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CAST_EiJ_v1

Organism name:
Mus musculus castaneus (southeastern Asian house mouse)
Infraspecific name:
Strain: CAST/EiJ
Sex:
female
BioSample:
SAMN04489822
BioProject:
PRJNA310854
Submitter:
Wellcome Trust Sanger Institute
Date:
2016/04/26
Assembly level:
Chromosome
Genome representation:
full
GenBank assembly accession:
GCA_001624445.1 (latest)
RefSeq assembly accession:
n/a
RefSeq assembly and GenBank assembly identical:
n/a
WGS Project:
LVXN01
Assembly method:
SGA v. 0.9.19; SOAP denovo2 v. r240; Dovetail Genomics v. August-2015; Ragout v. 2.0b
Expected final version:
no
Reference guided assembly:
GCA_000001635.2
Genome coverage:
60.0x
Sequencing technology:
Illumina

IDs: 731271 [UID] 3209048 [GenBank]

See Genome Information for Mus musculus

There are 24 assemblies for this organism

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History (Show revision history)

Global statistics

Total sequence length2,653,990,650
Total ungapped length2,286,959,630
Gaps between scaffolds0
Number of scaffolds2,977
Scaffold N50133,752,109
Scaffold L509
Number of contigs391,250
Contig N5011,642
Contig L5056,171
Total number of chromosomes and plasmids21
Number of component sequences (WGS or clone)52,352

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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 (GCA_001624455.1)
Molecule nameGenBank sequenceRefSeq sequenceUnlocalized
sequences count
Chromosome 1CM003994.1n/an/a0
Chromosome 2CM003995.1n/an/a0
Chromosome 3CM003996.1n/an/a0
Chromosome 4CM003997.1n/an/a1
Chromosome 5CM003998.1n/an/a0
Chromosome 6CM003999.1n/an/a0
Chromosome 7CM004000.1n/an/a0
Chromosome 8CM004001.1n/an/a0
Chromosome 9CM004002.1n/an/a0
Chromosome 10CM004003.1n/an/a0
Chromosome 11CM004004.1n/an/a0
Chromosome 12CM004005.1n/an/a0
Chromosome 13CM004006.1n/an/a0
Chromosome 14CM004007.1n/an/a0
Chromosome 15CM004008.1n/an/a0
Chromosome 16CM004009.1n/an/a0
Chromosome 17CM004010.1n/an/a0
Chromosome 18CM004011.1n/an/a0
Chromosome 19CM004012.1n/an/a0
Chromosome XCM004013.1n/an/a1
unplacedn/an/an/a2,954

Assembly statistics

MoleculeSequence RoleTotal
Length
Scaffold
Count
Ungapped
Length
Scaffold
N50
Spanned
Gaps
Unspanned
Gaps
AllAssembled molecule2,653,974,3512,9762,286,943,331133,752,109388,2730
Chromosome 1Assembled molecule200,424,5681173,044,753200,424,56829,3610
Chromosome 2Assembled molecule184,952,9601162,254,868184,952,96024,3920
Chromosome 3Assembled molecule162,825,5431139,566,438162,825,54324,8740
Chromosome 4AllAssembled moleculeUnlocalized scaffolds156,174,714156,060,657114,057211134,646,649134,559,30087,349156,060,657156,060,657114,05722,49222,45339000
Chromosome 5Assembled molecule156,282,1851133,150,298156,282,18523,0410
Chromosome 6Assembled molecule152,789,6391131,379,906152,789,63921,5370
Chromosome 7Assembled molecule142,579,3511120,100,084142,579,35120,7040
Chromosome 8Assembled molecule132,173,0231114,458,548132,173,02318,5580
Chromosome 9Assembled molecule126,342,0131111,948,661126,342,01315,3320
Chromosome 10Assembled molecule133,752,1091115,729,108133,752,10919,5210
Chromosome 11Assembled molecule126,372,5551112,245,097126,372,55515,4890
Chromosome 12Assembled molecule116,209,7491100,470,271116,209,74916,6680
Chromosome 13Assembled molecule121,085,6971103,431,650121,085,69717,0240
Chromosome 14Assembled molecule119,554,5851102,832,570119,554,58517,9050
Chromosome 15Assembled molecule106,035,878192,052,149106,035,87815,2970
Chromosome 16Assembled molecule99,123,743186,515,74799,123,74314,4410
Chromosome 17Assembled molecule98,844,223183,249,50998,844,22315,0600
Chromosome 18Assembled molecule91,110,059180,105,30891,110,05912,3450
Chromosome 19Assembled molecule61,167,864153,765,10361,167,8647,6020
Chromosome XAllAssembled moleculeUnlocalized scaffolds147,916,378147,371,385544,993211123,872,957123,384,626488,331147,371,385147,371,385544,99330,60430,51490000
unplacedAssembled molecule18,257,5152,95412,123,6578,9256,0260
MoleculeTotal
Length
Scaffold
Count
Ungapped
Length
Scaffold
N50
Spanned
Gaps
Unspanned
Gaps
Mitochondrion MT16,299116,29916,29900
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