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Mouse Genome Assembly GRCm38.p6

Information on tiling path files (TPFs) for the assembly is available at TPF Overview.

Other assembly versions:
Chromosome lengths are calculated by summing the length of the placed scaffolds and estimated gaps.
Chromosome Total length (bp) GenBank accession RefSeq accession
1 195,471,971 CM000994.2 NC_000067.6
2 182,113,224 CM000995.2 NC_000068.7
3 160,039,680 CM000996.2 NC_000069.6
4 156,508,116 CM000997.2 NC_000070.6
5 151,834,684 CM000998.2 NC_000071.6
6 149,736,546 CM000999.2 NC_000072.6
7 145,441,459 CM001000.2 NC_000073.6
8 129,401,213 CM001001.2 NC_000074.6
9 124,595,110 CM001002.2 NC_000075.6
10 130,694,993 CM001003.2 NC_000076.6
11 122,082,543 CM001004.2 NC_000077.6
12 120,129,022 CM001005.2 NC_000078.6
13 120,421,639 CM001006.2 NC_000079.6
14 124,902,244 CM001007.2 NC_000080.6
15 104,043,685 CM001008.2 NC_000081.6
16 98,207,768 CM001009.2 NC_000082.6
17 94,987,271 CM001010.2 NC_000083.6
18 90,702,639 CM001011.2 NC_000084.6
19 61,431,566 CM001012.2 NC_000085.6
X 171,031,299 CM001013.2 NC_000086.7
Y 91,744,698 CM001014.2 NC_000087.7
Total lengths are calculated by summing the length of the sequenced bases and estimated gaps.
Chromosome All scaffolds Placed scaffolds Unplaced scaffolds
1 196,283,350 195,471,971 811,379
2 182,113,224 182,113,224 0
3 160,039,680 160,039,680 0
4 157,219,549 156,508,116 711,433
5 153,573,022 151,834,684 1,738,338
6 149,736,546 149,736,546 0
7 145,617,427 145,441,459 175,968
8 129,401,213 129,401,213 0
9 124,595,110 124,595,110 0
10 130,694,993 130,694,993 0
11 122,082,543 122,082,543 0
12 120,129,022 120,129,022 0
13 120,421,639 120,421,639 0
14 124,902,244 124,902,244 0
15 104,043,685 104,043,685 0
16 98,207,768 98,207,768 0
17 94,987,271 94,987,271 0
18 90,702,639 90,702,639 0
19 61,431,566 61,431,566 0
X 171,368,232 171,031,299 336,933
Y 92,500,857 91,744,698 756,159
Un 803,895 na 803,895
Genome 2,730,855,475 2,725,521,370 5,334,105
Region Location Sequence types Scaffold length
4933416I08Rik chrX:53444973-53687352 FIX 155,470
Ahnak2 chr12:112701299-112815832 FIX 111,720
Airn chr17:12729292-12861171 ALT 138,490
Anxa13 chr15:57983529-58517868 FIX 542,789
Atg4a chrX:140784762-141363409 FIX 460,895
Auts2 chr5:131326290-132550462 FIX 1,224,174
Baalc chr15:38582635-39142852 FIX 423,369
Dgkk chrX:6763452-7054396 FIX 245,130
DiGeorge chr16:17742495-19065968 ALT, FIX 2,049,231
Dnah12 chr14:26629355-26911986 FIX 283,434
DownSynCrit_region_1 chr16:94114272-95747459 ALT 1,618,162
DownSynCrit_region_2 chr16:95846204-96221063 ALT 374,389
DownSynCrit_region_3 chr16:97054368-97223607 ALT 170,763
Efcab7 chr4:99625547-100035456 FIX 378,870
