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MGSCv37

This assembly has been updated. See current version

Organism name:: Mus musculus (house mouse)
Infraspecific name:: Strain: C57BL/6J
BioProject:: PRJNA20689
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

Pathogen Detection Resources

There are 24 assemblies for this organism

History (Show revision history)

GenBank Assembly Accession		RefSeq Assembly Accession	Assembly Name	Assembly Level	Status
GCA_000001635.9	=	GCF_000001635.27	GRCm39	Chromosome	Latest GenBank, Latest RefSeq
GCA_000001635.8	=	GCF_000001635.26	GRCm38.p6	Chromosome	Replaced GenBank, Replaced RefSeq
GCA_000001635.7	=	GCF_000001635.25	GRCm38.p5	Chromosome	Replaced GenBank, Replaced RefSeq
GCA_000001635.6	=	GCF_000001635.24	GRCm38.p4	Chromosome	Replaced GenBank, Replaced RefSeq
GCA_000001635.5	=	GCF_000001635.23	GRCm38.p3	Chromosome	Replaced GenBank, Replaced RefSeq
GCA_000001635.4	=	GCF_000001635.22	GRCm38.p2	Chromosome	Replaced GenBank, Replaced RefSeq
GCA_000001635.3	=	GCF_000001635.21	GRCm38.p1	Chromosome	Replaced GenBank, Replaced RefSeq
GCA_000001635.2	=	GCF_000001635.20	GRCm38	Chromosome	Replaced GenBank, Replaced RefSeq
GCA_000001635.1	=	GCF_000001635.18	MGSCv37	Chromosome	Replaced GenBank, Replaced RefSeq
GCA_000001635.1	≠	GCF_000001635.16	MGSCv37	Chromosome	Replaced GenBank, Replaced RefSeq
n/a	n/a	GCF_000001635.15	MGSCv36	Chromosome	Replaced RefSeq
n/a	n/a	GCF_000001635.14	MGSCv35	Chromosome	Replaced RefSeq
n/a	n/a	GCF_000001635.13	MGSCv34	Chromosome	Replaced RefSeq
n/a	n/a	GCF_000001635.12	MGSCv3	Chromosome	Replaced RefSeq

Comment

Global statistics*

Number of regions with alternate loci or patches	60
Total sequence length	2,716,949,182
Total ungapped length	2,620,329,768
Gaps between scaffolds	126
Number of scaffolds	315
Scaffold N50	39,293,786
Scaffold L50	20
Number of contigs	1,029
Contig N50	25,603,741
Contig L50	30
Total number of chromosomes and plasmids	21
Number of component sequences (WGS or clone)	20,330

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

Name	Location
region1	1:60697653-61195514
region2	1:61754170-61941338
region3	1:63440029-63634836
region4	1:78410334-78684064
Ren2	1:135135713-135386019
Ifi_cluster	1:175631261-175981314
region29	2:102863803-103229146
region30	3:36705645-37462525
region31	3:47250927-47483886
region32	3:99757788-99890338
region33	3:100124682-100629140
region34	3:100709803-101111508
region35	3:103394301-103719496
region36	3:108919638-109610603
olfactory_region_2	4:43775564-43869886
Mup_region_1	4:60433222-61702235
Mup_region_2	4:61706289-61898563
region40	4:66718636-66856206
region41	4:129222696-129387052
region42	4:129673209-129813999
Padi_cluster	4:140277012-140517363
region44	5:91082154-91255787
region45	5:151674830-151925798
region46	6:50729501-50869226
region47	6:82834040-82989835
vomeronasal_region_1	6:90040061-90240457
region49	6:120327240-120965219
region50	6:144953971-145181710
region51	7:28528234-28611868
Hbb_cluster	7:110959995-111009204
olfactory_region_3	7:114032224-114070764
region54	8:42378188-42567887
Large	8:75589541-75842949
Grm1	10:10581444-10647182
olfactory_region_1	11:58426683-58600787
region9	11:69708974-70768432
region10	11:72722413-72881612
region11	11:88404152-88462832
Mapt	11:104064572-104223846
Igh	12:105978478-115696908
Naip2_Naip5	13:100922006-101021810
Ipo11	13:107591153-107722976
Fhit	14:11148176-11650860
region17	14:52482687-52593237
Tcra_Tcrd	14:52971974-54848751
region19	15:80333302-80502798
DiGeorge	16:17742588-19066061
DownSynCrit	16:94114517-95701295
Airn	17:12922132-13054037
region23	17:27450268-27705657
region24	17:27792385-29352922
MHC_region_1	17:33888191-35744546
MHC_region_2	17:36230820-38050373
Impact	18:11308623-11423912
region28	19:5679043-5707799
Odz1	X:40330809-40652019
region57	X:69411520-69608545
Xlr_region_1	X:70248990-70367303
Xlr_region_2	X:70430764-70508135
Xic	X:100784623-101037209

