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GRCm38.p6

Description:
Genome Reference Consortium Mouse Build 38 patch release 6 (GRCm38.p6)
Organism name:
Mus musculus (house mouse)
Infraspecific name:
Strain: C57BL/6J
BioProject:
PRJNA20689
Submitter:
Genome Reference Consortium
Date:
2017/09/15
Assembly type:
haploid-with-alt-loci
Release type:
patch
Assembly level:
Chromosome
Genome representation:
full
RefSeq category:
reference genome
GenBank assembly accession:
GCA_000001635.8 (latest)
RefSeq assembly accession:
GCF_000001635.26 (latest)
RefSeq assembly and GenBank assembly identical:
yes

IDs: 1198761 [UID] 5015798 [GenBank] 5034988 [RefSeq]

See Genome Information for Mus musculus

There are 24 assemblies for this organism

See more

History (Show revision history)

Comment

The DNA sequence is composed of genomic sequence, primarily finished clones that were sequenced as part of the Mouse Genome Project. PCR products and WGS shotgun sequence have been added where necessary to fill gaps or correct errors. All ... such additions are manually curated by GRC staff. For more information see: http://genomereference.org.  more

Global statistics

Number of regions with alternate loci or patches129
Total sequence length2,730,855,475
Total assembly gap length78,088,216
Gaps between scaffolds191
Number of scaffolds162
Scaffold N5054,517,951
Scaffold L5017
Number of contigs605
Contig N5032,813,180
Contig L5025
Total number of chromosomes and plasmids21
Number of component sequences (WGS or clone)20,423