Grm1 chr10:10861646-10927384 ALT 77,891
Hbb_cluster chr7:103811478-103860690 ALT 55,856
Ide chr19:37204249-37492988 FIX 299,789
Ifi_cluster chr1:173701136-174051183 ALT 495,160
Igh chr12:113067904-114458697 ALT 1,874,038
Impact chr18:11238883-11458280 ALT, FIX 438,003
Intu chr3:40505691-40944643 FIX 339,234
Ipo11 chr13:106801073-106932896 ALT 138,435
Jakmip3 chr7:138934711-139370933 FIX 414,410
Large chr8:73065642-73319050 ALT 251,056
MHC chr17:33681276-38548659 ALT 13,006,275
Mapt chr11:104203258-104362532 ALT 161,334
Meg3 chr12:109373903-109689534 FIX 316,140
Muc2 chr7:141683154-141786694 FIX 71,460
Mup_region_1 chr4:61778759-62041201 ALT 264,822
Mup_region_2 chr4:62045255-62237529 ALT 191,695
Mup_region_3 chr4:59870283-60154907 ALT 284,739
Mup_region_4 chr4:60250666-61586638 ALT, FIX 737,784
NOD_mouse_Idd10.1 chr3:99953865-101307585 ALT 1,153,325
NOD_mouse_Idd16.1 chr17:27313323-29215977 ALT 1,908,920
NOD_mouse_Idd18.1 chr3:109116720-109807685 ALT 689,363
NOD_mouse_Idd18.2 chr3:103590378-104055839 ALT 466,430
NOD_mouse_Idd3.1 chr3:36806723-37563603 ALT 1,047,914
NOD_mouse_Idd4.1 chr11:69895472-71336724 ALT, NOVEL 2,730,113
NOD_mouse_Idd4.2 chr11:72908911-74370562 ALT 1,462,311
NOD_mouse_Idd4.2Q chr11:86869779-89954755 ALT, FIX 3,417,855
NOD_mouse_Idd5.1 chr1:60640809-63588262 ALT, NOVEL 1,460,657
NOD_mouse_Idd5.3 chr1:65597865-69265254 ALT 3,760,957
NOD_mouse_Idd5.4 chr1:130311064-130653047 ALT 326,027
NOD_mouse_Idd6.1+2 chr6:143536594-149568188 ALT 5,956,088
NOD_mouse_Idd6.3 chr6:129636567-130656471 ALT 1,759,414
NOD_mouse_Idd9.1 chr4:128397119-131686709 ALT, FIX 3,285,011
NOD_mouse_Idd9.1M chr4:135021547-135237421 ALT 215,601
NOD_mouse_Idd9.2_Idd9.3 chr4:146068508-151320022 ALT, FIX 5,363,538
Nadk2 chr15:9054779-9266110 FIX 211,337
Naip2_Naip5 chr13:100075065-100330017 ALT 280,055
Nlrp4g chr9:124268539-124479149 FIX 210,641
Odz1 chrX:42891057-43298842 ALT 414,761
Padi_cluster chr4:140721097-140961448 ALT 240,498
Prame_region_1 chr4:144179444-144348902 ALT 170,592
Pstpip2 chr18:77623953-78117342 FIX 448,905
Ptpmt1 chr2:90853948-91049681 FIX 195,735
Rab3a_Ifi30 chr8:70673831-70845694 FIX 171,859
Ren2 chr1:133239136-133489442 ALT 281,255
Rims1 chr1:22159855-22877939 FIX 686,942
Serpin_region_1 chr12:103722705-103922810 ALT 84,250
Sftpb chr6:72296717-72451483 FIX 154,766
Sgms2 chr3:131299856-131505512 FIX 117,769
Slc1a1 chr19:28892559-28918752 ALT 25,407
Slc26a6 chr9:108784955-108953239 FIX 120,154
Spata5l1 chr2:122566305-122720961 FIX 166,096
Tcl1_region_1 chr12:105147714-105196166 ALT 83,612
Tcra_Tcrd chr14:52352473-54229076 ALT 1,666,365
Tdpoz_cluster chr3:93583858-93685263 ALT 124,933
Tmem134 chr19:4013986-4260737 FIX 246,751