Molecule name	GenBank sequence		RefSeq sequence	Unlocalized sequences count
Chromosome 1	CM000994.1	=	NC_000067.5	5
Chromosome 2	CM000995.1	=	NC_000068.6	0
Chromosome 3	CM000996.1	=	NC_000069.5	1
Chromosome 4	CM000997.1	=	NC_000070.5	2
Chromosome 5	CM000998.1	=	NC_000071.5	2
Chromosome 6	CM000999.1	=	NC_000072.5	0
Chromosome 7	CM001000.1	=	NC_000073.5	2
Chromosome 8	CM001001.1	=	NC_000074.5	4
Chromosome 9	CM001002.1	=	NC_000075.5	2
Chromosome 10	CM001003.1	=	NC_000076.5	0
Chromosome 11	CM001004.1	=	NC_000077.5	0
Chromosome 12	CM001005.1	=	NC_000078.5	0
Chromosome 13	CM001006.1	=	NC_000079.5	2
Chromosome 14	CM001007.1	=	NC_000080.5	0
Chromosome 15	CM001008.1	=	NC_000081.5	0
Chromosome 16	CM001009.1	=	NC_000082.5	1
Chromosome 17	CM001010.1	=	NC_000083.5	3
Chromosome 18	CM001011.1	=	NC_000084.5	0
Chromosome 19	CM001012.1	=	NC_000085.5	0
Chromosome X	CM001013.1	=	NC_000086.6	11
Chromosome Y	CM001014.1	=	NC_000087.6	102
unplaced	n/a	n/a	n/a	52

Scaffold name	Chromosome assignment	GenBank ID		RefSeq ID
Mm2_39263_37	2	GL456024.1	=	NT_039223.2
Mm6_39413_37	6	GL456025.1	=	NT_039373.1
Mm6_39422_37	6	GL456026.1	=	NT_039382.3
Mm14_39653_37	14	GL456027.1	=	NT_039613.3
Mm16_39670_37	16	GL456028.1	=	NT_039630.4
Mm17_39704_37	17	GL456029.1	=	NT_039664.1
Mm17_39705_37	17	GL456030.1	=	NT_039665.1
MmX_39784_37	X	GL456032.1	=	NT_039744.2
MmX_39787_37	X	GL456033.1	=	NT_039747.3
MmX_110790_37	X	GL456031.1	=	NT_111920.1

