Genome assembly GRCm39
reference

FTP
Actions
NCBI RefSeq assembly
GCF_000001635.27
Submitted GenBank assembly
GCA_000001635.9
Taxon
Mus musculus (house mouse)
Strain
C57BL/6J
Synonym
mm39
Assembly type
haploid
Submitter
Genome Reference Consortium
Date
Jun 24, 2020

Assembly statistics

RefSeqGenBank
Genome size2.7 Gb2.7 Gb
Total ungapped length2.7 Gb2.7 Gb
Gaps between scaffolds143143
Number of chromosomes2121
Number of organelles11
Number of scaffolds101101
Scaffold N50106.1 Mb106.1 Mb
Scaffold L501111
Number of contigs305305
Contig N5059.5 Mb59.5 Mb
Contig L501515
GC percent4242
Assembly levelChromosomeChromosome
View sequencesview RefSeq sequencesview GenBank sequences

Additional genomes

Browse all Mus musculus genomes (70)

BioProject

PRJNA20689

Genome sequence finishing for Mus musculus, currently maintained by the Genome Reference Consortium (GRC)

Annotation details

See full annotation report
RefSeq
ProviderNCBI RefSeq
NameGCF_000001635.27-RS_2024_02
DateFeb 1, 2024
Genes50,763
Protein-coding22,198
Software version10.2

Quality analysis

BUSCO analysis (4.1.4)

C:99.5%[S:98.6%,D:0.9%],F:0.2%,M:0.4%,n:13798

glires_odb10 (13798)

Chromosomes

Chromosome
GenBank
RefSeq
Size (bp)
GC content (%)
Unlocalized count
Action
1CM000994.3NC_000067.7195,154,27941.56
2CM000995.3NC_000068.8181,755,01742.50
3CM000996.3NC_000069.7159,745,31640.50
4CM000997.3NC_000070.7156,860,68642.51
5CM000998.3NC_000071.7151,758,14942.55
6CM000999.3NC_000072.7149,588,04441.50
7CM001000.3NC_000073.7144,995,196431
8CM001001.3NC_000074.7130,127,69442.50
9CM001002.3NC_000075.7124,359,700430
10CM001003.3NC_000076.7130,530,86241.50
11CM001004.3NC_000077.7121,973,369440
12CM001005.3NC_000078.7120,092,757420
13CM001006.3NC_000079.7120,883,17541.50
14CM001007.3NC_000080.7125,139,656410
15CM001008.3NC_000081.7104,073,951420
16CM001009.3NC_000082.798,008,968410
17CM001010.3NC_000083.795,294,69942.50
18CM001011.3NC_000084.790,720,76341.50
19CM001012.3NC_000085.761,420,004430
XCM001013.3NC_000086.8169,476,59239.51
YCM001014.3NC_000087.891,455,967394
MTAY172335.1NC_005089.116,29936.50

Note: This genome assembly includes 21 unplaced scaffolds.

Revision history

GenBank
RefSeq
Name
Level
Date
Action
GCA_000001635.9GCF_000001635.27GRCm39ChromosomeJun 24, 2020
GCA_000001635.8GCF_000001635.26GRCm38.p6ChromosomeSep 15, 2017
GCA_000001635.7GCF_000001635.25GRCm38.p5ChromosomeJun 29, 2016
GCA_000001635.6GCF_000001635.24GRCm38.p4ChromosomeMar 23, 2015
GCA_000001635.5GCF_000001635.23GRCm38.p3ChromosomeMar 20, 2014
GCA_000001635.4GCF_000001635.22GRCm38.p2ChromosomeMar 7, 2013
GCA_000001635.3GCF_000001635.21GRCm38.p1ChromosomeAug 21, 2012
GCA_000001635.2GCF_000001635.20GRCm38ChromosomeJan 9, 2012
GCA_000001635.1GCF_000001635.18MGSCv37ChromosomeOct 21, 2010
GCA_000001635.1GCF_000001635.16MGSCv37ChromosomeJun 21, 2007

n/a

GCF_000001635.15MGSCv36ChromosomeMay 26, 2006

n/a

GCF_000001635.14MGSCv35ChromosomeDec 5, 2005

n/a

GCF_000001635.13MGSCv34ChromosomeMay 16, 2005

n/a

GCF_000001635.12MGSCv3ChromosomeMay 15, 2002