15CM000870.1=NC_013910.161
Chromosome 16CM000871.1=NC_013911.164
Chromosome 17CM000872.1=NC_013912.149
Chromosome 18CM000873.1=NC_013913.151
Chromosome 19CM000874.1=NC_013914.128
Chromosome 20CM000875.1=NC_013915.168
Chromosome 21CM000876.1=NC_013916.142
Chromosome 22CM000877.1=NC_013917.1129
Chromosome XCM000878.1=NC_013918.1279
Chromosome YCM000879.1=NC_013919.149
unplacedn/an/an/a11,556

Assembly statistics

MoleculeSequence RoleTotal
Length		Scaffold
Count		Ungapped
Length		Scaffold
N50		Spanned
Gaps		Unspanned
Gaps
AllAssembled molecule2,914,958,54416,3992,752,505,8005,167,444184,9722,242
Chromosome 1AllAssembled moleculeUnlocalized scaffolds215,927,180210,400,6355,526,545501229272204,289,788199,159,6085,130,1804,078,1464,078,14641,67313,45213,0154372302300
Chromosome 2AllAssembled moleculeUnlocalized scaffolds207,607,435204,313,9513,293,484294134160197,006,822193,958,9293,047,8936,268,8086,268,80841,39512,01111,7392721351350
Chromosome 3AllAssembled moleculeUnlocalized scaffolds192,728,775190,850,7961,877,97919586109183,907,627182,151,6781,755,9497,736,7107,736,71031,7389,9409,81013087870
Chromosome 4AllAssembled moleculeUnlocalized scaffolds174,673,594171,630,2743,043,320254101153166,354,324163,489,1812,865,1437,547,6417,566,73246,1709,6539,4302231021020
Chromosome 5AllAssembled moleculeUnlocalized scaffolds161,704,552159,171,4112,533,141296148148152,065,395149,672,1882,393,2074,422,2014,422,20127,47011,97611,7791971491490
Chromosome 6AllAssembled moleculeUnlocalized scaffolds160,852,914158,406,7342,446,180255100155152,643,443150,392,5492,250,8948,265,9708,265,97026,0278,9758,7891861011010
Chromosome 7AllAssembled moleculeUnlocalized scaffolds157,268,708155,834,2431,434,46518982107148,662,074147,318,1371,343,9377,194,4647,194,46420,57910,49110,37012183830
Chromosome 8AllAssembled moleculeUnlocalized scaffolds129,240,703128,169,2931,071,4101496782122,375,159121,367,3521,007,8076,591,4686,591,46819,8757,0706,9809068680
Chromosome 9AllAssembled moleculeUnlocalized scaffolds126,052,641124,281,9921,770,649265127138118,794,215117,157,6261,636,5896,027,9056,640,99719,4038,2708,1241461281280
Chromosome 10AllAssembled moleculeUnlocalized scaffolds133,990,898132,174,5271,816,37120498106126,576,572124,851,7271,724,8455,855,1306,230,96045,9308,3708,22914199990
Chromosome 11AllAssembled moleculeUnlocalized scaffolds132,298,687130,397,2571,901,43020288114124,392,285122,636,1041,756,1816,651,8226,651,82228,4138,5008,33017089890
Chromosome 12AllAssembled moleculeUnlocalized scaffolds123,473,099121,768,1011,704,99822413787116,236,772114,670,7361,566,0363,099,9243,099,92434,7928,4478,3061411381380
Chromosome 13AllAssembled moleculeUnlocalized scaffolds118,961,469117,903,8541,057,6151507476112,945,031111,969,328975,7035,396,1205,396,12019,1676,4646,3947075750
Chromosome 14AllAssembled moleculeUnlocalized scaffolds110,008,065108,792,8651,215,2001788098104,841,431103,709,6891,131,7424,218,7214,218,72119,6966,4566,3639381810
Chromosome 15AllAssembled moleculeUnlocalized scaffolds99,215,59998,464,013751,586103426195,175,07294,476,333698,7396,978,4126,978,41222,6075,5935,5375643430
Chromosome 16AllAssembled moleculeUnlocalized scaffolds97,861,70096,796,9701,064,730104406493,635,02692,655,659979,3676,908,9536,908,95329,9225,4595,3689141410
Chromosome 17AllAssembled moleculeUnlocalized scaffolds75,472,40274,750,902721,50066174972,239,60471,586,435653,16916,666,13716,666,13721,8223,9233,8616218180
Chromosome 18AllAssembled moleculeUnlocalized scaffolds48,664,39547,448,7591,215,63694435146,600,66645,436,7691,163,8974,989,1014,989,10144,3013,0522,9876544440
Chromosome 19AllAssembled moleculeUnlocalized scaffolds50,019,79149,578,535441,25669412847,769,72847,372,264397,4643,828,9673,828,96726,1193,1143,0862842420
Chromosome 20AllAssembled moleculeUnlocalized scaffolds46,338,00144,557,9581,780,043107396843,948,36542,319,8521,628,5134,074,4374,074,43783,3123,2733,11915440400
Chromosome 21AllAssembled moleculeUnlocalized scaffolds51,266,54450,472,720793,82489474248,111,30347,372,052739,2515,152,9425,152,94238,7102,8722,8244848480
Chromosome 22AllAssembled moleculeUnlocalized scaffolds51,931,09849,145,3162,785,78224811912945,598,39143,045,2902,553,1011,016,1661,119,25948,5696,8176,5182991201200
Chromosome XAllAssembled moleculeUnlocalized scaffolds146,981,136142,054,2084,926,928532253279136,372,298131,921,4814,450,8171,997,5382,039,87625,01310,76910,2884812542540
Chromosome YAllAssembled moleculeUnlocalized scaffolds3,528,0732,853,901674,1727526493,179,2642,606,259573,0052,038,3642,038,36418,5673312428927270
unplacedAssembled molecule98,891,08511,55688,785,14513,4089,6940