Scaffold name	Chromosome assignment	GenBank ID		RefSeq ID
Mm1_39238_37	1	GL455993.1	=	NT_039198.1
Mm1_39232_37	1	GL455991.1	=	NT_039192.2
Mm1_39234_37	1	GL455992.1	=	NT_039194.4
Mm4_39331_37	4	GL455994.1	=	NT_039291.1
Mm5_39374_37	5	GL455995.1	=	NT_039334.1
Mm8_39509_37	8	GL455996.1	=	NT_039469.1
Mm8_39510_37	8	GL455997.1	=	NT_039470.1
Mm11_78748_37	11	GL455998.1	=	NT_078683.1
Mm13_39634_37	13	GL455999.1	=	NT_039594.2
Mm15_39662_37	15	GL456000.1	=	NT_039622.1
Mm16_39674_37	16	GL456001.1	=	NT_039634.3
Mm17_39706_37	17	GL456002.1	=	NT_039666.1
MmX_39779_37	X	GL456003.1	=	NT_039739.1
MmX_98661_37	X	GL456004.1	=	NT_099024.1

Scaffold name	Chromosome assignment	GenBank ID		RefSeq ID
Mm1_39235_37	1	GL456005.1	=	NT_039195.1
Mm3_80254_37	3	GL456008.1	=	NT_080257.1
Mm3_39296_37	3	GL456007.1	=	NT_039256.1
Mm3_39288_37	3	GL456006.1	=	NT_039248.1
Mm4_39336_37	4	GL456010.1	=	NT_039296.1
Mm4_108188_37	4	GL456009.1	=	NT_109318.2
Mm5_108469_37	5	GL456011.1	=	NT_109599.1
Mm6_39412_37	6	GL456012.1	=	NT_039372.1
Mm7_78637_37	7	GL456014.1	=	NT_078572.1
Mm7_39483_37	7	GL456013.1	=	NT_039443.1
Mm10_78716_37	10	GL456015.1	=	NT_078651.1
Mm11_39565_37	11	GL456016.1	=	NT_039525.1
Mm12_39612_37	12	GL456018.1	=	NT_039572.1
Mm12_112696_37	12	GL456017.1	=	NT_114985.2
Mm14_96434_37	14	GL456020.1	=	NT_096797.1
Mm14_39654_37	14	GL456019.1	=	NT_039614.1
Mm17_39702_37	17	GL456022.1	=	NT_039662.2
Mm17_39703_37	17	GL456023.1	=	NT_039663.1
Mm17_39701_37	17	GL456021.1	=	NT_039661.3

Scaffold name	Chromosome assignment	GenBank ID		RefSeq ID
Mm4_163469_37	4	GL456077.1	=	NT_166295.1
Mm4_163467_37	4	GL456075.1	=	NT_166293.1
Mm4_163468_37	4	GL456076.1	=	NT_166294.1
Mm12_163496_37	12	GL456078.1	=	NT_166322.1

Scaffold name	Chromosome assignment	GenBank ID		RefSeq ID
AKR/J_MMCHRY_CTG1	Y	GL456080.1	=	NT_166394.1
AKR/J_MMCHRY_CTG2	Y	GL456081.1	=	NT_166397.1
AKR/J_MMCHRY_CTG3	Y	GL456082.1	=	NT_166400.1

Scaffold name	Chromosome assignment	GenBank ID		RefSeq ID
MmY_163570_37	Y	GL456071.1	=	NT_166396.1
MmY_163572_37	Y	GL456072.1	=	NT_166398.1
MmY_163573_37	Y	GL456073.1	=	NT_166399.1

