Genome assembly GRCm39reference
- 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
RefSeq | GenBank | |
---|---|---|
Genome size | 2.7 Gb | 2.7 Gb |
Total ungapped length | 2.7 Gb | 2.7 Gb |
Gaps between scaffolds | 143 | 143 |
Number of chromosomes | 21 | 21 |
Number of organelles | 1 | 1 |
Number of scaffolds | 101 | 101 |
Scaffold N50 | 106.1 Mb | 106.1 Mb |
Scaffold L50 | 11 | 11 |
Number of contigs | 305 | 305 |
Contig N50 | 59.5 Mb | 59.5 Mb |
Contig L50 | 15 | 15 |
GC percent | 42 | 42 |
Assembly level | Chromosome | Chromosome |
View sequences | view RefSeq sequences | view GenBank sequences |
Additional genomes
Browse all Mus musculus genomes (70)BioProject
PRJNA20689Genome sequence finishing for Mus musculus, currently maintained by the Genome Reference Consortium (GRC)
Annotation details
See full annotation reportRefSeq | |
---|---|
Provider | NCBI RefSeq |
Name | GCF_000001635.27-RS_2024_02 |
Date | Feb 1, 2024 |
Genes | 50,763 |
Protein-coding | 22,198 |
Software version | 10.2 |
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 |
---|---|---|---|---|---|---|
1 | CM000994.3 | NC_000067.7 | 195,154,279 | 41.5 | 6 | |
2 | CM000995.3 | NC_000068.8 | 181,755,017 | 42.5 | 0 | |
3 | CM000996.3 | NC_000069.7 | 159,745,316 | 40.5 | 0 | |
4 | CM000997.3 | NC_000070.7 | 156,860,686 | 42.5 | 1 | |
5 | CM000998.3 | NC_000071.7 | 151,758,149 | 42.5 | 5 | |
6 | CM000999.3 | NC_000072.7 | 149,588,044 | 41.5 | 0 | |
7 | CM001000.3 | NC_000073.7 | 144,995,196 | 43 | 1 | |
8 | CM001001.3 | NC_000074.7 | 130,127,694 | 42.5 | 0 | |
9 | CM001002.3 | NC_000075.7 | 124,359,700 | 43 | 0 | |
10 | CM001003.3 | NC_000076.7 | 130,530,862 | 41.5 | 0 | |
11 | CM001004.3 | NC_000077.7 | 121,973,369 | 44 | 0 | |
12 | CM001005.3 | NC_000078.7 | 120,092,757 | 42 | 0 | |
13 | CM001006.3 | NC_000079.7 | 120,883,175 | 41.5 | 0 | |
14 | CM001007.3 | NC_000080.7 | 125,139,656 | 41 | 0 | |
15 | CM001008.3 | NC_000081.7 | 104,073,951 | 42 | 0 | |
16 | CM001009.3 | NC_000082.7 | 98,008,968 | 41 | 0 | |
17 | CM001010.3 | NC_000083.7 | 95,294,699 | 42.5 | 0 | |
18 | CM001011.3 | NC_000084.7 | 90,720,763 | 41.5 | 0 | |
19 | CM001012.3 | NC_000085.7 | 61,420,004 | 43 | 0 | |
X | CM001013.3 | NC_000086.8 | 169,476,592 | 39.5 | 1 | |
Y | CM001014.3 | NC_000087.8 | 91,455,967 | 39 | 4 | |
MT | AY172335.1 | NC_005089.1 | 16,299 | 36.5 | 0 |
Note: This genome assembly includes 21 unplaced scaffolds.
Revision history
GenBank | RefSeq | Name | Level | Date | Action |
---|---|---|---|---|---|
GCA_000001635.9 | GCF_000001635.27 | GRCm39 | Chromosome | Jun 24, 2020 | |
GCA_000001635.8 | GCF_000001635.26 | GRCm38.p6 | Chromosome | Sep 15, 2017 | |
GCA_000001635.7 | GCF_000001635.25 | GRCm38.p5 | Chromosome | Jun 29, 2016 | |
GCA_000001635.6 | GCF_000001635.24 | GRCm38.p4 | Chromosome | Mar 23, 2015 | |
GCA_000001635.5 | GCF_000001635.23 | GRCm38.p3 | Chromosome | Mar 20, 2014 | |
GCA_000001635.4 | GCF_000001635.22 | GRCm38.p2 | Chromosome | Mar 7, 2013 | |
GCA_000001635.3 | GCF_000001635.21 | GRCm38.p1 | Chromosome | Aug 21, 2012 | |
GCA_000001635.2 | GCF_000001635.20 | GRCm38 | Chromosome | Jan 9, 2012 | |
GCA_000001635.1 | GCF_000001635.18 | MGSCv37 | Chromosome | Oct 21, 2010 | |
GCA_000001635.1 | GCF_000001635.16 | MGSCv37 | Chromosome | Jun 21, 2007 | |
n/a | GCF_000001635.15 | MGSCv36 | Chromosome | May 26, 2006 | |
n/a | GCF_000001635.14 | MGSCv35 | Chromosome | Dec 5, 2005 | |
n/a | GCF_000001635.13 | MGSCv34 | Chromosome | May 16, 2005 | |
n/a | GCF_000001635.12 | MGSCv3 | Chromosome | May 15, 2002 |