Traf5 chr1:191793213-192106925 FIX 266,016
Trerf1 chr17:47094952-47423636 FIX 328,684
Xic chrX:103589284-103841870 ALT 247,850
Xlr_region_1 chrX:73003651-73121964 ALT 123,835
Xlr_region_2 chrX:73185425-73263090 ALT 78,689
olfactory_region_1 chr11:58613181-58787285 ALT 170,397
olfactory_region_2 chr4:43762692-43857014 ALT 76,099
olfactory_region_3 chr7:106888710-106927250 ALT 34,498
region17 chr14:51863012-51973562 ALT 105,813
region19 chr15:80502872-80672368 ALT 88,442
region28 chr19:5679043-5707799 ALT 46,440
region29 chr2:102983310-103388989 ALT 410,905
region31 chr3:47447005-47679964 ALT 243,366
region4 chr1:78413759-78687489 ALT 272,653
region40 chr4:67057602-67195172 ALT 138,473
region44 chr5:90653128-90826761 ALT 180,394
region45 chr5:150872255-151123781 ALT 262,166
region46 chr6:50779502-50919227 ALT 145,152
region47 chr6:82734575-83039841 ALT 312,568
region49 chr6:120377222-121015201 ALT 636,141
region51 chr7:27743215-27826849 ALT 91,251
region54 chr8:41292834-41482533 ALT 183,135
region57 chrX:72166181-72363206 ALT 194,271
region60 chr11:48799134-49141362 ALT, NOVEL 648,905
region61 chr11:58115562-58302084 ALT 186,379
region65 chr15:79892564-79986558 ALT 89,177
region70 chr18:60125920-60496981 ALT 231,969
region71 chr4:143214657-143582942 FIX 368,286
region72 chr7:3000001-3475222 FIX 473,738
region73 chrY:45842743-46337667 FIX 544,189
region74 chrY:66019703-66188541 FIX 221,588
region75 chr5:15457667-15635395 FIX 205,713
region76 chrY:49216909-49556418 FIX 331,480
region77 chrX:37690395-37986547 FIX 203,377
region78 chr17:54687402-55747384 FIX 1,059,955
region79 chr4:122217500-122473817 FIX 316,842
region80 chr3:15760691-15949398 FIX 214,957
region81 chr10:58205866-58311233 FIX 129,865
region82 chr15:3050001-3186530 FIX 166,012
region83 chr19:6183084-6688105 FIX 506,812
region84 chrX:60271962-60763715 FIX 490,000
region85 chrX:29000987-29562451 FIX 480,168
region86 chr1:178144751-178344759 FIX 200,008
region87 chr3:50686235-50904915 FIX 171,653
region88 chr4:121426261-122034165 FIX 583,977
region89 chr4:141987963-142697802 FIX 709,099
region90 chr10:7346541-7776389 FIX 355,613
region91 chr10:67228314-67653670 FIX 425,386
region92 chr11:7560598-7879512 FIX 318,915
region93 chr11:82933464-83353797 NOVEL 1,061,161
region94 chr14:24646407-24762340 FIX 66,290
region95 chr15:103658568-103917132 FIX 380,404
region96 chr17:7391520-7693199 FIX 253,113
region97 chr17:47916958-48583287 FIX 662,433
region98 chr18:76466242-76775534 FIX 263,917
region99 chrX:111104003-111543375 FIX 305,464
vomeronasal_region_1 chr6:89851149-90290463 ALT 198,515
N50 is a measure of contiguity. 50% of the bases reside in a scaffold of this length or greater.
