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GRCm38

Description:: Genome Reference Consortium Mouse Build 38
Organism name:: Mus musculus
Submitter:: Genome Reference Consortium
Synonym:: mm10
Assembly type:: haploid-with-alt-loci
Assembly level:: Chromosome
Genome representation:: full
GenBank Assembly ID:: GCA_000001635.2 (replaced)
RefSeq Assembly ID:: GCF_000001635.20 (replaced)
RefSeq Assembly and GenBank Assembly Identical:: yes

See Genome Information for Mus musculus

There are 6 assemblies for this organism

History (Show revision history)

GenBank Assembly ID		RefSeq Assembly ID	Assembly Name	Assembly Level	Status
GCA_000001635.3	=	GCF_000001635.21	GRCm38.p1	Chromosome	Latest GenBank, Latest 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
n/a	n/a	GCF_000001635.16	MGSCv37	Chromosome	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

Global statistics

Number of regions with alternate loci or patches	72
Total sequence length	2,793,712,140
Total assembly gap length	79,289,460
Gaps between scaffolds	191
Number of scaffolds	262
Scaffold N50	52,589,046
Number of contigs	726
Contig N50	32,273,079
Total number of chromosomes and plasmids	22

Assembly Definition
Assembly Statistics

Global assembly definitionDownload 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)
129P2/OlaHsd
129S1/SvImJ
129S2/SvPas
129S6/SvEvTac
129S7/SvEvBrd-Hprt-b-m2
129X1/SvJ
A/J
AKR/J
BALB/c
CAST/Ei
NOD/MrkTac
NOD/ShiLtJ
RIII
UNKNOWN
non-nuclear

Regions

Name	Location
Odz1	X:42891057-43298842
region57	X:72166181-72363206
Xic	X:103589284-103841870
Xlr_region_1	X:73003651-73121964
Xlr_region_2	X:73185425-73263090
Ifi_cluster	1:173701136-174051183
NOD_mouse_Idd5.1	1:60640809-63588262
NOD_mouse_Idd5.3	1:65597865-69265254
NOD_mouse_Idd5.4	1:130311064-130653047
region4	1:78413759-78687489
Ren2	1:133239136-133489442
region29	2:102983310-103388989
NOD_mouse_Idd10.1	3:99953865-101307585
NOD_mouse_Idd18.1	3:109116720-109807685
NOD_mouse_Idd18.2	3:103590378-104055839
NOD_mouse_Idd3.1	3:36806723-37563603
region31	3:47447005-47679964
Tdpoz_cluster	3:93583858-93685263
Mup_region_1	4:61778759-62041201
Mup_region_2	4:62045255-62237529
Mup_region_3	4:59870283-60154907
Mup_region_4	4:60374393-61285346
NOD_mouse_Idd9.1	4:128397119-131686709
NOD_mouse_Idd9.1M	4:135021547-135237421
NOD_mouse_Idd9.2_Idd9.3	4:146068508-151320022
olfactory_region_2	4:43762692-43857014
Padi_cluster	4:140721097-140961448
Prame_region_1	4:144179444-144348902
region40	4:67057602-67195172
region44	5:90653128-90826761
region45	5:150872255-151123781
NOD_mouse_Idd6.1+2	6:143536594-149568188
NOD_mouse_Idd6.3	6:129636567-130656471
region46	6:50779502-50919227
region47	6:82734575-83039841
region49	6:120377222-121015201
vomeronasal_region_1	6:89851149-90290463
Hbb_cluster	7:103811478-103860690
olfactory_region_3	7:106888710-106927250
region51	7:27743215-27826849
Large	8:73065642-73319050
region54	8:41292834-41482533
Grm1	10:10861646-10927384
Mapt	11:104203258-104362532
NOD_mouse_Idd4.1	11:69895472-71298870
NOD_mouse_Idd4.2	11:72908911-74370562
NOD_mouse_Idd4.2Q	11:86869779-89954755
olfactory_region_1	11:58613181-58787285
region60	11:48799134-49141362
region61	11:58115562-58302084
Igh	12:113067904-114458697
Serpin_region_1	12:103722705-103922810
Tcl1_region_1	12:105147714-105196166
Ipo11	13:106801073-106932896
Naip2_Naip5	13:100075065-100330017
region17	14:51863012-51973562
Tcra_Tcrd	14:52352473-54229076
region19	15:80502872-80672368
region65	15:79892564-79986558
DiGeorge	16:17742495-19065968
DownSynCrit_region_1	16:94114272-95747459
DownSynCrit_region_2	16:95846204-96221063
DownSynCrit_region_3	16:97054368-97223607
Airn	17:12729292-12861171
MHC	17:33681276-38548659
NOD_mouse_Idd16.1	17:27313323-29215977
Impact	18:11308625-11318460
region70	18:60125920-60496981
region28	19:5679043-5707799
Slc1a1	19:28892559-28918752