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
Rims11:22159855-22877939
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
region861:178144751-178344759
Traf51:191793213-192106925
Ptpmt12:90853948-91049681
region292:102983310-103388989
Spata5l12:122566305-122720961
region803:15760691-15949398
NOD_mouse_Idd3.13:36806723-37563603
Intu3:40505691-40944643
region313:47447005-47679964
region873:50686235-50904915
Tdpoz_cluster3:93583858-93685263
NOD_mouse_Idd10.13:99953865-101307585
NOD_mouse_Idd18.23:103590378-104055839
NOD_mouse_Idd18.13:109116720-109807685
Sgms23:131299856-131505512
olfactory_region_24:43762692-43857014
Mup_region_34:59870283-60154907
Mup_region_44:60250666-61586638
Mup_region_14:61778759-62041201
Mup_region_24:62045255-62237529
region404:67057602-67195172
Efcab74:99625547-100035456
region884:121426261-122034165
region794:122217500-122473817
NOD_mouse_Idd9.14:128397119-131686709
NOD_mouse_Idd9.1M4:135021547-135237421
Padi_cluster4:140721097-140961448
region894:141987963-142697802
region714:143214657-143582942
Prame_region_14:144179444-144348902
NOD_mouse_Idd9.2_Idd9.34:146068508-151320022
region755:15457667-15635395
region445:90653128-90826761
Auts25:131326290-132550462
region455:150872255-151123781
region466:50779502-50919227
Sftpb6:72296717-72451483
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
Jakmip37:138934711-139370933
Muc27:141683154-141786694
region548:41292834-41482533
Rab3a_Ifi308:70673831-70845694
Large8:73065642-73319050
Slc26a69:108784955-108953239
Nlrp4g9:124268539-124479149
region9010:7346541-7776389
Grm110:10861646-10927384
region8110:58205866-58311233
region9110:67228314-67653670
region9211:7560598-7879512
region6011:48799134-49141362
region6111:58115562-58302084
olfactory_region_111:58613181-58787285
NOD_mouse_Idd4.111:69895472-71336724
NOD_mouse_Idd4.211:72908911-74370562
region9311:82933464-83353797
NOD_mouse_Idd4.2Q11:86869779-89954755
Mapt11:104203258-104362532
Serpin_region_112:103722705-103922810
Tcl1_region_112:105147714-105196166
Meg312:109373903-109689534
Ahnak212:112701299-112815832
Igh12:113067904-114458697
Naip2_Naip513:100075065-100330017
Ipo1113:106801073-106932896
region9414:24646407-24762340
Dnah1214:26629355-26911986
region1714:51863012-51973562
Tcra_Tcrd14:52352473-54229076
region8215:3050001-3186530
Nadk215:9054779-9266110
Baalc15:38582635-39142852
Anxa1315:57983529-58517868
region6515:79892564-79986558
region1915:80502872-80672368
region9515:103658568-103917132
DiGeorge16:17742495-19065968
DownSynCrit_region_116:94114272-95747459
DownSynCrit_region_216:95846204-96221063
DownSynCrit_region_316:97054368-97223607
region9617:7391520-7693199
Airn17:12729292-12861171
NOD_mouse_Idd16.117:27313323-29215977
MHC17:33681276-38548659
Trerf117:47094952-47423636
region9717:47916958-48583287
region7817:54687402-55747384
Impact18:11238883-11458280
region7018:60125920-60496981
region9818:76466242-76775534
Pstpip218:77623953-78117342
Tmem13419:4013986-4260737
region2819:5679043-5707799
region8319:6183084-6688105
Slc1a119:28892559-28918752
Ide19:37204249-37492988
DgkkX:6763452-7054396
region85X:29000987-29562451
region77X:37690395-37986547
Odz1X:42891057-43298842
4933416I08RikX:53444973-53687352
region84X:60271962-60763715
region57X:72166181-72363206
Xlr_region_1X:73003651-73121964
Xlr_region_2X:73185425-73263090
XicX:103589284-103841870
region99X:111104003-111543375
Atg4aX:140784762-141363409
PARX:169969759-170931299
region73Y:45842743-46337667
region76Y:49216909-49556418
region74Y:66019703-66188541
PARY:90745845-91644698
region1aMMCHR6_CHORI29_IDD6_3:709988-1759414
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
AllAssembled molecule2,730,855,4751622,652,767,25954,517,951443191
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
Rims11:22159855-228779391686,942686,942686,9420
NOD_mouse_Idd5.11:60640809-6358826221,460,6571,310,6571,003,8593
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
region861:178144751-1783447591200,008200,008200,0080
Traf51:191793213-1921069251266,016265,916266,0161
Ptpmt12:90853948-910496811195,735195,735195,7350
region292:102983310-1033889891410,905410,905410,9050
Spata5l12:122566305-1227209611166,096166,096166,0960
region803:15760691-159493981214,957214,957214,9570
NOD_mouse_Idd3.13:36806723-3756360341,047,9141,047,914292,4160
Intu3:40505691-409446431339,234339,234339,2340
region313:47447005-476799641243,366243,366243,3660
region873:50686235-509049151171,653171,653171,6530
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
Sgms23:131299856-1315055121117,769117,769117,7690
olfactory_region_24:43762692-43857014176,09976,09976,0990
Mup_region_34:59870283-601549071284,739284,739284,7390
Mup_region_44:60250666-615866384737,784737,784399,2650
Mup_region_14:61778759-620412011264,822264,822264,8220