Chromosome All scaffolds Placed scaffolds Unplaced scaffolds
1 52,589,046 52,589,046 206,961
2 116,378,660 116,378,660 0
3 109,125,955 109,125,955 0
4 86,266,799 86,266,799 207,968
5 37,423,120 37,423,120 953,012
6 108,860,100 108,860,100 0
7 43,149,176 43,149,176 175,968
8 25,646,931 25,646,931 0
9 40,307,006 40,307,006 0
10 72,389,128 72,389,128 0
11 87,300,923 87,300,923 0
12 78,455,223 78,455,223 0
13 28,633,993 28,633,993 0
14 105,332,540 105,332,540 0
15 65,061,235 65,061,235 0
16 62,256,588 62,256,588 0
17 81,232,659 81,232,659 0
18 73,480,409 73,480,409 0
19 54,517,951 54,517,951 0
X 28,873,115 28,873,115 336,933
Y 17,801,351 17,801,351 182,347
Un 38,659 na 38,659
Genome 54,517,951 54,517,951 199,368
Region Location Sequence types Scaffold length
4933416I08Rik chrX:53444973-53687352 FIX 155,470
Ahnak2 chr12:112701299-112815832 FIX 111,720
Airn chr17:12729292-12861171 ALT 138,490
Anxa13 chr15:57983529-58517868 FIX 542,789
Atg4a chrX:140784762-141363409 FIX 460,895
Auts2 chr5:131326290-132550462 FIX 1,224,174
Baalc chr15:38582635-39142852 FIX 423,369
Dgkk chrX:6763452-7054396 FIX 245,130
DiGeorge chr16:17742495-19065968 ALT, FIX 261,336
Dnah12 chr14:26629355-26911986 FIX 283,434
DownSynCrit_region_1 chr16:94114272-95747459 ALT 1,618,162
DownSynCrit_region_2 chr16:95846204-96221063 ALT 374,389
DownSynCrit_region_3 chr16:97054368-97223607 ALT 170,763
Efcab7 chr4:99625547-100035456 FIX 378,870
Grm1 chr10:10861646-10927384 ALT 77,891
Hbb_cluster chr7:103811478-103860690 ALT 55,856
Ide chr19:37204249-37492988 FIX 299,789
Ifi_cluster chr1:173701136-174051183 ALT 154,284
Igh chr12:113067904-114458697 ALT 1,714,434
Impact chr18:11238883-11458280 ALT, FIX 352,455
Intu chr3:40505691-40944643 FIX 339,234
Ipo11 chr13:106801073-106932896 ALT 138,435
Jakmip3 chr7:138934711-139370933 FIX 414,410
Large chr8:73065642-73319050 ALT 251,056
MHC chr17:33681276-38548659 ALT 4,256,209
Mapt chr11:104203258-104362532 ALT 161,334
Meg3 chr12:109373903-109689534 FIX 316,140
Muc2 chr7:141683154-141786694 FIX 71,460
Mup_region_1 chr4:61778759-62041201 ALT 264,822
Mup_region_2 chr4:62045255-62237529 ALT 191,695
Mup_region_3 chr4:59870283-60154907 ALT 284,739
Mup_region_4 chr4:60250666-61586638 ALT, FIX 399,265
NOD_mouse_Idd10.1 chr3:99953865-101307585 ALT 1,153,325
NOD_mouse_Idd16.1 chr17:27313323-29215977 ALT 1,908,920
NOD_mouse_Idd18.1 chr3:109116720-109807685 ALT 689,363
NOD_mouse_Idd18.2 chr3:103590378-104055839 ALT 466,430
NOD_mouse_Idd3.1 chr3:36806723-37563603 ALT 292,416
NOD_mouse_Idd4.1 chr11:69895472-71336724 ALT, NOVEL 1,550,185
NOD_mouse_Idd4.2 chr11:72908911-74370562 ALT 1,462,311
NOD_mouse_Idd4.2Q chr11:86869779-89954755 ALT, FIX 3,086,744
NOD_mouse_Idd5.1 chr1:60640809-63588262 ALT, NOVEL 1,003,859
NOD_mouse_Idd5.3 chr1:65597865-69265254 ALT 3,760,957
NOD_mouse_Idd5.4 chr1:130311064-130653047 ALT 326,027
NOD_mouse_Idd6.1+2 chr6:143536594-149568188 ALT 5,956,088
NOD_mouse_Idd6.3 chr6:129636567-130656471 ALT 1,759,414
NOD_mouse_Idd9.1 chr4:128397119-131686709 ALT, FIX 3,050,841
NOD_mouse_Idd9.1M chr4:135021547-135237421 ALT 215,601
NOD_mouse_Idd9.2_Idd9.3 chr4:146068508-151320022 ALT, FIX 3,205,425
Nadk2 chr15:9054779-9266110 FIX 211,337
Naip2_Naip5 chr13:100075065-100330017 ALT 179,252
Nlrp4g chr9:124268539-124479149 FIX 210,641
Odz1 chrX:42891057-43298842 ALT 414,761
Padi_cluster chr4:140721097-140961448 ALT 240,498