Assembly Unit: Primary Assembly (C57BL/6J)

Molecule name	GenBank ID		RefSeq ID	Unlocalized sequences count
1	CM000994.2	=	NC_000067.6	5
2	CM000995.2	=	NC_000068.7	0
3	CM000996.2	=	NC_000069.6	0
4	CM000997.2	=	NC_000070.6	6
5	CM000998.2	=	NC_000071.6	5
6	CM000999.2	=	NC_000072.6	0
7	CM001000.2	=	NC_000073.6	1
8	CM001001.2	=	NC_000074.6	0
9	CM001002.2	=	NC_000075.6	0
10	CM001003.2	=	NC_000076.6	0
11	CM001004.2	=	NC_000077.6	0
12	CM001005.2	=	NC_000078.6	0
13	CM001006.2	=	NC_000079.6	0
14	CM001007.2	=	NC_000080.6	0
15	CM001008.2	=	NC_000081.6	0
16	CM001009.2	=	NC_000082.6	0
17	CM001010.2	=	NC_000083.6	0
18	CM001011.2	=	NC_000084.6	0
19	CM001012.2	=	NC_000085.6	0
X	CM001013.2	=	NC_000086.7	1
Y	CM001014.2	=	NC_000087.7	4
unplaced				22

Molecule name	GenBank ID		RefSeq ID	Unlocalized sequences count
MT	AY172335.1	=	NC_005089.1	0

Scaffold Name	Chromosome Assignment	GenBank ID		RefSeq ID
129P2/OLAHSD_MMCHR19_CTG1	19	GL456079.1	=	NT_039697.1

Assembly Unit: 129S1/SvImJ

Scaffold Name	Chromosome Assignment	GenBank ID		RefSeq ID
129S1/SVIMJ_MMCHR2_CTG2	2	GL456024.2	=	NT_039223.3
129S1/SVIMJ_MMCHR3_CTG2	3	GL456007.1	=	NT_039256.1
129S1/SVIMJ_MMCHR3_CTG3	3	GL456006.1	=	NT_039248.1
129S1/SVIMJ_MMCHR3_CTG4	3	GL456008.1	=	NT_080257.1
129S1/SVIMJ_MMCHR5_CTG5	5	GL456011.1	=	NT_109599.1
129S1/SVIMJ_MMCHR6_CTG1	6	GL456025.1	=	NT_039373.1
129S1/SVIMJ_MMCHR6_CTG5	6	GL456026.2	=	NT_039382.4
129S1/SVIMJ_MMCHR7_CTG1	7	GL456014.1	=	NT_078572.1
129S1/SVIMJ_MMCHR12_CTG3	12	GL456074.1	=	NT_114988.1
129S1/SVIMJ_MMCHR12_CTG1	12	GL456017.2	=	NT_114985.3
129S1/SVIMJ_MMCHR13_CTG1	13	JH584305.1	=	NT_187006.1
129S1/SVIMJ_MMCHR14_CTG3	14	GL456019.1	=	NT_039614.1
129S1/SVIMJ_MMCHR16_CTG1	16	JH584306.1	=	NT_187007.1
129S1/SVIMJ_MMCHR16_CTG2	16	JH584307.1	=	NT_187008.1
129S1/SVIMJ_MMCHR17_CTG2	17	JH590470.1	=	NT_187009.1
129S1/SVIMJ_MMCHR17_CTG3	17	JH584308.1	=	NT_187010.1
129S1/SVIMJ_MMCHR17_CTG4	17	JH584309.1	=	NT_187011.1
129S1/SVIMJ_MMCHRX_CTG3	X	GL456032.1	=	NT_039744.2
129S1/SVIMJ_MMCHRX_CTG7	X	GL456033.2	=	NT_039747.4
129S1/SVIMJ_MMCHRX_CTG10	X	GL456031.1	=	NT_111920.1

