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GRCm38.p1

Description:
Genome Reference Consortium Mouse Build 38 patch release 1 (GRCm38.p1)
Organism name:
Mus musculus (house mouse)
Infraspecific name:
Strain: C57BL/6J
Submitter:
Genome Reference Consortium
Date:
2012/08/21
Assembly type:
haploid-with-alt-loci
Release type:
patch
Assembly level:
Chromosome
Genome representation:
full
GenBank assembly accession:
GCA_000001635.3 (replaced)
RefSeq assembly accession:
GCF_000001635.21 (replaced)
RefSeq assembly and GenBank assembly identical:
yes

IDs: 418928 [UID] 416688 [GenBank] 418928 [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 patches80
Total sequence length2,796,638,596
Total assembly gap length79,291,755
Gaps between scaffolds191
Number of scaffolds271
Scaffold N5052,589,046
Scaffold L5018
Number of contigs759
Contig N5032,273,079
Contig L5026
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)
PATCHES
129P2/OlaHsd
129S1/SvImJ
129S2/SvPas
129S6/SvEvTac
129X1/SvJ
A/J
AKR/J
BALB/c
CAST/Ei
NOD/MrkTac
NOD/ShiLtJ
RIII
UNKNOWN
129S7/SvEvBrd-Hprt-b-m2
non-nuclear

Regions

NameLocation
NOD_mouse_Idd5.11:60640809-63588262
NOD_mouse_Idd5.31:65597865-69265254
region41:78413759-78687489
NOD_mouse_Idd5.41:130311064-130653047
Ren21:133239136-133489442
Ifi_cluster1:173701136-174051183
region292:102983310-103388989
NOD_mouse_Idd3.13:36806723-37563603
region313:47447005-47679964
Tdpoz_cluster3:93583858-93685263
NOD_mouse_Idd10.13:99953865-101307585
NOD_mouse_Idd18.23:103590378-104055839
NOD_mouse_Idd18.13:109116720-109807685
olfactory_region_24:43762692-43857014
Mup_region_34:59870283-60154907
Mup_region_44:60374393-61285346
Mup_region_14:61778759-62041201
Mup_region_24:62045255-62237529
region404:67057602-67195172
NOD_mouse_Idd9.14:128397119-131686709
NOD_mouse_Idd9.1M4:135021547-135237421
Padi_cluster4:140721097-140961448
region714:143214657-143582942
Prame_region_14:144179444-144348902
NOD_mouse_Idd9.2_Idd9.34:146068508-151320022
region755:15457667-15635395
region445:90653128-90826761
region455:150872255-151123781
region466:50779502-50919227
region476:82734575-83039841
vomeronasal_region_16:89851149-90290463
region496:120377222-121015201
NOD_mouse_Idd6.36:129636567-130656471
NOD_mouse_Idd6.1+26:143536594-149568188
region727:3000001-3475222
region517:27743215-27826849
Hbb_cluster7:103811478-103860690
olfactory_region_37:106888710-106927250
region548:41292834-41482533
Large8:73065642-73319050
Grm110:10861646-10927384
region6011:48799134-49141362
region6111:58115562-58302084
olfactory_region_111:58613181-58787285
NOD_mouse_Idd4.111:69895472-71298870
NOD_mouse_Idd4.211:72908911-74370562
NOD_mouse_Idd4.2Q11:86869779-89954755
Mapt11:104203258-104362532
Serpin_region_112:103722705-103922810
Tcl1_region_112:105147714-105196166
Igh12:113067904-114458697
Naip2_Naip513:100075065-100330017
Ipo1113:106801073-106932896
region1714:51863012-51973562
Tcra_Tcrd14:52352473-54229076
region6515:79892564-79986558
region1915:80502872-80672368
DiGeorge16:17742495-19065968
DownSynCrit_region_116:94114272-95747459
DownSynCrit_region_216:95846204-96221063
DownSynCrit_region_316:97054368-97223607
Airn17:12729292-12861171
NOD_mouse_Idd16.117:27313323-29215977
MHC17:33681276-38548659
Impact18:11238883-11458280
region7018:60125920-60496981
Tmem13419:4013986-4260737
region2819:5679043-5707799
Slc1a119:28892559-28918752
region77X:37804742-37986547
Odz1X:42891057-43298842
region57X:72166181-72363206
Xlr_region_1X:73003651-73121964
Xlr_region_2X:73185425-73263090
XicX:103589284-103841870
PARX:169969759-170931299
region73Y:45842743-46337667
region76Y:49216909-49556418
region74Y:66019703-66188541
PARY:90745845-91644698
Assembly Unit: Primary Assembly (C57BL/6J) (GCF_000000055.19)
Molecule nameGenBank sequenceRefSeq sequenceUnlocalized
sequences count
Chromosome 1CM000994.2=NC_000067.65
Chromosome 2CM000995.2=NC_000068.70
Chromosome 3CM000996.2=NC_000069.60
Chromosome 4CM000997.2=NC_000070.66
Chromosome 5CM000998.2=NC_000071.65
Chromosome 6CM000999.2=NC_000072.60
Chromosome 7CM001000.2=NC_000073.61
Chromosome 8CM001001.2=NC_000074.60
Chromosome 9CM001002.2=NC_000075.60
Chromosome 10CM001003.2=NC_000076.60
Chromosome 11CM001004.2=NC_000077.60
Chromosome 12CM001005.2=NC_000078.60
Chromosome 13CM001006.2=NC_000079.60
Chromosome 14CM001007.2=NC_000080.60
Chromosome 15CM001008.2=NC_000081.60
Chromosome 16CM001009.2=NC_000082.60
Chromosome 17CM001010.2=NC_000083.60
Chromosome 18CM001011.2=NC_000084.60
Chromosome 19CM001012.2=NC_000085.60
Chromosome XCM001013.2=NC_000086.71
Chromosome YCM001014.2=NC_000087.74
unplacedn/an/an/a22