Prame_region_1 chr4:144179444-144348902 ALT 170,592
Pstpip2 chr18:77623953-78117342 FIX 448,905
Ptpmt1 chr2:90853948-91049681 FIX 195,735
Rab3a_Ifi30 chr8:70673831-70845694 FIX 171,859
Ren2 chr1:133239136-133489442 ALT 281,255
Rims1 chr1:22159855-22877939 FIX 686,942
Serpin_region_1 chr12:103722705-103922810 ALT 84,250
Sftpb chr6:72296717-72451483 FIX 154,766
Sgms2 chr3:131299856-131505512 FIX 117,769
Slc1a1 chr19:28892559-28918752 ALT 25,407
Slc26a6 chr9:108784955-108953239 FIX 120,154
Spata5l1 chr2:122566305-122720961 FIX 166,096
Tcl1_region_1 chr12:105147714-105196166 ALT 83,612
Tcra_Tcrd chr14:52352473-54229076 ALT 1,666,365
Tdpoz_cluster chr3:93583858-93685263 ALT 124,933
Tmem134 chr19:4013986-4260737 FIX 246,751
Traf5 chr1:191793213-192106925 FIX 266,016
Trerf1 chr17:47094952-47423636 FIX 328,684
Xic chrX:103589284-103841870 ALT 247,850
Xlr_region_1 chrX:73003651-73121964 ALT 123,835
Xlr_region_2 chrX:73185425-73263090 ALT 78,689
olfactory_region_1 chr11:58613181-58787285 ALT 170,397
olfactory_region_2 chr4:43762692-43857014 ALT 76,099
olfactory_region_3 chr7:106888710-106927250 ALT 34,498
region17 chr14:51863012-51973562 ALT 105,813
region19 chr15:80502872-80672368 ALT 88,442
region28 chr19:5679043-5707799 ALT 46,440
region29 chr2:102983310-103388989 ALT 410,905
region31 chr3:47447005-47679964 ALT 243,366
region4 chr1:78413759-78687489 ALT 272,653
region40 chr4:67057602-67195172 ALT 138,473
region44 chr5:90653128-90826761 ALT 180,394
region45 chr5:150872255-151123781 ALT 262,166
region46 chr6:50779502-50919227 ALT 145,152
region47 chr6:82734575-83039841 ALT 312,568
region49 chr6:120377222-121015201 ALT 636,141
region51 chr7:27743215-27826849 ALT 91,251
region54 chr8:41292834-41482533 ALT 183,135
region57 chrX:72166181-72363206 ALT 194,271
region60 chr11:48799134-49141362 ALT, NOVEL 215,264
region61 chr11:58115562-58302084 ALT 186,379
region65 chr15:79892564-79986558 ALT 89,177
region70 chr18:60125920-60496981 ALT 231,969
region71 chr4:143214657-143582942 FIX 368,286
region72 chr7:3000001-3475222 FIX 473,738
region73 chrY:45842743-46337667 FIX 544,189
region74 chrY:66019703-66188541 FIX 221,588
region75 chr5:15457667-15635395 FIX 205,713
region76 chrY:49216909-49556418 FIX 331,480
region77 chrX:37690395-37986547 FIX 203,377
region78 chr17:54687402-55747384 FIX 1,059,955
region79 chr4:122217500-122473817 FIX 316,842
region80 chr3:15760691-15949398 FIX 214,957
region81 chr10:58205866-58311233 FIX 129,865
region82 chr15:3050001-3186530 FIX 166,012
region83 chr19:6183084-6688105 FIX 506,812
region84 chrX:60271962-60763715 FIX 490,000
region85 chrX:29000987-29562451 FIX 260,447
region86 chr1:178144751-178344759 FIX 200,008
region87 chr3:50686235-50904915 FIX 171,653
region88 chr4:121426261-122034165 FIX 583,977
region89 chr4:141987963-142697802 FIX 709,099
region90 chr10:7346541-7776389 FIX 355,613
region91 chr10:67228314-67653670 FIX 425,386
region92 chr11:7560598-7879512 FIX 318,915
region93 chr11:82933464-83353797 NOVEL 368,967
region94 chr14:24646407-24762340 FIX 66,290
region95 chr15:103658568-103917132 FIX 380,404
region96 chr17:7391520-7693199 FIX 253,113
region97 chr17:47916958-48583287 FIX 662,433
region98 chr18:76466242-76775534 FIX 263,917
region99 chrX:111104003-111543375 FIX 305,464
vomeronasal_region_1 chr6:89851149-90290463 ALT 198,515
Ungapped lengths are calculated by summing the length of sequenced bases only. 'Ns' are excluded.
