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MGSCv35

Organism name:
Mus musculus (house mouse)
Infraspecific name:
Strain: C57BL/6J
BioProject:
PRJNA20689
Submitter:
Genome Reference Consortium
Date:
2005/12/05
Synonyms:
mm7
Assembly type:
haploid-with-alt-loci
Assembly level:
Chromosome
Genome representation:
full
GenBank assembly accession:
n/a
RefSeq assembly accession:
GCF_000001635.14 (replaced)
RefSeq assembly and GenBank assembly identical:
n/a

IDs: 5728 [UID] 5728 [RefSeq]

See Genome Information for Mus musculus

There are 65 assemblies for this organism

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History (Show revision history)

Comment

Global statistics*

Total sequence length2,691,661,974
Total ungapped length2,582,925,725
Gaps between scaffolds213
Number of scaffolds5,041
Scaffold N5026,734,816
Scaffold L5029
Number of contigs26,071
Contig N501,647,665
Contig L50306
Total number of chromosomes and plasmids21
Number of component sequences (WGS or clone)44,040

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

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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
129_substrain
A/J
B6/CBAF1J
Balb/c
C3H
NOD
unknown
Assembly Unit: Primary Assembly (GCF_000000055.14)
Molecule nameGenBank sequenceRefSeq sequenceUnlocalized
sequences count
Chromosome 1n/an/aNC_000067.3303
Chromosome 2n/an/aNC_000068.40
Chromosome 3n/an/aNC_000069.3238
Chromosome 4n/an/aNC_000070.30
Chromosome 5n/an/aNC_000071.3208
Chromosome 6n/an/aNC_000072.3274
Chromosome 7n/an/aNC_000073.3229
Chromosome 8n/an/aNC_000074.3169
Chromosome 9n/an/aNC_000075.3159
Chromosome 10n/an/aNC_000076.3305
Chromosome 11n/an/aNC_000077.30
Chromosome 12n/an/aNC_000078.3178
Chromosome 13n/an/aNC_000079.3199
Chromosome 14n/an/aNC_000080.3216
Chromosome 15n/an/aNC_000081.3112
Chromosome 16n/an/aNC_000082.3148
Chromosome 17n/an/aNC_000083.3131
Chromosome 18n/an/aNC_000084.395
Chromosome 19n/an/aNC_000085.337
Chromosome Xn/an/aNC_000086.40
Chromosome Yn/an/aNC_000087.390
unplacedn/an/an/a1,738

Assembly statistics

MoleculeSequence RoleTotal
Length		Scaffold
Count		Ungapped
Length		Scaffold
N50		Spanned
Gaps		Unspanned
Gaps
AllAssembled molecule2,691,661,9745,0412,582,925,72526,734,81621,035213
Chromosome 1AllAssembled moleculeUnlocalized scaffolds198,663,866194,923,5353,740,33131613303193,402,076189,661,7453,740,33121,593,52321,593,52346,9071,5061,506013130
Chromosome 2Assembled molecule182,548,2678178,438,26736,476,222159
Chromosome 3AllAssembled moleculeUnlocalized scaffolds162,467,622159,849,0392,618,58325214238157,323,806154,705,2232,618,58326,091,22326,091,22333,8521,1201,120014140
Chromosome 4Assembled molecule155,175,44312150,925,44321,931,4121212
Chromosome 5AllAssembled moleculeUnlocalized scaffolds154,227,713150,670,3233,557,39022719208148,703,831145,246,4413,457,39018,828,59718,828,597195,9931,1691,167219190
Chromosome 6AllAssembled moleculeUnlocalized scaffolds152,288,955149,646,8342,642,12128612274147,852,421145,210,3002,642,12116,953,15516,953,15529,586850850012120
Chromosome 7AllAssembled moleculeUnlocalized scaffolds144,392,857141,766,3522,626,50525324229137,645,414135,018,9092,626,50522,474,45622,474,45637,2851,3151,315024240
Chromosome 8AllAssembled moleculeUnlocalized scaffolds129,983,084127,874,0532,109,03118011169124,990,350122,881,3192,109,03129,247,26529,247,26548,9541,3001,300011110
Chromosome 9AllAssembled moleculeUnlocalized scaffolds125,673,340123,828,2361,845,10417112159120,631,468118,786,3641,845,10426,734,81626,734,81635,7472,0512,051012120
Chromosome 10AllAssembled moleculeUnlocalized scaffolds131,935,635130,066,7661,868,8693127305127,646,725125,777,8561,868,86936,126,36536,126,36518,3161,0841,0840770
Chromosome 11Assembled molecule122,091,5872118,641,58787,556,17852
Chromosome 12AllAssembled moleculeUnlocalized scaffolds119,686,543117,814,1031,872,44018810178114,568,323112,695,8831,872,44073,453,50573,453,50530,7171,7561,756010100
Chromosome 13AllAssembled moleculeUnlocalized scaffolds119,075,244116,696,5282,378,71620910199113,702,400111,323,6842,378,71619,252,87819,252,87832,3911,9231,923010100
Chromosome 14AllAssembled moleculeUnlocalized scaffolds122,309,637119,226,8403,082,7972215216117,264,446114,181,6493,082,79768,358,70768,358,70771,1391,9681,9680550
Chromosome 15AllAssembled moleculeUnlocalized scaffolds105,173,234103,647,3851,525,8491153112101,495,95099,970,1011,525,84964,752,15064,752,15034,4427447440330
Chromosome 16AllAssembled moleculeUnlocalized scaffolds100,106,28798,481,0191,625,268152414895,614,60193,989,3331,625,26862,164,85962,164,85935,7091,4921,4920440
Chromosome 17AllAssembled moleculeUnlocalized scaffolds95,316,99093,276,9252,040,0651441313189,785,86787,745,8022,040,06511,969,77516,522,20745,0852,0592,059013130
Chromosome 18AllAssembled moleculeUnlocalized scaffolds91,988,89090,918,7141,070,17610059588,422,00387,351,8271,070,17673,768,17373,768,17328,0004224220550
Chromosome 19AllAssembled moleculeUnlocalized scaffolds62,022,48561,223,509798,9763923758,596,66257,797,686798,97654,590,03054,590,030220,1432192190220
Chromosome XAssembled molecule164,906,25225159,246,25217,968,0881925
Chromosome YAllAssembled moleculeUnlocalized scaffolds40,585,93115,523,45325,062,4789119026,985,7311,923,25325,062,478310,3272,223,453305,629550110
unplacedAssembled molecule11,042,1121,73811,042,10220,97110
Unit NameScaffold
Count		Total
Length		Ungapped
Length		Scaffold
N50		Spanned
Gaps
129_substrain20239,854,17439,842,152262,06298
A/J1100,803100,803100,8030
B6/CBAF1J137,34937,34937,3490
Balb/c155,85655,85655,8560
C3H1176,641176,641176,6410
NOD194,380,3174,380,317276,1030
unknown486,574,0016,573,035191,6294