Scaffold name	Chromosome assignment	GenBank ID		RefSeq ID
Mm1_39240_37	1	GL456039.1	=	NT_039200.1
Mm1_163271_37	1	GL456036.1	=	NT_165757.1
Mm1_39239_37	1	GL456038.1	=	NT_039199.1
Mm1_39237_37	1	GL456037.1	=	NT_039197.1
Mm1_39241_37	1	GL456040.1	=	NT_039201.1
Mm3_111969_37	3	GL456043.1	=	NT_114258.1
Mm3_80253_37	3	GL456050.1	=	NT_080256.1
Mm3_39292_37	3	GL456048.1	=	NT_039252.1
Mm3_39287_37	3	GL456045.1	=	NT_039247.1
Mm3_39297_37	3	GL456049.1	=	NT_039257.3
Mm3_108181_37	3	GL456041.1	=	NT_109311.1
Mm3_39290_37	3	GL456046.1	=	NT_039250.1
Mm3_39291_37	3	GL456047.1	=	NT_039251.2
Mm3_163461_37	3	GL456044.1	=	NT_166287.1
Mm3_111968_37	3	GL456042.1	=	NT_114257.3
Mm4_163473_37	4	GL456053.1	=	NT_166299.1
Mm4_163472_37	4	GL456052.1	=	NT_166298.1
Mm4_163471_37	4	GL456051.1	=	NT_166297.1
Mm6_163479_37	6	GL456054.1	=	NT_166305.1
Mm11_112594_37	11	GL456058.1	=	NT_114883.1
Mm11_109495_37	11	GL456055.1	=	NT_110625.3
Mm11_163288_37	11	GL456059.1	=	NT_165774.1
Mm11_109496_37	11	GL456056.1	=	NT_110626.2
Mm11_163491_37	11	GL456060.1	=	NT_166317.1
Mm11_112593_37	11	GL456057.1	=	NT_114882.1
Mm17_163503_37	17	GL456063.1	=	NT_166329.1
Mm17_163295_37	17	GL456061.1	=	NT_165781.2
Mm17_163296_37	17	GL456062.1	=	NT_165782.2

Scaffold name	Chromosome assignment	GenBank ID		RefSeq ID
MmY_163567_37	Y	GL456034.1	=	NT_166393.1
MmY_163569_37	Y	GL456035.1	=	NT_166395.1

Scaffold name	Chromosome assignment	GenBank ID		RefSeq ID
Mm4_39332_37	4	GL456064.1	=	NT_039292.1
Mm6_39407_37	6	GL456065.1	=	NT_039367.1
Mm12_95992_37	12	GL456068.1	=	NT_096355.1
Mm12_163493_37	12	GL456066.1	=	NT_166319.1
Mm12_163494_37	12	GL456067.1	=	NT_166320.1
Mm17_96973_37	17	GL456069.1	=	NT_097336.1
Mm18_163298_37	18	GL456070.1	=	NT_165784.1

