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MGSCv37

Organism name:
Mus musculus (house mouse)
Infraspecific name:
Strain: C57BL/6J
Submitter:
Genome Reference Consortium
Date:
2010/10/21
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_000001635.18 (replaced)
RefSeq assembly and GenBank assembly identical:
yes

IDs: 165668 [UID] 171598 [GenBank] 165668 [RefSeq]

See Genome Information for Mus musculus

There are 22 assemblies for this organism

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History (Show revision history)

Global statistics

Number of regions with alternate loci or patches60
Total sequence length2,745,142,291
Total assembly gap length96,621,235
Gaps between scaffolds126
Number of scaffolds410
Scaffold N5037,678,470
Scaffold L5021
Number of contigs1,141
Contig N5025,603,741
Contig L5030
Total number of chromosomes and plasmids22

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/J
129/Sv
129/SvEvTac
129/SvJ
129P2/OlaHsd
129S7/SvEv
A/J
AKR/J
Balb/c
Cast/Ei
NOD
Spret/Ei
unknown strain
non-nuclear

Regions

NameLocation
region11:60697653-61195514
region21:61754170-61941338
region31:63440029-63634836
region41:78410334-78684064
Ren21:135135713-135386019
Ifi_cluster1:175631261-175981314
region292:102863803-103229146
region303:36705645-37462525
region313:47250927-47483886
region323:99757788-99890338
region333:100124682-100629140
region343:100709803-101111508
region353:103394301-103719496
region363:108919638-109610603
olfactory_region_24:43775564-43869886
Mup_region_14:60433222-61702235
Mup_region_24:61706289-61898563
region404:66718636-66856206
region414:129222696-129387052
region424:129673209-129813999
Padi_cluster4:140277012-140517363
region445:91082154-91255787
region455:151674830-151925798
region466:50729501-50869226
region476:82834040-82989835
vomeronasal_region_16:90040061-90240457
region496:120327240-120965219
region506:144953971-145181710
region517:28528234-28611868
Hbb_cluster7:110959995-111009204
olfactory_region_37:114032224-114070764
region548:42378188-42567887
Large8:75589541-75842949
Grm110:10581444-10647182
olfactory_region_111:58426683-58600787
region911:69708974-70768432
region1011:72722413-72881612
region1111:88404152-88462832
Mapt11:104064572-104223846
Igh12:105978478-115696908
Naip2_Naip513:100922006-101021810
Ipo1113:107591153-107722976
Fhit14:11148176-11650860
region1714:52482687-52593237
Tcra_Tcrd14:52971974-54848751
region1915:80333302-80502798
DiGeorge16:17742588-19066061
DownSynCrit16:94114517-95701295
Airn17:12922132-13054037
region2317:27450268-27705657
region2417:27792385-29352922
MHC_region_117:33888191-35744546
MHC_region_217:36230820-38050373
Impact18:11308623-11423912
region2819:5679043-5707799
Odz1X:40330809-40652019
region57X:69411520-69608545
Xlr_region_1X:70248990-70367303
Xlr_region_2X:70430764-70508135
XicX:100784623-101037209
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
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
MoleculeTotal
Length
Mitochondrion MT16,299
Region
Name
LocationScaffold
Count
Total
Length
Ungapped
Length
Scaffold
N50
Spanned
Gaps
region11:60697653-611955143923,979923,979289,6620
region21:61754170-619413381187,142187,142187,1420
region31:63440029-636348361199,536199,536199,5360
region41:78410334-786840641272,653272,653272,6530
Ren21:135135713-1353860191281,255281,255281,2550
Ifi_cluster1:175631261-1759813142390,047390,022235,7631
region292:102863803-1032291461370,505370,505370,5050
region303:36705645-3746252541,047,9141,047,914292,4160
region313:47250927-474838861243,366243,366243,3660
region323:99757788-998903381141,661141,661141,6610
region333:100124682-1006291401509,460509,460509,4600
region343:100709803-1011115081402,204402,204402,2040
region353:103394301-1037194961325,555325,555325,5550
region363:108919638-1096106031689,363689,363689,3630
olfactory_region_24:43775564-43869886176,09976,09976,0990
Mup_region_14:60433222-617022351264,822264,822264,8220
Mup_region_24:61706289-618985631191,695191,695191,6950
region404:66718636-668562061138,473138,473138,4730
region414:129222696-1293870521165,559165,559165,5590
region424:129673209-1298139991140,602140,602140,6020
Padi_cluster4:140277012-1405173631240,498240,433240,4982
region445:91082154-912557871180,394180,394180,3940
region455:151674830-1519257981262,166262,166262,1660
region466:50729501-508692261145,152145,152145,1520
region476:82834040-829898351162,691162,691162,6910
vomeronasal_region_16:90040061-902404571198,515198,515198,5150
region496:120327240-1209652191636,098636,098636,0980
region506:144953971-1451817101231,326231,326231,3260
region517:28528234-28611868191,25191,25191,2510
Hbb_cluster7:110959995-111009204155,85655,85655,8560
olfactory_region_37:114032224-114070764134,49834,49834,4980
region548:42378188-425678871183,135183,135183,1350
Large8:75589541-758429491251,056251,056251,0560
Grm110:10581444-10647182177,89177,89177,8910
olfactory_region_111:58426683-586007871170,397170,397170,3970
region911:69708974-707684323875,078875,078472,0260
region1011:72722413-728816121159,511159,511159,5110
region1111:88404152-88462832110,75510,75510,7550
Mapt11:104064572-1042238461161,334161,334161,3340
Igh12:105978478-11569690851,906,5221,906,5221,380,7170
Naip2_Naip513:100922006-1010218101100,803100,803100,8030
Ipo1113:107591153-1077229761138,434138,434138,4340
Fhit14:11148176-116508601503,103503,103503,1030
region1714:52482687-525932371105,813105,813105,8130
Tcra_Tcrd14:52971974-5484875111,666,3651,666,3651,666,3650
region1915:80333302-80502798188,44288,44288,4420
DiGeorge16:17742588-1906606111,312,1511,312,1511,312,1510
DownSynCrit16:94114517-9570129511,351,3771,351,3771,351,3770
Airn17:12922132-130540371138,490138,490138,4900
region2317:27450268-277056571258,652258,652258,6520
region2417:27792385-2935292221,565,5461,565,546893,6850
MHC_region_117:33888191-3574454621,963,2371,963,2371,736,6430
MHC_region_217:36230820-3805037332,055,1902,055,1901,281,1220
Impact18:11308623-11423912185,54885,54885,5480
region2819:5679043-5707799146,44046,44046,4400
Odz1X:40330809-406520191328,187328,187328,1870
region57X:69411520-696085451194,271194,271194,2710
Xlr_region_1X:70248990-703673031123,835123,835123,8350
Xlr_region_2X:70430764-70508135178,78578,68978,7851
XicX:100784623-1010372091247,850247,850247,8500
Unit NameScaffold
Count
Total
Length
Ungapped
Length
Scaffold
N50
Spanned
Gaps
129/J184,25084,25084,2500
129/Sv103,712,1993,712,103636,0981
129/SvEvTac144,472,9464,472,650328,1872
129/SvJ198,419,0588,417,6291,380,71717
129P2/OlaHsd146,44046,44046,4400
129S7/SvEv4639,698639,698191,6950
A/J1100,803100,803100,8030
AKR/J3586,502586,502191,5210
Balb/c155,85655,85655,8560
Cast/Ei3589,796589,796196,0140
NOD288,199,0578,199,057325,5550
Spret/Ei2347,950347,950179,6510
unknown strain7922,255922,255149,3710
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