Assembly statistics

MoleculeSequence RoleTotal
Length
Scaffold
Count
Ungapped
Length
Scaffold
N50
Spanned
Gaps
Unspanned
Gaps
Chromosome 1AllAssembled moleculeUnlocalized scaffolds196,283,350195,471,971811,3791385192,720,578191,909,199811,37952,589,04652,589,046206,9613434011110
Chromosome 2Assembled molecule182,113,2247178,326,651116,378,6601711
Chromosome 3Assembled molecule160,039,6804156,398,866109,125,95557
Chromosome 4AllAssembled moleculeUnlocalized scaffolds157,219,549156,508,116711,433936152,764,072152,055,611708,46186,266,79986,266,799207,96844359880
Chromosome 5AllAssembled moleculeUnlocalized scaffolds153,573,022151,834,6841,738,33817125149,658,012147,919,6741,738,33837,423,12037,423,120953,0121919015150
Chromosome 6Assembled molecule149,736,5464146,336,546108,860,10019
Chromosome 7AllAssembled moleculeUnlocalized scaffolds145,617,427145,441,459175,968651142,031,376141,855,408175,96843,149,17643,149,176175,96825250880
Chromosome 8Assembled molecule129,401,2135125,611,43225,646,93168
Chromosome 9Assembled molecule124,595,1107121,157,01840,307,0062610
Chromosome 10Assembled molecule130,694,9933127,067,66472,389,128247
Chromosome 11Assembled molecule122,082,5432118,745,94587,300,92316
Chromosome 12Assembled molecule120,129,0222116,922,42278,455,22315
Chromosome 13Assembled molecule120,421,6395117,121,19328,633,99338
Chromosome 14Assembled molecule124,902,2442121,442,113105,332,54085
Chromosome 15Assembled molecule104,043,6853100,653,31565,061,23557
Chromosome 16Assembled molecule98,207,768295,019,76862,256,58815
Chromosome 17Assembled molecule94,987,271391,707,46481,232,659336
Chromosome 18Assembled molecule90,702,639387,452,63973,480,40916
Chromosome 19Assembled molecule61,431,566258,205,85654,517,95125
Chromosome XAllAssembled moleculeUnlocalized scaffolds171,368,232171,031,299336,93321201163,801,988163,488,006313,98228,873,11528,873,115336,93399722725250
Chromosome YAllAssembled moleculeUnlocalized scaffolds92,500,85791,744,698756,1592016488,880,85788,124,698756,15917,801,35117,801,351182,3471313019190
unplacedAssembled molecule803,89522741,48438,659750
MoleculeTotal
Length
Mitochondrion MT16,299
Region
Name
LocationScaffold
Count
Total
Length
Ungapped
Length
Scaffold
N50
Spanned
Gaps
NOD_mouse_Idd5.11:60640809-6358826211,003,859853,8591,003,8593
NOD_mouse_Idd5.31:65597865-6926525413,760,9573,710,9573,760,9571
region41:78413759-786874891272,653272,653272,6530
NOD_mouse_Idd5.41:130311064-1306530471326,027326,027326,0270
Ren21:133239136-1334894421281,255281,255281,2550
Ifi_cluster1:173701136-1740511833495,160495,160154,2840
region292:102983310-1033889891410,905410,905410,9050
NOD_mouse_Idd3.13:36806723-3756360341,047,9141,047,914292,4160
region313:47447005-476799641243,366243,366243,3660
Tdpoz_cluster3:93583858-936852631124,933124,933124,9330
NOD_mouse_Idd10.13:99953865-10130758511,153,3251,053,3251,153,3252
NOD_mouse_Idd18.23:103590378-1040558391466,430466,430466,4300
NOD_mouse_Idd18.13:109116720-1098076851689,363689,363689,3630
olfactory_region_24:43762692-43857014176,09976,09976,0990
Mup_region_34:59870283-601549071284,739284,739284,7390
Mup_region_44:60374393-612853462152,971152,97183,2180
Mup_region_14:61778759-620412011264,822264,822264,8220
Mup_region_24:62045255-622375291191,695191,695191,6950
region404:67057602-671951721138,473138,473138,4730
NOD_mouse_Idd9.14:128397119-13168670913,050,8412,950,8413,050,8412
NOD_mouse_Idd9.1M4:135021547-1352374211215,601215,601215,6010
Padi_cluster4:140721097-1409614481240,498240,433240,4982
region714:143214657-1435829421368,286368,286368,2860
Prame_region_14:144179444-1443489021170,592170,592170,5920