Molecule	Sequence Role	Total Length	Scaffold Count	Ungapped Length	Scaffold N50	Spanned Gaps	Unspanned Gaps
All	Assembled molecule	2,716,949,182	315	2,620,329,768	39,293,786	714	126
Chromosome 1	AllAssembled moleculeUnlocalized scaffolds	198,227,129197,195,4321,031,697	1275	192,486,238191,477,4361,008,802	52,628,78152,628,781241,735	522131	770
Chromosome 2	Assembled molecule	181,748,087	6	178,392,072	116,366,104	18	6
Chromosome 3	AllAssembled moleculeUnlocalized scaffolds	159,641,682159,599,78341,899	651	156,435,822156,393,92341,899	80,458,78980,458,78941,899	440	550
Chromosome 4	AllAssembled moleculeUnlocalized scaffolds	155,740,714155,630,120110,594	13112	151,994,466151,886,844107,622	21,899,95521,899,95566,673	29209	11110
Chromosome 5	AllAssembled moleculeUnlocalized scaffolds	152,844,609152,537,259307,350	20182	148,028,535147,721,185307,350	37,319,36237,319,362159,935	29290	18180
Chromosome 6	Assembled molecule	149,517,037	5	146,317,037	91,924,394	0	5
Chromosome 7	AllAssembled moleculeUnlocalized scaffolds	152,837,043152,524,553312,490	862	142,190,701141,878,211312,490	36,356,19436,356,194175,968	58580	660
Chromosome 8	AllAssembled moleculeUnlocalized scaffolds	132,438,464131,738,871699,593	1064	125,496,364124,796,771699,593	18,157,43118,157,431177,422	330	660
Chromosome 9	AllAssembled moleculeUnlocalized scaffolds	124,475,575124,076,172399,403	972	121,102,885120,720,222382,663	26,676,75426,676,754243,717	785424	770
Chromosome 10	Assembled molecule	129,993,255	3	126,847,852	72,324,642	24	3
Chromosome 11	Assembled molecule	121,843,856	3	118,743,556	33,384,931	3	3
Chromosome 12	Assembled molecule	121,257,530	3	117,459,312	39,293,786	22	3
Chromosome 13	AllAssembled moleculeUnlocalized scaffolds	120,634,623120,284,312350,311	752	116,706,770116,370,905335,865	28,633,59528,633,595186,869	422616	550
Chromosome 14	Assembled molecule	125,194,864	4	121,635,312	97,629,908	36	4
Chromosome 15	Assembled molecule	103,494,974	3	100,439,974	64,780,978	0	3
Chromosome 16	AllAssembled moleculeUnlocalized scaffolds	98,323,14498,319,1503,994	321	95,008,93395,004,9393,994	62,254,92362,254,9233,994	11110	220
Chromosome 17	AllAssembled moleculeUnlocalized scaffolds	95,801,39095,272,651528,739	633	92,426,94391,898,204528,739	81,466,43781,466,437195,669	40400	330
Chromosome 18	Assembled molecule	90,772,031	4	87,600,131	73,639,148	9	4
Chromosome 19	Assembled molecule	61,342,430	2	58,142,230	54,454,325	2	2
Chromosome X	AllAssembled moleculeUnlocalized scaffolds	167,935,371166,650,2961,285,075	322111	163,343,027162,080,9031,262,124	28,862,97528,862,975224,892	876027	20200
Chromosome Y	AllAssembled moleculeUnlocalized scaffolds	69,535,01615,902,55553,632,461	1042102	56,335,0162,702,55553,632,461	620,0432,195,326586,359	110	330
unplaced	Assembled molecule	3,350,358	52	3,196,592	187,641	166	0