Mup_region_24:62045255-622375291191,695191,695191,6950
region404:67057602-671951721138,473138,473138,4730
Efcab74:99625547-1000354561378,870378,870378,8700
region884:121426261-1220341651583,977583,977583,9770
region794:122217500-1224738171316,842316,842316,8420
NOD_mouse_Idd9.14:128397119-13168670933,285,0113,184,7893,050,8414
NOD_mouse_Idd9.1M4:135021547-1352374211215,601215,601215,6010
Padi_cluster4:140721097-1409614481240,498240,433240,4982
region894:141987963-1426978021709,099709,099709,0990
region714:143214657-1435829421368,286368,286368,2860
Prame_region_14:144179444-1443489021170,592170,592170,5920
NOD_mouse_Idd9.2_Idd9.34:146068508-15132002235,363,5385,097,5383,205,4256
region755:15457667-156353951205,713205,713205,7130
region445:90653128-908267611180,394180,394180,3940
Auts25:131326290-13255046211,224,1741,224,1741,224,1740
region455:150872255-1511237811262,166262,166262,1660
region466:50779502-509192271145,152145,152145,1520
Sftpb6:72296717-724514831154,766154,766154,7660
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
Jakmip37:138934711-1393709331414,410414,410414,4100
Muc27:141683154-141786694171,46071,46071,4600
region548:41292834-414825331183,135183,135183,1350
Rab3a_Ifi308:70673831-708456941171,859171,859171,8590
Large8:73065642-733190501251,056251,056251,0560
Slc26a69:108784955-1089532391120,154120,154120,1540
Nlrp4g9:124268539-1244791491210,641195,862210,64112
region9010:7346541-77763891355,613355,613355,6130
Grm110:10861646-10927384177,89177,89177,8910
region8110:58205866-583112331129,865129,865129,8650
region9110:67228314-676536701425,386425,318425,3863
region9211:7560598-78795121318,915318,915318,9150
region6011:48799134-491413623648,905648,905215,2640
region6111:58115562-583020841186,379186,379186,3790
olfactory_region_111:58613181-587872851170,397170,397170,3970
NOD_mouse_Idd4.111:69895472-7133672442,730,1132,730,1131,550,1850
NOD_mouse_Idd4.211:72908911-7437056211,462,3111,462,3111,462,3110
region9311:82933464-8335379731,061,1611,061,161368,9670
NOD_mouse_Idd4.2Q11:86869779-8995475523,417,8553,417,8553,086,7440
Mapt11:104203258-1043625321161,334161,334161,3340
Serpin_region_112:103722705-103922810184,25084,25084,2500
Tcl1_region_112:105147714-105196166183,61283,61283,6120
Meg312:109373903-1096895341316,140316,140316,1400
Ahnak212:112701299-1128158321111,720111,720111,7200
Igh12:113067904-11445869731,874,0381,872,6991,714,4341
Naip2_Naip513:100075065-1003300172280,055280,055179,2520
Ipo1113:106801073-1069328961138,435138,435138,4350
region9414:24646407-24762340166,29066,29066,2900
Dnah1214:26629355-269119861283,434283,434283,4340
region1714:51863012-519735621105,813105,813105,8130
Tcra_Tcrd14:52352473-5422907611,666,3651,666,3651,666,3650
region8215:3050001-31865301166,012166,012166,0120
Nadk215:9054779-92661101211,337211,337211,3370
Baalc15:38582635-391428521423,369423,369423,3690
Anxa1315:57983529-585178681542,789542,694542,7891
region6515:79892564-79986558189,17789,17789,1770
region1915:80502872-80672368188,44288,44288,4420
region9515:103658568-1039171321380,404380,404380,4040
DiGeorge16:17742495-1906596872,049,2312,049,231261,3360
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
region9617:7391520-76931991253,113253,113253,1130
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
Trerf117:47094952-474236361328,684328,684328,6840
region9717:47916958-485832871662,433662,433662,4330
region7817:54687402-5574738411,059,9551,059,9551,059,9550
Impact18:11238883-114582802438,003438,003352,4550
region7018:60125920-604969811231,969231,969231,9690
region9818:76466242-767755341263,917263,917263,9170
Pstpip218:77623953-781173421448,905448,905448,9050
Tmem13419:4013986-42607371246,751246,751246,7510
region2819:5679043-5707799146,44046,44046,4400
region8319:6183084-66881051506,812506,812506,8120
Slc1a119:28892559-28918752125,40725,40725,4070
Ide19:37204249-374929881299,789299,789299,7890
DgkkX:6763452-70543961245,130245,130245,1300
region85X:29000987-295624512480,168480,168260,4470
region77X:37690395-379865471203,377203,377203,3770
Odz1X:42891057-432988421414,761414,761414,7610
4933416I08RikX:53444973-536873521155,470155,470155,4700
region84X:60271962-607637151490,000490,000490,0000
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
region99X:111104003-1115433751305,464305,464305,4640
Atg4aX:140784762-1413634091460,895460,895460,8950
region73Y:45842743-463376671544,189544,189544,1890
region76Y:49216909-495564181331,480331,480331,4800
region74Y:66019703-661885411221,588221,588221,5880
region1a6:709988-175941400000
Unit NameScaffold
Count
Total
Length
Ungapped
Length
Scaffold
N50
Spanned
Gaps
PATCHES7425,262,40825,118,591394,02661
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
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