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MGSCv37

Organism name:
Mus musculus (house mouse)
Infraspecific name:
Strain: C57BL/6J
BioProject:
PRJNA20689
Submitter:
Genome Reference Consortium
Date:
2007/06/21
Synonyms:
mm9
Assembly type:
haploid-with-alt-loci
Assembly level:
Chromosome
Genome representation:
full
GenBank assembly accession:
GCA_000001635.1 (replaced)
RefSeq assembly accession:
GCF_000001635.16 (replaced)
RefSeq assembly and GenBank assembly identical:
no (hide details)
  • Only in GenBank: chromosome MT (in non-nuclear assembly-unit)
  • Only in RefSeq: 193 unlocalized scaffolds.
  • Data displayed for RefSeq version

IDs: 3188 [UID] 171598 [GenBank] 3188 [RefSeq]

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 length2,716,949,182
Total ungapped length2,620,329,768
Gaps between scaffolds126
Number of scaffolds315
Scaffold N5039,293,786
Scaffold L5020
Number of contigs1,029
Contig N5025,603,741
Contig L5030
Total number of chromosomes and plasmids21
Number of component sequences (WGS or clone)20,330

*Note: Statistics shown for the primary assembly-unit. See the statistics report for additional statistics.

Supplemental Content

PubMed articles for this assembly

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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)
129
129/J
129/Ola
129/Sv
129/SvEvTac
129/SvJ
129S7/SvEv
A/J
AKR/J
B6/CBAF1J
Balb/c
C3H
Cast/Ei
NOD
SJL/J
Spret/Ei
unknown
Assembly Unit: Primary Assembly (C57BL/6J) (GCF_000000055.16)
Molecule nameGenBank sequenceRefSeq sequenceUnlocalized
sequences count
Chromosome 1CM000994.1=NC_000067.55
Chromosome 2CM000995.1=NC_000068.60
Chromosome 3CM000996.1=NC_000069.51
Chromosome 4CM000997.1=NC_000070.52
Chromosome 5CM000998.1=NC_000071.52
Chromosome 6CM000999.1=NC_000072.50
Chromosome 7CM001000.1=NC_000073.52
Chromosome 8CM001001.1=NC_000074.54
Chromosome 9CM001002.1=NC_000075.52
Chromosome 10CM001003.1=NC_000076.50
Chromosome 11CM001004.1=NC_000077.50
Chromosome 12CM001005.1=NC_000078.50
Chromosome 13CM001006.1=NC_000079.52
Chromosome 14CM001007.1=NC_000080.50
Chromosome 15CM001008.1=NC_000081.50
Chromosome 16CM001009.1=NC_000082.51
Chromosome 17CM001010.1=NC_000083.53
Chromosome 18CM001011.1=NC_000084.50
Chromosome 19CM001012.1=NC_000085.50
Chromosome XCM001013.1=NC_000086.611
Chromosome YCM001014.1=NC_000087.6102
unplacedn/an/an/a52

Assembly statistics

MoleculeSequence RoleTotal
Length
Scaffold
Count
Ungapped
Length
Scaffold
N50
Spanned
Gaps
Unspanned
Gaps
AllAssembled molecule2,716,949,1823152,620,329,76839,293,786714126
Chromosome 1AllAssembled moleculeUnlocalized scaffolds198,227,129197,195,4321,031,6971275192,486,238191,477,4361,008,80252,628,78152,628,781241,735522131770
Chromosome 2Assembled molecule181,748,0876178,392,072116,366,104186
Chromosome 3AllAssembled moleculeUnlocalized scaffolds159,641,682159,599,78341,899651156,435,822156,393,92341,89980,458,78980,458,78941,899440550
Chromosome 4AllAssembled moleculeUnlocalized scaffolds155,740,714155,630,120110,59413112151,994,466151,886,844107,62221,899,95521,899,95566,6732920911110
Chromosome 5AllAssembled moleculeUnlocalized scaffolds152,844,609152,537,259307,35020182148,028,535147,721,185307,35037,319,36237,319,362159,9352929018180
Chromosome 6Assembled molecule149,517,0375146,317,03791,924,39405
Chromosome 7AllAssembled moleculeUnlocalized scaffolds152,837,043152,524,553312,490862142,190,701141,878,211312,49036,356,19436,356,194175,96858580660
Chromosome 8AllAssembled moleculeUnlocalized scaffolds132,438,464131,738,871699,5931064125,496,364124,796,771699,59318,157,43118,157,431177,422330660
Chromosome 9AllAssembled moleculeUnlocalized scaffolds124,475,575124,076,172399,403972121,102,885120,720,222382,66326,676,75426,676,754243,717785424770
Chromosome 10Assembled molecule129,993,2553126,847,85272,324,642243
Chromosome 11Assembled molecule121,843,8563118,743,55633,384,93133
Chromosome 12Assembled molecule121,257,5303117,459,31239,293,786223
Chromosome 13AllAssembled moleculeUnlocalized scaffolds120,634,623120,284,312350,311752116,706,770116,370,905335,86528,633,59528,633,595186,869422616550
Chromosome 14Assembled molecule125,194,8644121,635,31297,629,908364
Chromosome 15Assembled molecule103,494,9743100,439,97464,780,97803
Chromosome 16AllAssembled moleculeUnlocalized scaffolds98,323,14498,319,1503,99432195,008,93395,004,9393,99462,254,92362,254,9233,99411110220
Chromosome 17AllAssembled moleculeUnlocalized scaffolds95,801,39095,272,651528,73963392,426,94391,898,204528,73981,466,43781,466,437195,66940400330
Chromosome 18Assembled molecule90,772,031487,600,13173,639,14894
Chromosome 19Assembled molecule61,342,430258,142,23054,454,32522
Chromosome XAllAssembled moleculeUnlocalized scaffolds167,935,371166,650,2961,285,075322111163,343,027162,080,9031,262,12428,862,97528,862,975224,89287602720200
Chromosome YAllAssembled moleculeUnlocalized scaffolds69,535,01615,902,55553,632,461104210256,335,0162,702,55553,632,461620,0432,195,326586,359110330
unplacedAssembled molecule3,350,358523,196,592187,6411660
Unit NameScaffold
Count
Total
Length
Ungapped
Length
Scaffold
N50
Spanned
Gaps
1293179,229179,22991,7480
129/J184,25084,25084,2500
129/Ola6304,110304,08546,8721
129/Sv6111,848,97811,843,500262,06227
129/SvEvTac4712,118,77412,118,398281,2554
129/SvJ6713,887,94513,883,418273,36947
129S7/SvEv121,256,1091,256,109113,5410
A/J1100,803100,803100,8030
AKR/J3586,502586,502191,5210
B6/CBAF1J137,34937,34937,3490
Balb/c2756,816756,816700,9600
C3H1176,641176,641176,6410
Cast/Ei4789,807789,807200,0110
NOD288,199,0578,199,057325,5550
SJL/J1144,780144,780144,7800
Spret/Ei2347,950347,950179,6510
unknown476,294,3786,294,127183,1926
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