Scaffold Name	Chromosome Assignment	GenBank ID		RefSeq ID
129S2/SVPAS_MMCHR7_CTG1	7	GL456013.1	=	NT_039443.1

Assembly Unit: 129S6/SvEvTac

Scaffold Name	Chromosome Assignment	GenBank ID		RefSeq ID
129S6/SVEVTAC_MMCHR1_CTG1	1	GL455993.1	=	NT_039198.1
129S6/SVEVTAC_MMCHR1_CTG3	1	GL455991.1	=	NT_039192.2
129S6/SVEVTAC_MMCHR1_CTG4	1	GL455992.2	=	NT_039194.5
129S6/SVEVTAC_MMCHR4_CTG1	4	GL455994.1	=	NT_039291.1
129S6/SVEVTAC_MMCHR5_CTG1	5	GL455995.1	=	NT_039334.1
129S6/SVEVTAC_MMCHR8_CTG1	8	GL455996.1	=	NT_039469.1
129S6/SVEVTAC_MMCHR8_CTG2	8	GL455997.1	=	NT_039470.1
129S6/SVEVTAC_MMCHR11_CTG1	11	GL455998.1	=	NT_078683.1
129S6/SVEVTAC_MMCHR13_CTG1	13	GL455999.2	=	NT_039594.3
129S6/SVEVTAC_MMCHR15_CTG1	15	GL456000.1	=	NT_039622.1
129S6/SVEVTAC_MMCHR16_CTG1	16	JH584310.1	=	NT_187012.1
129S6/SVEVTAC_MMCHR16_CTG2	16	JH584311.1	=	NT_187013.1
129S6/SVEVTAC_MMCHR16_CTG3	16	JH584312.1	=	NT_187014.1
129S6/SVEVTAC_MMCHR16_CTG6	16	GL456001.2	=	NT_039634.4
129S6/SVEVTAC_MMCHR16_CTG4	16	JH584313.1	=	NT_187015.1
129S6/SVEVTAC_MMCHR16_CTG5	16	JH584314.1	=	NT_187016.1
129S6/SVEVTAC_MMCHR17_CTG1	17	GL456021.2	=	NT_039661.4
129S6/SVEVTAC_MMCHR17_CTG2	17	GL456002.2	=	NT_039666.2
129S6/SVEVTAC_MMCHRX_CTG2	X	GL456003.2	=	NT_039739.2
129S6/SVEVTAC_MMCHRX_CTG6	X	GL456004.1	=	NT_099024.1

Assembly Unit: 129S7/SvEvBrd-Hprt-b-m2

Scaffold Name	Chromosome Assignment	GenBank ID		RefSeq ID
129S7/SVEVBRD-HPRT-B-M2_MMCHR4_CTG6	4	JH584269.1	=	NT_187000.1
129S7/SVEVBRD-HPRT-B-M2_MMCHR4_CTG5	4	JH584268.1	=	NT_186999.1
129S7/SVEVBRD-HPRT-B-M2_MMCHR4_CTG4	4	GL456077.1	=	NT_166295.1
129S7/SVEVBRD-HPRT-B-M2_MMCHR4_CTG2	4	GL456075.1	=	NT_166293.1
129S7/SVEVBRD-HPRT-B-M2_MMCHR4_CTG3	4	GL456076.1	=	NT_166294.1
129S7/SVEVBRD-HPRT-B-M2_MMCHR12_CTG2	12	GL456078.1	=	NT_166322.1
129S7/SVEVBRD-HPRT-B-M2_MMCHR15_CTG1	15	JH584270.1	=	NT_187001.1

Assembly Unit: 129X1/SvJ

Scaffold Name	Chromosome Assignment	GenBank ID		RefSeq ID
129X1/SVJ_MMCHR1_CTG1	1	JH584315.1	=	NT_187017.1
129X1/SVJ_MMCHR1_CTG2	1	GL456005.1	=	NT_039195.1
129X1/SVJ_MMCHR4_CTG2	4	GL456010.1	=	NT_039296.1
129X1/SVJ_MMCHR6_CTG1	6	GL456012.2	=	NT_039372.2
129X1/SVJ_MMCHR6_CTG3	6	GL456065.1	=	NT_039367.1
129X1/SVJ_MMCHR11_CTG3	11	GL456016.1	=	NT_039525.1
129X1/SVJ_MMCHR14_CTG1	14	GL456020.1	=	NT_096797.1
129X1/SVJ_MMCHR16_CTG1	16	GL456028.2	=	NT_039630.5
129X1/SVJ_MMCHR17_CTG2	17	GL456022.2	=	NT_039662.3