Chromosome All scaffolds Placed scaffolds Unplaced scaffolds
1 192,720,578 191,909,199 811,379
2 178,326,651 178,326,651 0
3 156,398,866 156,398,866 0
4 152,764,072 152,055,611 708,461
5 149,658,012 147,919,674 1,738,338
6 146,336,546 146,336,546 0
7 142,031,376 141,855,408 175,968
8 125,611,432 125,611,432 0
9 121,157,018 121,157,018 0
10 127,067,664 127,067,664 0
11 118,745,945 118,745,945 0
12 116,922,422 116,922,422 0
13 117,121,193 117,121,193 0
14 121,442,113 121,442,113 0
15 100,653,315 100,653,315 0
16 95,019,768 95,019,768 0
17 91,707,464 91,707,464 0
18 87,452,639 87,452,639 0
19 58,205,856 58,205,856 0
X 163,801,988 163,488,006 313,982
Y 88,880,857 88,124,698 756,159
Un 741,484 na 741,484
Genome 2,652,767,259 2,647,521,488 5,245,771
Region Location Sequence types Scaffold length
4933416I08Rik chrX:53444973-53687352 FIX 155,470
Ahnak2 chr12:112701299-112815832 FIX 111,720
Airn chr17:12729292-12861171 ALT 138,490
Anxa13 chr15:57983529-58517868 FIX 542,694
Atg4a chrX:140784762-141363409 FIX 460,895
Auts2 chr5:131326290-132550462 FIX 1,224,174
Baalc chr15:38582635-39142852 FIX 423,369
Dgkk chrX:6763452-7054396 FIX 245,130
DiGeorge chr16:17742495-19065968 ALT, FIX 2,049,231
Dnah12 chr14:26629355-26911986 FIX 283,434
DownSynCrit_region_1 chr16:94114272-95747459 ALT 1,618,162
DownSynCrit_region_2 chr16:95846204-96221063 ALT 374,389
DownSynCrit_region_3 chr16:97054368-97223607 ALT 170,763
Efcab7 chr4:99625547-100035456 FIX 378,870
Grm1 chr10:10861646-10927384 ALT 77,891
Hbb_cluster chr7:103811478-103860690 ALT 55,856
Ide chr19:37204249-37492988 FIX 299,789
Ifi_cluster chr1:173701136-174051183 ALT 495,160
Igh chr12:113067904-114458697 ALT 1,872,699
Impact chr18:11238883-11458280 ALT, FIX 438,003
Intu chr3:40505691-40944643 FIX 339,234
Ipo11 chr13:106801073-106932896 ALT 138,435
Jakmip3 chr7:138934711-139370933 FIX 414,410
Large chr8:73065642-73319050 ALT 251,056
MHC chr17:33681276-38548659 ALT 12,906,275
Mapt chr11:104203258-104362532 ALT 161,334
Meg3 chr12:109373903-109689534 FIX 316,140
Muc2 chr7:141683154-141786694 FIX 71,460
Mup_region_1 chr4:61778759-62041201 ALT 264,822
Mup_region_2 chr4:62045255-62237529 ALT 191,695
Mup_region_3 chr4:59870283-60154907 ALT 284,739
Mup_region_4 chr4:60250666-61586638 ALT, FIX 737,784
NOD_mouse_Idd10.1 chr3:99953865-101307585 ALT 1,053,325