Region Name	Location	Scaffold Count	Total Length	Ungapped Length	Scaffold N50	Spanned Gaps
region1	1:60697653-61195514	3	923,979	923,979	289,662	0
region2	1:61754170-61941338	1	187,142	187,142	187,142	0
region3	1:63440029-63634836	1	199,536	199,536	199,536	0
region4	1:78410334-78684064	1	272,653	272,653	272,653	0
Ren2	1:135135713-135386019	1	281,255	281,255	281,255	0
Ifi_cluster	1:175631261-175981314	2	390,047	390,022	235,763	1
region29	2:102863803-103229146	1	370,505	370,505	370,505	0
region30	3:36705645-37462525	4	1,047,914	1,047,914	292,416	0
region31	3:47250927-47483886	1	243,366	243,366	243,366	0
region32	3:99757788-99890338	1	141,661	141,661	141,661	0
region33	3:100124682-100629140	1	509,460	509,460	509,460	0
region34	3:100709803-101111508	1	402,204	402,204	402,204	0
region35	3:103394301-103719496	1	325,555	325,555	325,555	0
region36	3:108919638-109610603	1	689,363	689,363	689,363	0
olfactory_region_2	4:43775564-43869886	1	76,099	76,099	76,099	0
Mup_region_1	4:60433222-61702235	1	264,822	264,822	264,822	0
Mup_region_2	4:61706289-61898563	1	191,695	191,695	191,695	0
region40	4:66718636-66856206	1	138,473	138,473	138,473	0
region41	4:129222696-129387052	1	165,559	165,559	165,559	0
region42	4:129673209-129813999	1	140,602	140,602	140,602	0
Padi_cluster	4:140277012-140517363	1	240,498	240,433	240,498	2
region44	5:91082154-91255787	1	180,394	180,394	180,394	0
region45	5:151674830-151925798	1	262,166	262,166	262,166	0
region46	6:50729501-50869226	1	145,152	145,152	145,152	0
region47	6:82834040-82989835	1	162,691	162,691	162,691	0
vomeronasal_region_1	6:90040061-90240457	1	198,515	198,515	198,515	0
region49	6:120327240-120965219	1	636,098	636,098	636,098	0
region50	6:144953971-145181710	1	231,326	231,326	231,326	0
region51	7:28528234-28611868	1	91,251	91,251	91,251	0
Hbb_cluster	7:110959995-111009204	1	55,856	55,856	55,856	0
olfactory_region_3	7:114032224-114070764	1	34,498	34,498	34,498	0
region54	8:42378188-42567887	1	183,135	183,135	183,135	0
Large	8:75589541-75842949	1	251,056	251,056	251,056	0
Grm1	10:10581444-10647182	1	77,891	77,891	77,891	0
olfactory_region_1	11:58426683-58600787	1	170,397	170,397	170,397	0
region9	11:69708974-70768432	3	875,078	875,078	472,026	0
region10	11:72722413-72881612	1	159,511	159,511	159,511	0
region11	11:88404152-88462832	1	10,755	10,755	10,755	0
Mapt	11:104064572-104223846	1	161,334	161,334	161,334	0
Igh	12:105978478-115696908	5	1,906,522	1,906,522	1,380,717	0
Naip2_Naip5	13:100922006-101021810	1	100,803	100,803	100,803	0
Ipo11	13:107591153-107722976	1	138,434	138,434	138,434	0
Fhit	14:11148176-11650860	1	503,103	503,103	503,103	0
region17	14:52482687-52593237	1	105,813	105,813	105,813	0
Tcra_Tcrd	14:52971974-54848751	1	1,666,365	1,666,365	1,666,365	0
region19	15:80333302-80502798	1	88,442	88,442	88,442	0
DiGeorge	16:17742588-19066061	1	1,312,151	1,312,151	1,312,151	0
DownSynCrit	16:94114517-95701295	1	1,351,377	1,351,377	1,351,377	0
Airn	17:12922132-13054037	1	138,490	138,490	138,490	0
region23	17:27450268-27705657	1	258,652	258,652	258,652	0
region24	17:27792385-29352922	2	1,565,546	1,565,546	893,685	0
MHC_region_1	17:33888191-35744546	2	1,963,237	1,963,237	1,736,643	0
MHC_region_2	17:36230820-38050373	3	2,055,190	2,055,190	1,281,122	0
Impact	18:11308623-11423912	1	85,548	85,548	85,548	0
region28	19:5679043-5707799	1	46,440	46,440	46,440	0
Odz1	X:40330809-40652019	1	328,187	328,187	328,187	0
region57	X:69411520-69608545	1	194,271	194,271	194,271	0
Xlr_region_1	X:70248990-70367303	1	123,835	123,835	123,835	0
Xlr_region_2	X:70430764-70508135	1	78,785	78,689	78,785	1
Xic	X:100784623-101037209	1	247,850	247,850	247,850	0

Unit Name	Scaffold Count	Total Length	Ungapped Length	Scaffold N50	Spanned Gaps
129/J	1	84,250	84,250	84,250	0
129/Sv	10	3,712,199	3,712,103	636,098	1
129/SvEvTac	14	4,472,946	4,472,650	328,187	2
129/SvJ	19	8,419,058	8,417,629	1,380,717	17
129P2/OlaHsd	1	46,440	46,440	46,440	0
129S7/SvEv	4	639,698	639,698	191,695	0
A/J	1	100,803	100,803	100,803	0
AKR/J	3	586,502	586,502	191,521	0
Balb/c	1	55,856	55,856	55,856	0
Cast/Ei	3	589,796	589,796	196,014	0
NOD	28	8,199,057	8,199,057	325,555	0
Spret/Ei	2	347,950	347,950	179,651	0
unknown strain	7	922,255	922,255	149,371	0

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MGSCv37

See Genome Information for Mus musculus

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There are 24 assemblies for this organism

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