Scaffold Name	Chromosome Assignment	GenBank ID		RefSeq ID
A/J_MMCHR13_CTG1	13	GL455990.1	=	NT_039593.1

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
BALB/C_MMCHR7_CTG1	7	GL455989.1	=	NT_095534.1
BALB/C_MMCHR12_CTG1	12	GL456068.1	=	NT_096355.1

Assembly Unit: CAST/Ei

Scaffold Name	Chromosome Assignment	GenBank ID		RefSeq ID
CAST/EI_MMCHR11_CTG1	11	JH584316.1	=	NT_187028.1
CAST/EI_MMCHR11_CTG3	11	JH584317.1	=	NT_187029.1
CAST/EI_MMCHR18_CTG1	18	JH584318.1	=	NT_187030.1
CAST/EI_MMCHRY_CTG1	Y	GL456071.1	=	NT_166396.1
CAST/EI_MMCHRY_CTG2	Y	GL456072.1	=	NT_166398.1
CAST/EI_MMCHRY_CTG3	Y	GL456073.1	=	NT_166399.1

Assembly Unit: NOD/MrkTac

Showing 16 out of 17 records

Scaffold Name	Chromosome Assignment	GenBank ID		RefSeq ID
MMCHR1_NOD_IDD5_1	1	JH584320.1	=	NT_187019.1
MMCHR1_NOD_IDD5_3	1	JH584321.1	=	NT_187020.1
MMCHR1_NOD_IDD5_4	1	JH584322.1	=	NT_187021.1
MMCHR3_NOD_IDD3_1	3	GL456048.1	=	NT_039252.1
MMCHR3_NODMRKTAC_CTG1	3	GL456045.2	=	NT_039247.2
MMCHR3_NODMRKTAC_CTG2	3	GL456049.2	=	NT_039257.4
MMCHR3_NOD_IDD10_1	3	JH584323.1	=	NT_187022.1
MMCHR3_NOD_IDD18_2	3	GL456044.2	=	NT_166287.2
MMCHR3_NOD_IDD18_1	3	GL456042.2	=	NT_114257.4
MMCHR4_NOD_IDD9_1	4	JH584324.1	=	NT_187023.1
MMCHR4_NOD_IDD9_1M	4	JH584325.1	=	NT_187024.1
MMCHR4_NOD_IDD9_2	4	GL456053.2	=	NT_166299.2
MMCHR4_NOD_IDD9_3	4	JH584326.1	=	NT_187025.1
MMCHR11_NOD_IDD4_1	11	JH584327.1	=	NT_187026.1
MMCHR11_NOD_IDD4_2	11	GL456060.2	=	NT_166317.2
MMCHR17_NOD_IDD1	17	JH584328.1	=	NT_187027.1

Assembly Unit: NOD/ShiLtJ

Scaffold Name	Chromosome Assignment	GenBank ID		RefSeq ID
MMCHR6_CHORI29_IDD6_3	6	JH584264.1	=	NT_187002.1
MMCHR6_CHORI29_IDD6_1+2	6	GL456054.2	=	NT_166305.2
MMCHR11_CHORI29_IDD4_2Q	11	JH584265.1	=	NT_187003.1
MMCHR17_CHORI29_IDD16_1	17	JH584267.1	=	NT_187005.1
MMCHR17_CHO_IDD1	17	JH584266.1	=	NT_187004.1

Scaffold Name	Chromosome Assignment	GenBank ID		RefSeq ID
RIII_MMCHR12_CTG1	12	GL456349.1	=	NT_166433.1
RIII_MMCHR18_CTG1	18	GL456070.1	=	NT_165784.1

Assembly Unit: UNKNOWN

Scaffold Name	Chromosome Assignment	GenBank ID		RefSeq ID
UNKNOWN_MMCHR4_CTG1	4	GL456064.1	=	NT_039292.1
UNKNOWN_MMCHR4_CTG7	4	GL456009.1	=	NT_109318.2
UNKNOWN_MMCHR10_CTG3	10	GL456015.1	=	NT_078651.1
UNKNOWN_MMCHR17_CTG3	17	GL456069.1	=	NT_097336.1
UNKNOWN_MMCHR19_CTG2	19	JH584319.1	=	NT_187018.1