NOD_mouse_Idd9.2_Idd9.34:146068508-15132002224,830,9664,580,9663,205,4255
region755:15457667-156353951205,713205,713205,7130
region445:90653128-908267611180,394180,394180,3940
region455:150872255-1511237811262,166262,166262,1660
region466:50779502-509192271145,152145,152145,1520
region476:82734575-830398411312,568312,568312,5680
vomeronasal_region_16:89851149-902904631198,515198,515198,5150
region496:120377222-1210152011636,141636,141636,1410
NOD_mouse_Idd6.36:129636567-13065647111,759,4141,609,4141,759,4143
NOD_mouse_Idd6.1+26:143536594-14956818815,956,0885,656,0885,956,0886
region727:3000001-34752221473,738473,738473,7380
region517:27743215-27826849191,25191,25191,2510
Hbb_cluster7:103811478-103860690155,85655,85655,8560
olfactory_region_37:106888710-106927250134,49834,49834,4980
region548:41292834-414825331183,135183,135183,1350
Large8:73065642-733190501251,056251,056251,0560
Grm110:10861646-10927384177,89177,89177,8910
region6011:48799134-491413621247,497247,497247,4970
region6111:58115562-583020841186,379186,379186,3790
olfactory_region_111:58613181-587872851170,397170,397170,3970
NOD_mouse_Idd4.111:69895472-7129887011,550,1851,550,1851,550,1850
NOD_mouse_Idd4.211:72908911-7437056211,462,3111,462,3111,462,3110
NOD_mouse_Idd4.2Q11:86869779-8995475513,086,7443,086,7443,086,7440
Mapt11:104203258-1043625321161,334161,334161,3340
Serpin_region_112:103722705-103922810184,25084,25084,2500
Tcl1_region_112:105147714-105196166183,61283,61283,6120
Igh12:113067904-11445869731,874,0381,872,6991,714,4341
Naip2_Naip513:100075065-1003300172280,055280,055179,2520
Ipo1113:106801073-1069328961138,435138,435138,4350
region1714:51863012-519735621105,813105,813105,8130
Tcra_Tcrd14:52352473-5422907611,666,3651,666,3651,666,3650
region6515:79892564-79986558189,17789,17789,1770
region1915:80502872-80672368188,44288,44288,4420
DiGeorge16:17742495-1906596861,543,3551,543,355250,5950
DownSynCrit_region_116:94114272-9574745911,618,1621,618,1621,618,1620
DownSynCrit_region_216:95846204-962210631374,389374,389374,3890
DownSynCrit_region_316:97054368-972236071170,763170,763170,7630
Airn17:12729292-128611711138,490138,490138,4900
NOD_mouse_Idd16.117:27313323-2921597711,908,9201,908,9201,908,9200
MHC17:33681276-38548659813,006,27512,906,2754,256,2092
Impact18:11238883-114582802438,003438,003352,4550
region7018:60125920-604969811231,969231,969231,9690
Tmem13419:4013986-42607371246,751246,751246,7510
region2819:5679043-5707799146,44046,44046,4400
Slc1a119:28892559-28918752125,40725,40725,4070
region77X:37804742-379865471182,256182,256182,2560
Odz1X:42891057-432988421414,761414,761414,7610
region57X:72166181-723632061194,271194,271194,2710
Xlr_region_1X:73003651-731219641123,835123,835123,8350
Xlr_region_2X:73185425-73263090178,68978,68978,6890
XicX:103589284-1038418701247,850247,850247,8500
region73Y:45842743-463376671544,189544,189544,1890
region76Y:49216909-495564181331,480331,480331,4800
region74Y:66019703-661885411221,588221,588221,5880
Unit NameScaffold
Count
Total
Length
Ungapped
Length
Scaffold
N50
Spanned
Gaps
PATCHES92,926,4562,926,456352,4550
129P2/OlaHsd146,44046,44046,4400
129S1/SvImJ208,669,4378,666,7981,154,07815
129S2/SvPas134,49834,49834,4980
129S6/SvEvTac205,590,0855,589,414281,2553
129X1/SvJ93,340,0173,340,0171,934,4100
A/J1100,803100,803100,8030
AKR/J3586,502586,502191,5210
BALB/c2115,497115,49759,6410
CAST/Ei61,255,6411,255,641204,6630
NOD/MrkTac1723,606,01822,956,0183,050,84113
NOD/ShiLtJ517,622,14217,072,1424,910,97611
RIII2169,160169,16085,5480
UNKNOWN5620,759620,530138,4904
129S7/SvEvBrd-Hprt-b-m271,083,3671,083,367264,8220