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MGSCv36

Organism name:
Mus musculus (house mouse)
Infraspecific name:
Strain: C57BL/6J
BioProject:
PRJNA20689
Submitter:
Genome Reference Consortium
Date:
2006/05/26
Synonyms:
mm8
Assembly type:
haploid-with-alt-loci
Assembly level:
Chromosome
Genome representation:
full
GenBank assembly accession:
n/a
RefSeq assembly accession:
GCF_000001635.15 (replaced)
RefSeq assembly and GenBank assembly identical:
n/a

IDs: 3168 [UID] 3168 [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 length2,661,188,789
Total ungapped length2,567,267,557
Gaps between scaffolds123
Number of scaffolds200
Scaffold N5040,319,553
Scaffold L5019
Number of contigs1,427
Contig N5017,840,746
Contig L5035
Total number of chromosomes and plasmids21
Number of component sequences (WGS or clone)20,382

*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 (C57BL/6J)
129_substrain
A/J
B6/CBAF1J
Balb/c
C3H
NOD
unknown
Assembly Unit: Primary Assembly (C57BL/6J) (GCF_000000055.15)
Molecule nameGenBank sequenceRefSeq sequenceUnlocalized
sequences count
Chromosome 1n/an/aNC_000067.43
Chromosome 2n/an/aNC_000068.50
Chromosome 3n/an/aNC_000069.40
Chromosome 4n/an/aNC_000070.40
Chromosome 5n/an/aNC_000071.48
Chromosome 6n/an/aNC_000072.40
Chromosome 7n/an/aNC_000073.44
Chromosome 8n/an/aNC_000074.41
Chromosome 9n/an/aNC_000075.41
Chromosome 10n/an/aNC_000076.41
Chromosome 11n/an/aNC_000077.40
Chromosome 12n/an/aNC_000078.40
Chromosome 13n/an/aNC_000079.42
Chromosome 14n/an/aNC_000080.40
Chromosome 15n/an/aNC_000081.42
Chromosome 16n/an/aNC_000082.40
Chromosome 17n/an/aNC_000083.42
Chromosome 18n/an/aNC_000084.40
Chromosome 19n/an/aNC_000085.40
Chromosome Xn/an/aNC_000086.51
Chromosome Yn/an/aNC_000087.533
unplacedn/an/an/a19

Assembly statistics

MoleculeSequence RoleTotal
Length		Scaffold
Count		Ungapped
Length		Scaffold
N50		Spanned
Gaps		Unspanned
Gaps
AllAssembled molecule2,661,188,7892002,567,267,55740,319,5531,228123
Chromosome 1AllAssembled moleculeUnlocalized scaffolds197,142,236197,069,96272,2741073191,522,546191,450,27272,27452,567,97852,567,97853,23528280770
Chromosome 2Assembled molecule181,976,7626178,271,939113,363,752236
Chromosome 3Assembled molecule159,872,1124156,356,812108,969,45754
Chromosome 4Assembled molecule155,029,70112151,137,47921,899,6581912
Chromosome 5AllAssembled moleculeUnlocalized scaffolds154,574,310152,003,0632,571,24724168149,734,934147,163,6872,571,24712,068,67236,574,280436,5094848016160
Chromosome 6Assembled molecule149,525,6856146,293,58533,356,98416
Chromosome 7AllAssembled moleculeUnlocalized scaffolds145,228,004145,134,09493,9101064140,716,246140,622,33693,91022,508,26822,508,26824,89439390660
Chromosome 8AllAssembled moleculeUnlocalized scaffolds132,292,059132,085,098206,961761125,220,355125,013,394206,96118,144,08918,144,089206,96120200660
Chromosome 9AllAssembled moleculeUnlocalized scaffolds124,017,901124,000,66917,232871120,614,357120,597,12517,23226,658,68926,658,68917,2321331330770
Chromosome 10AllAssembled moleculeUnlocalized scaffolds129,969,929129,959,14810,781541126,759,683126,748,90210,78150,271,34650,271,34610,78128280440
Chromosome 11Assembled molecule121,798,6323118,711,73233,383,01913
Chromosome 12Assembled molecule120,463,1592116,603,18578,006,7941522
Chromosome 13AllAssembled moleculeUnlocalized scaffolds121,000,569120,614,378386,191752116,663,519116,277,328386,19128,586,49128,586,491222,7491631630550
Chromosome 14Assembled molecule123,978,8703120,037,66698,400,2161843
Chromosome 15AllAssembled moleculeUnlocalized scaffolds103,548,509103,492,57755,932532100,492,699100,436,76755,93264,780,05364,780,05329,373990330
Chromosome 16Assembled molecule98,252,459294,825,98062,189,938612
Chromosome 17AllAssembled moleculeUnlocalized scaffolds95,216,51195,177,42039,09153291,293,83391,254,74239,09181,771,67381,771,67328,0952752750330
Chromosome 18Assembled molecule90,736,837487,552,07773,604,859144
Chromosome 19Assembled molecule61,321,190258,121,09054,440,53112
Chromosome XAllAssembled moleculeUnlocalized scaffolds165,596,165165,556,46939,69622211160,240,651160,200,95539,69628,957,32328,957,32339,6962222021210
Chromosome YAllAssembled moleculeUnlocalized scaffolds29,007,13616,029,40412,977,7323413315,457,1362,479,40412,977,732418,0782,729,404407,439220110
unplacedAssembled molecule640,05319640,053160,41000
Unit NameScaffold
Count		Total
Length		Ungapped
Length		Scaffold
N50		Spanned
Gaps
129_substrain20541,059,75341,046,633251,056108
A/J1100,803100,803100,8030
B6/CBAF1J137,34937,34937,3490
Balb/c2756,816756,816700,9600
C3H1176,641176,641176,6410
NOD246,540,6286,540,628292,4160
unknown496,658,6576,657,691186,3144