Scaffold Name	Chromosome Assignment	GenBank ID		RefSeq ID
MMCHR1_NOD_IDD5_3	1	JH584321.1	=	NT_187020.1

Scaffold Name	Chromosome Assignment	GenBank ID		RefSeq ID
MMCHR1_NOD_IDD5_4	1	JH584322.1	=	NT_187021.1

Scaffold Name	Chromosome Assignment	GenBank ID		RefSeq ID
129S6/SVEVTAC_MMCHR1_CTG3	1	GL455991.1	=	NT_039192.2

Region: Ifi_cluster

Scaffold Name	Chromosome Assignment	GenBank ID		RefSeq ID
129S6/SVEVTAC_MMCHR1_CTG4	1	GL455992.2	=	NT_039194.5
129X1/SVJ_MMCHR1_CTG1	1	JH584315.1	=	NT_187017.1
129X1/SVJ_MMCHR1_CTG2	1	GL456005.1	=	NT_039195.1

Scaffold Name	Chromosome Assignment	GenBank ID		RefSeq ID
UNKNOWN_MMCHR10_CTG3	10	GL456015.1	=	NT_078651.1

Scaffold Name	Chromosome Assignment	GenBank ID		RefSeq ID
CAST/EI_MMCHR11_CTG3	11	JH584317.1	=	NT_187029.1

Scaffold Name	Chromosome Assignment	GenBank ID		RefSeq ID
129S6/SVEVTAC_MMCHR11_CTG1	11	GL455998.1	=	NT_078683.1

Scaffold Name	Chromosome Assignment	GenBank ID		RefSeq ID
MMCHR11_NOD_IDD4_1	11	JH584327.1	=	NT_187026.1

Scaffold Name	Chromosome Assignment	GenBank ID		RefSeq ID
MMCHR11_NOD_IDD4_2	11	GL456060.2	=	NT_166317.2

Scaffold Name	Chromosome Assignment	GenBank ID		RefSeq ID
MMCHR11_CHORI29_IDD4_2Q	11	JH584265.1	=	NT_187003.1

Scaffold Name	Chromosome Assignment	GenBank ID		RefSeq ID
129X1/SVJ_MMCHR11_CTG3	11	GL456016.1	=	NT_039525.1

Scaffold Name	Chromosome Assignment	GenBank ID		RefSeq ID
129S1/SVIMJ_MMCHR12_CTG3	12	GL456074.1	=	NT_114988.1

Scaffold Name	Chromosome Assignment	GenBank ID		RefSeq ID
RIII_MMCHR12_CTG1	12	GL456349.1	=	NT_166433.1

Region: Igh

Scaffold Name	Chromosome Assignment	GenBank ID		RefSeq ID
BALB/C_MMCHR12_CTG1	12	GL456068.1	=	NT_096355.1
129S7/SVEVBRD-HPRT-B-M2_MMCHR12_CTG2	12	GL456078.1	=	NT_166322.1
129S1/SVIMJ_MMCHR12_CTG1	12	GL456017.2	=	NT_114985.3

Scaffold Name	Chromosome Assignment	GenBank ID		RefSeq ID
A/J_MMCHR13_CTG1	13	GL455990.1	=	NT_039593.1
129S1/SVIMJ_MMCHR13_CTG1	13	JH584305.1	=	NT_187006.1

Scaffold Name	Chromosome Assignment	GenBank ID		RefSeq ID
129S6/SVEVTAC_MMCHR13_CTG1	13	GL455999.2	=	NT_039594.3

Scaffold Name	Chromosome Assignment	GenBank ID		RefSeq ID
129X1/SVJ_MMCHR14_CTG1	14	GL456020.1	=	NT_096797.1

Scaffold Name	Chromosome Assignment	GenBank ID		RefSeq ID
129S1/SVIMJ_MMCHR14_CTG3	14	GL456019.1	=	NT_039614.1

Scaffold Name	Chromosome Assignment	GenBank ID		RefSeq ID
129S7/SVEVBRD-HPRT-B-M2_MMCHR15_CTG1	15	JH584270.1	=	NT_187001.1

Scaffold Name	Chromosome Assignment	GenBank ID		RefSeq ID
129S6/SVEVTAC_MMCHR15_CTG1	15	GL456000.1	=	NT_039622.1

