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GRCm39

Description:
Genome Reference Consortium Mouse Build 39
Organism name:
Mus musculus (house mouse)
Infraspecific name:
Strain: C57BL/6J
BioProject:
PRJNA20689
Submitter:
Genome Reference Consortium
Date:
2020/06/24
Synonyms:
mm39
Assembly level:
Chromosome
Genome representation:
full
RefSeq category:
reference genome
GenBank assembly accession:
GCA_000001635.9 (latest)
RefSeq assembly accession:
GCF_000001635.27 (latest)
RefSeq assembly and GenBank assembly identical:
yes

IDs: 7358741 [UID] 20371618 [GenBank] 20412818 [RefSeq]

See Genome Information for Mus musculus

Pathogen Detection Resources

There are 65 assemblies for this organism

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History (Show revision history)

Comment

Genome-Annotation-Data

##Genome-Annotation-Data-START##
Annotation Provider::NCBI RefSeq
Annotation Status::Updated annotation
Annotation Name::GCF_000001635.27-RS_2024_02
Annotation Pipeline::NCBI eukaryotic genome annotation pipeline
Annotation Software Version::10.2
URL Organism::Mus_musculus
Annotation Method::Best-placed RefSeq; Gnomon; RefSeqFE; cmsearch; tRNAscan-SE
Features Annotated::Gene; mRNA; CDS; ncRNA
##Genome-Annotation-Data-END##

Global statistics

Number of regions with alternate loci or patches3
Total sequence length2,728,222,451
Total ungapped length2,654,621,837
Gaps between scaffolds143
Number of scaffolds102
Scaffold N50106,145,001
Scaffold L5011
Number of contigs306
Contig N5059,462,871
Contig L5015
Total number of chromosomes and plasmids22
Number of component sequences (WGS or clone)21,255

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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 (C57BL/6J)
non-nuclear

Regions

NameLocation
PARX:168752755-169376592
CENYY:4072168-4161965
PARY:90757114-91355967
Assembly Unit: Primary Assembly (C57BL/6J) (GCF_000000055.20)
Molecule nameGenBank sequenceRefSeq sequenceUnlocalized
sequences count
Chromosome 1CM000994.3=NC_000067.76
Chromosome 2CM000995.3=NC_000068.80
Chromosome 3CM000996.3=NC_000069.70
Chromosome 4CM000997.3=NC_000070.71
Chromosome 5CM000998.3=NC_000071.75
Chromosome 6CM000999.3=NC_000072.70
Chromosome 7CM001000.3=NC_000073.71
Chromosome 8CM001001.3=NC_000074.70
Chromosome 9CM001002.3=NC_000075.70
Chromosome 10CM001003.3=NC_000076.70
Chromosome 11CM001004.3=NC_000077.70
Chromosome 12CM001005.3=NC_000078.70
Chromosome 13CM001006.3=NC_000079.70
Chromosome 14CM001007.3=NC_000080.70
Chromosome 15CM001008.3=NC_000081.70
Chromosome 16CM001009.3=NC_000082.70
Chromosome 17CM001010.3=NC_000083.70
Chromosome 18CM001011.3=NC_000084.70
Chromosome 19CM001012.3=NC_000085.70
Chromosome XCM001013.3=NC_000086.81
Chromosome YCM001014.3=NC_000087.84
unplacedn/an/an/a21

Assembly statistics

MoleculeSequence RoleTotal
Length		Scaffold
Count		Ungapped
Length		Scaffold
N50		Spanned
Gaps		Unspanned
Gaps
AllAssembled molecule2,728,206,1521012,654,605,538106,145,001204143
Chromosome 1AllAssembled moleculeUnlocalized scaffolds195,974,786195,154,279820,507826192,774,546191,954,039820,507109,679,455109,679,455206,961660660
Chromosome 2Assembled molecule181,755,0175178,354,017172,291,09429
Chromosome 3Assembled molecule159,745,3161156,538,186156,645,31644
Chromosome 4AllAssembled moleculeUnlocalized scaffolds156,862,662156,860,6861,976321152,711,764152,709,7881,97686,185,03686,185,0361,97629290660
Chromosome 5AllAssembled moleculeUnlocalized scaffolds153,496,487151,758,1491,738,338615149,744,487148,006,1491,738,338148,608,149148,608,149953,012330550
Chromosome 6Assembled molecule149,588,0442146,383,044101,774,07116
Chromosome 7AllAssembled moleculeUnlocalized scaffolds145,171,164144,995,196175,968321141,850,664141,674,696175,968106,145,001106,145,001175,968440660
Chromosome 8Assembled molecule130,127,6942125,677,394108,725,50066
Chromosome 9Assembled molecule124,359,7002121,184,854120,961,46675
Chromosome 10Assembled molecule130,530,8621127,155,762127,380,86225
Chromosome 11Assembled molecule121,973,3691118,822,369118,823,36915
Chromosome 12Assembled molecule120,092,7571116,922,757116,942,75715
Chromosome 13Assembled molecule120,883,1751117,256,175117,733,17535
Chromosome 14Assembled molecule125,139,6562121,174,156105,519,88436
Chromosome 15Assembled molecule104,073,9511100,923,951100,923,95105
Chromosome 16Assembled molecule98,008,968194,850,96894,858,96835
Chromosome 17Assembled molecule95,294,699291,815,49981,319,82556
Chromosome 18Assembled molecule90,720,763187,605,76387,620,76314
Chromosome 19Assembled molecule61,420,004258,220,00454,530,07906
Chromosome XAllAssembled moleculeUnlocalized scaffolds170,035,695169,476,592559,10315141164,715,435164,206,332509,10344,068,26944,068,269559,1035049119190
Chromosome YAllAssembled moleculeUnlocalized scaffolds92,212,12691,455,967756,1592016489,242,12688,485,967756,15917,801,35117,801,351182,34788019190
unplacedAssembled molecule739,25721681,61731,704650
MoleculeTotal
Length
Mitochondrion MT16,299
Region
Name		LocationScaffold
Count		Total
Length		Ungapped
Length		Scaffold
N50		Spanned
Gaps
CENYY:4072168-416196500000