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MGSCv34

Organism name:
Mus musculus (house mouse)
BioProject:
PRJNA20689
Submitter:
Genome Reference Consortium
Date:
2005/05/16
Assembly type:
haploid-with-alt-loci
Assembly level:
Chromosome
Genome representation:
full
GenBank assembly accession:
n/a
RefSeq assembly accession:
GCF_000001635.13 (replaced)
RefSeq assembly and GenBank assembly identical:
n/a

IDs: 5678 [UID] 5678 [RefSeq]

See Genome Information for Mus musculus

There are 23 assemblies for this organism

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History (Show revision history)

Comment

Global statistics*

Total sequence length2,710,735,632
Total ungapped length2,596,437,591
Gaps between scaffolds253
Number of scaffolds33,321
Scaffold N5025,747,655
Scaffold L5035
Number of contigs77,750
Contig N50683,385
Contig L50618
Total number of chromosomes and plasmids21
Number of component sequences (WGS or clone)93,049

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

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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
129_substrain
A/J
B6/CBAF1J
Balb/c
C3H
NOD
unknown
Assembly Unit: Primary Assembly (GCF_000000055.13)
Molecule nameGenBank sequenceRefSeq sequenceUnlocalized
sequences count
Chromosome 1n/an/aNC_000067.2641
Chromosome 2n/an/aNC_000068.30
Chromosome 3n/an/aNC_000069.2716
Chromosome 4n/an/aNC_000070.20
Chromosome 5n/an/aNC_000071.2504
Chromosome 6n/an/aNC_000072.2497
Chromosome 7n/an/aNC_000073.2560
Chromosome 8n/an/aNC_000074.2441
Chromosome 9n/an/aNC_000075.2253
Chromosome 10n/an/aNC_000076.2293
Chromosome 11n/an/aNC_000077.20
Chromosome 12n/an/aNC_000078.2389
Chromosome 13n/an/aNC_000079.2414
Chromosome 14n/an/aNC_000080.2368
Chromosome 15n/an/aNC_000081.2304
Chromosome 16n/an/aNC_000082.2310
Chromosome 17n/an/aNC_000083.2261
Chromosome 18n/an/aNC_000084.2359
Chromosome 19n/an/aNC_000085.2180
Chromosome Xn/an/aNC_000086.30
Chromosome Yn/an/aNC_000087.293
unplacedn/an/an/a26,486

Assembly statistics

MoleculeSequence RoleTotal
Length
Scaffold
Count
Ungapped
Length
Scaffold
N50
Spanned
Gaps
Unspanned
Gaps
AllAssembled molecule2,710,735,63233,3212,596,437,59125,747,65544,429253
Chromosome 1AllAssembled moleculeUnlocalized scaffolds197,759,336195,109,6122,649,72465716641191,079,569188,429,8452,649,72421,668,69421,668,6946,0103,3013,301016160
Chromosome 2Assembled molecule181,764,3139177,849,31336,424,2221210
Chromosome 3AllAssembled moleculeUnlocalized scaffolds163,221,595158,945,6754,275,92073014716156,515,677152,239,7574,275,92026,200,19826,200,19819,7952,5032,503014140
Chromosome 4Assembled molecule154,678,26411150,568,26421,931,4121211
Chromosome 5AllAssembled moleculeUnlocalized scaffolds152,858,577150,339,8312,518,74652420504146,008,216143,489,4702,518,74619,315,50319,315,50313,6922,8012,801020200
Chromosome 6AllAssembled moleculeUnlocalized scaffolds152,434,623150,245,8152,188,80851619497145,058,081142,869,2732,188,80817,008,41917,008,4196,1253,2333,233019190
Chromosome 7AllAssembled moleculeUnlocalized scaffolds143,409,833139,739,8273,670,00659030560135,026,981131,356,9753,670,00622,379,96722,379,96715,6022,9272,927030300
Chromosome 8AllAssembled moleculeUnlocalized scaffolds130,439,272127,867,6322,571,64045312441123,980,917121,409,2772,571,64029,804,51929,804,51915,3952,4912,491012120
Chromosome 9AllAssembled moleculeUnlocalized scaffolds125,140,570124,135,7091,004,86126512253119,063,347118,058,4861,004,86126,781,25926,781,2595,7063,8773,877012120
Chromosome 10AllAssembled moleculeUnlocalized scaffolds131,308,081130,291,7451,016,33630411293125,069,966124,053,6301,016,33616,089,87616,089,8764,2794,1614,161011110
Chromosome 11Assembled molecule121,803,6365118,593,63633,383,02515
Chromosome 12AllAssembled moleculeUnlocalized scaffolds118,711,433115,788,3032,923,13040415389112,291,667109,368,5372,923,13035,176,42857,274,33218,4333,3463,346015150
Chromosome 13AllAssembled moleculeUnlocalized scaffolds118,438,810114,687,1533,751,6574239414112,090,837108,339,1803,751,65719,999,56919,999,56923,8953,6183,6180990
Chromosome 14AllAssembled moleculeUnlocalized scaffolds120,928,008118,895,6602,032,3483735368114,986,982112,954,6342,032,34867,775,73767,775,73713,6423,4433,4430550
Chromosome 15AllAssembled moleculeUnlocalized scaffolds105,035,581103,639,4021,396,1793073304100,926,04599,529,8661,396,17964,849,91664,849,9168,6751,5861,5860330
Chromosome 16AllAssembled moleculeUnlocalized scaffolds99,128,43097,408,5581,719,872315531093,706,44191,986,5691,719,87230,623,34830,623,34814,0122,8532,8530550
Chromosome 17AllAssembled moleculeUnlocalized scaffolds94,429,97092,867,6601,562,3102822126188,100,54886,538,2381,562,31011,859,82911,859,82913,3603,0953,095021210
Chromosome 18AllAssembled moleculeUnlocalized scaffolds92,099,84090,308,3961,791,444364535988,474,07886,682,6341,791,44473,608,05973,608,05911,3477617610550
Chromosome 19AllAssembled moleculeUnlocalized scaffolds61,547,36760,626,890920,477183318057,868,93356,948,456920,47732,632,29532,632,29511,6603973970330
Chromosome XAssembled molecule163,688,98026157,668,98017,947,925727
Chromosome YAllAssembled moleculeUnlocalized scaffolds27,172,7722,207,72024,965,0529419326,772,7721,807,72024,965,052308,4262,207,720292,077440000
unplacedAssembled molecule54,736,34126,48654,736,3411,91200
Unit NameScaffold
Count
Total
Length
Ungapped
Length
Scaffold
N50
Spanned
Gaps
129_substrain18137,643,91437,639,892262,16618
A/J1100,803100,803100,8030
B6/CBAF1J137,34937,34937,3490
Balb/c155,85655,85655,8560
C3H1176,641176,641176,6410
NOD133,194,4753,194,475258,4670
unknown486,574,0016,573,035191,6294
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