Region: DiGeorge

Scaffold Name	Chromosome Assignment	GenBank ID		RefSeq ID
129S1/SVIMJ_MMCHR16_CTG1	16	JH584306.1	=	NT_187007.1
129S1/SVIMJ_MMCHR16_CTG2	16	JH584307.1	=	NT_187008.1
129S6/SVEVTAC_MMCHR16_CTG1	16	JH584310.1	=	NT_187012.1
129S6/SVEVTAC_MMCHR16_CTG2	16	JH584311.1	=	NT_187013.1
129S6/SVEVTAC_MMCHR16_CTG3	16	JH584312.1	=	NT_187014.1
129X1/SVJ_MMCHR16_CTG1	16	GL456028.2	=	NT_039630.5

Scaffold Name	Chromosome Assignment	GenBank ID		RefSeq ID
129S6/SVEVTAC_MMCHR16_CTG6	16	GL456001.2	=	NT_039634.4

Scaffold Name	Chromosome Assignment	GenBank ID		RefSeq ID
129S6/SVEVTAC_MMCHR16_CTG4	16	JH584313.1	=	NT_187015.1

Scaffold Name	Chromosome Assignment	GenBank ID		RefSeq ID
129S6/SVEVTAC_MMCHR16_CTG5	16	JH584314.1	=	NT_187016.1

Scaffold Name	Chromosome Assignment	GenBank ID		RefSeq ID
UNKNOWN_MMCHR17_CTG3	17	GL456069.1	=	NT_097336.1

Scaffold Name	Chromosome Assignment	GenBank ID		RefSeq ID
MMCHR17_CHORI29_IDD16_1	17	JH584267.1	=	NT_187005.1

Region: MHC

Scaffold Name	Chromosome Assignment	GenBank ID		RefSeq ID
MMCHR17_CHO_IDD1	17	JH584266.1	=	NT_187004.1
129S1/SVIMJ_MMCHR17_CTG2	17	JH590470.1	=	NT_187009.1
129S1/SVIMJ_MMCHR17_CTG3	17	JH584308.1	=	NT_187010.1
129S1/SVIMJ_MMCHR17_CTG4	17	JH584309.1	=	NT_187011.1
129S6/SVEVTAC_MMCHR17_CTG1	17	GL456021.2	=	NT_039661.4
129S6/SVEVTAC_MMCHR17_CTG2	17	GL456002.2	=	NT_039666.2
129X1/SVJ_MMCHR17_CTG2	17	GL456022.2	=	NT_039662.3
MMCHR17_NOD_IDD1	17	JH584328.1	=	NT_187027.1

Region: NOD_mouse_Idd3.1

Scaffold Name	Chromosome Assignment	GenBank ID		RefSeq ID
129S1/SVIMJ_MMCHR3_CTG2	3	GL456007.1	=	NT_039256.1
129S1/SVIMJ_MMCHR3_CTG3	3	GL456006.1	=	NT_039248.1
MMCHR3_NODMRKTAC_CTG1	3	GL456045.2	=	NT_039247.2
MMCHR3_NOD_IDD3_1	3	GL456048.1	=	NT_039252.1

Molecule	Object	Total Length	Scaffold Count	Ungapped Length	Scaffold N50	Spanned Gaps	Unspanned Gaps
1	AllChromosomeUnlocalized scaffolds	196,283,350195,471,971 811,379	1385	192,720,618191,909,239 811,379	52,589,04652,589,046 206,961	3030 0	1111 0
2	Chromosome	182,113,224	7	178,326,651	116,378,660	17	11
3	Chromosome	160,039,680	4	156,398,866	109,125,955	5	7
4	AllChromosomeUnlocalized scaffolds	157,219,549156,508,116 711,433	936	152,764,072152,055,611 708,461	86,266,79986,266,799 207,968	4435 9	88 0
5	AllChromosomeUnlocalized scaffolds	153,573,022151,834,684 1,738,338	17125	149,658,012147,919,674 1,738,338	37,423,12037,423,120 953,012	1919 0	1515 0
6	Chromosome	149,736,546	4	146,336,546	108,860,100	1	9
7	AllChromosomeUnlocalized scaffolds	145,617,427145,441,459 175,968	651	142,031,396141,855,428 175,968	43,149,17643,149,176 175,968	2424 0	88 0
8	Chromosome	129,401,213	5	125,611,432	25,646,931	6	8
9	Chromosome	124,595,110	7	121,157,018	40,307,006	26	10
10	Chromosome	130,694,993	3	127,067,764	72,389,128	23	7
11	Chromosome	122,082,543	2	118,745,945	87,300,923	1	6
12	Chromosome	120,129,022	2	116,922,422	78,455,223	1	5
13	Chromosome	120,421,639	5	117,121,193	28,633,993	3	8
14	Chromosome	124,902,244	2	121,442,113	105,332,540	8	5
15	Chromosome	104,043,685	3	100,653,315	65,061,235	5	7
16	Chromosome	98,207,768	2	95,019,768	62,256,588	1	5
17	Chromosome	94,987,271	3	91,707,464	81,232,659	33	6
18	Chromosome	90,702,639	3	87,452,639	73,480,409	1	6
19	Chromosome	61,431,566	2	58,205,856	54,517,951	2	5
X	AllChromosomeUnlocalized scaffolds	171,368,232171,031,299 336,933	21201	163,801,988163,488,006 313,982	28,873,11528,873,115 336,933	9972 27	2525 0
Y	AllChromosomeUnlocalized scaffolds	92,500,85791,744,698 756,159	20164	88,880,85788,124,698 756,159	17,801,35117,801,351 182,347	1313 0	1919 0
unplaced	Unplaced scaffolds	803,895	22	741,484	38,659	75	0

Region Name	Location	Scaffold Count	Total Length	Ungapped Length	Scaffold N50	Spanned Gaps
Odz1	X:42891057-43298842	1	414,761	414,761	414,761	0
region57	X:72166181-72363206	1	194,271	194,271	194,271	0
Xic	X:103589284-103841870	1	247,850	247,850	247,850	0
Xlr_region_1	X:73003651-73121964	1	123,835	123,835	123,835	0
Xlr_region_2	X:73185425-73263090	1	78,689	78,689	78,689	0
Ifi_cluster	1:173701136-174051183	3	495,160	495,160	154,284	0
NOD_mouse_Idd5.1	1:60640809-63588262	1	1,003,859	853,859	1,003,859	3
NOD_mouse_Idd5.3	1:65597865-69265254	1	3,760,957	3,710,957	3,760,957	1
NOD_mouse_Idd5.4	1:130311064-130653047	1	326,027	326,027	326,027	0
region4	1:78413759-78687489	1	272,653	272,653	272,653	0
Ren2	1:133239136-133489442	1	281,255	281,255	281,255	0
region29	2:102983310-103388989	1	410,905	410,905	410,905	0
NOD_mouse_Idd10.1	3:99953865-101307585	1	1,153,325	1,053,325	1,153,325	2
NOD_mouse_Idd18.1	3:109116720-109807685	1	689,363	689,363	689,363	0
NOD_mouse_Idd18.2	3:103590378-104055839	1	466,430	466,430	466,430	0
NOD_mouse_Idd3.1	3:36806723-37563603	4	1,047,914	1,047,914	292,416	0
region31	3:47447005-47679964	1	243,366	243,366	243,366	0
Tdpoz_cluster	3:93583858-93685263	1	124,933	124,933	124,933	0
Mup_region_1	4:61778759-62041201	1	264,822	264,822	264,822	0
Mup_region_2	4:62045255-62237529	1	191,695	191,695	191,695	0
Mup_region_3	4:59870283-60154907	1	284,739	284,739	284,739	0
Mup_region_4	4:60374393-61285346	2	152,971	152,971	83,218	0
NOD_mouse_Idd9.1	4:128397119-131686709	1	3,050,841	2,950,841	3,050,841	2
NOD_mouse_Idd9.1M	4:135021547-135237421	1	215,601	215,601	215,601	0
NOD_mouse_Idd9.2_Idd9.3	4:146068508-151320022	2	4,830,966	4,580,966	3,205,425	5
olfactory_region_2	4:43762692-43857014	1	76,099	76,099	76,099	0
Padi_cluster	4:140721097-140961448	1	240,498	240,433	240,498	2
Prame_region_1	4:144179444-144348902	1	170,592	170,592	170,592	0
region40	4:67057602-67195172	1	138,473	138,473	138,473	0
region44	5:90653128-90826761	1	180,394	180,394	180,394	0
region45	5:150872255-151123781	1	262,166	262,166	262,166	0
NOD_mouse_Idd6.1+2	6:143536594-149568188	1	5,956,088	5,656,088	5,956,088	6
NOD_mouse_Idd6.3	6:129636567-130656471	1	1,759,414	1,609,414	1,759,414	3
region46	6:50779502-50919227	1	145,152	145,152	145,152	0
region47	6:82734575-83039841	1	312,568	312,568	312,568	0
region49	6:120377222-121015201	1	636,141	636,141	636,141	0
vomeronasal_region_1	6:89851149-90290463	1	198,515	198,515	198,515	0
Hbb_cluster	7:103811478-103860690	1	55,856	55,856	55,856	0
olfactory_region_3	7:106888710-106927250	1	34,498	34,498	34,498	0
region51	7:27743215-27826849	1	91,251	91,251	91,251	0
Large	8:73065642-73319050	1	251,056	251,056	251,056	0
region54	8:41292834-41482533	1	183,135	183,135	183,135	0
Grm1	10:10861646-10927384	1	77,891	77,891	77,891	0
Mapt	11:104203258-104362532	1	161,334	161,334	161,334	0
NOD_mouse_Idd4.1	11:69895472-71298870	1	1,550,185	1,550,185	1,550,185	0
NOD_mouse_Idd4.2	11:72908911-74370562	1	1,462,311	1,462,311	1,462,311	0
NOD_mouse_Idd4.2Q	11:86869779-89954755	1	3,086,744	3,086,744	3,086,744	0
olfactory_region_1	11:58613181-58787285	1	170,397	170,397	170,397	0
region60	11:48799134-49141362	1	247,497	247,497	247,497	0
region61	11:58115562-58302084	1	186,379	186,379	186,379	0
Igh	12:113067904-114458697	3	1,874,038	1,872,699	1,714,434	1
Serpin_region_1	12:103722705-103922810	1	84,250	84,250	84,250	0
Tcl1_region_1	12:105147714-105196166	1	83,612	83,612	83,612	0
Ipo11	13:106801073-106932896	1	138,435	138,435	138,435	0
Naip2_Naip5	13:100075065-100330017	2	280,055	280,055	179,252	0
region17	14:51863012-51973562	1	105,813	105,813	105,813	0
Tcra_Tcrd	14:52352473-54229076	1	1,666,365	1,666,365	1,666,365	0
region19	15:80502872-80672368	1	88,442	88,442	88,442	0
region65	15:79892564-79986558	1	89,177	89,177	89,177	0
DiGeorge	16:17742495-19065968	6	1,543,355	1,543,355	250,595	0
DownSynCrit_region_1	16:94114272-95747459	1	1,618,162	1,618,162	1,618,162	0
DownSynCrit_region_2	16:95846204-96221063	1	374,389	374,389	374,389	0
DownSynCrit_region_3	16:97054368-97223607	1	170,763	170,763	170,763	0
Airn	17:12729292-12861171	1	138,490	138,490	138,490	0
MHC	17:33681276-38548659	8	13,006,275	12,906,275	4,256,209	2
NOD_mouse_Idd16.1	17:27313323-29215977	1	1,908,920	1,908,920	1,908,920	0
Impact	18:11308625-11318460	1	85,548	85,548	85,548	0
region70	18:60125920-60496981	1	231,969	231,969	231,969	0
region28	19:5679043-5707799	1	46,440	46,440	46,440	0
Slc1a1	19:28892559-28918752	1	25,407	25,407	25,407	0

Unit Name	Scaffold Count	Total Length	Ungapped Length	Scaffold N50	Spanned Gaps
129P2/OlaHsd	1	46,440	46,440	46,440	0
129S1/SvImJ	20	8,669,437	8,668,098	1,154,078	1
129S2/SvPas	1	34,498	34,498	34,498	0
129S6/SvEvTac	20	5,590,085	5,590,085	281,255	0
129S7/SvEvBrd-Hprt-b-m2	7	1,083,367	1,083,367	264,822	0
129X1/SvJ	9	3,340,017	3,340,017	1,934,410	0
A/J	1	100,803	100,803	100,803	0
AKR/J	3	586,502	586,502	191,521	0
BALB/c	2	115,497	115,497	59,641	0
CAST/Ei	6	1,255,641	1,255,641	204,663	0
NOD/MrkTac	17	23,606,018	22,956,018	3,050,841	13
NOD/ShiLtJ	5	17,622,142	17,072,142	4,910,976	11
non-nuclear	1	16,299	16,299	16,299	0
RIII	2	169,160	169,160	85,548	0
UNKNOWN	5	620,759	620,694	138,490	2

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GRCm38

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There are 6 assemblies for this organism

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