NOD_mouse_Idd16.1 chr17:27313323-29215977 ALT 1,908,920
NOD_mouse_Idd18.1 chr3:109116720-109807685 ALT 689,363
NOD_mouse_Idd18.2 chr3:103590378-104055839 ALT 466,430
NOD_mouse_Idd3.1 chr3:36806723-37563603 ALT 1,047,914
NOD_mouse_Idd4.1 chr11:69895472-71336724 ALT, NOVEL 2,730,113
NOD_mouse_Idd4.2 chr11:72908911-74370562 ALT 1,462,311
NOD_mouse_Idd4.2Q chr11:86869779-89954755 ALT, FIX 3,417,855
NOD_mouse_Idd5.1 chr1:60640809-63588262 ALT, NOVEL 1,310,657
NOD_mouse_Idd5.3 chr1:65597865-69265254 ALT 3,710,957
NOD_mouse_Idd5.4 chr1:130311064-130653047 ALT 326,027
NOD_mouse_Idd6.1+2 chr6:143536594-149568188 ALT 5,656,088
NOD_mouse_Idd6.3 chr6:129636567-130656471 ALT 1,609,414
NOD_mouse_Idd9.1 chr4:128397119-131686709 ALT, FIX 3,184,789
NOD_mouse_Idd9.1M chr4:135021547-135237421 ALT 215,601
NOD_mouse_Idd9.2_Idd9.3 chr4:146068508-151320022 ALT, FIX 5,097,538
Nadk2 chr15:9054779-9266110 FIX 211,337
Naip2_Naip5 chr13:100075065-100330017 ALT 280,055
Nlrp4g chr9:124268539-124479149 FIX 195,862
Odz1 chrX:42891057-43298842 ALT 414,761
Padi_cluster chr4:140721097-140961448 ALT 240,433
Prame_region_1 chr4:144179444-144348902 ALT 170,592
Pstpip2 chr18:77623953-78117342 FIX 448,905
Ptpmt1 chr2:90853948-91049681 FIX 195,735
Rab3a_Ifi30 chr8:70673831-70845694 FIX 171,859
Ren2 chr1:133239136-133489442 ALT 281,255
Rims1 chr1:22159855-22877939 FIX 686,942
Serpin_region_1 chr12:103722705-103922810 ALT 84,250
Sftpb chr6:72296717-72451483 FIX 154,766
Sgms2 chr3:131299856-131505512 FIX 117,769
Slc1a1 chr19:28892559-28918752 ALT 25,407
Slc26a6 chr9:108784955-108953239 FIX 120,154
Spata5l1 chr2:122566305-122720961 FIX 166,096
Tcl1_region_1 chr12:105147714-105196166 ALT 83,612
Tcra_Tcrd chr14:52352473-54229076 ALT 1,666,365
Tdpoz_cluster chr3:93583858-93685263 ALT 124,933
Tmem134 chr19:4013986-4260737 FIX 246,751
Traf5 chr1:191793213-192106925 FIX 265,916
Trerf1 chr17:47094952-47423636 FIX 328,684
Xic chrX:103589284-103841870 ALT 247,850
Xlr_region_1 chrX:73003651-73121964 ALT 123,835
Xlr_region_2 chrX:73185425-73263090 ALT 78,689
olfactory_region_1 chr11:58613181-58787285 ALT 170,397
olfactory_region_2 chr4:43762692-43857014 ALT 76,099
olfactory_region_3 chr7:106888710-106927250 ALT 34,498
region17 chr14:51863012-51973562 ALT 105,813
region19 chr15:80502872-80672368 ALT 88,442
region28 chr19:5679043-5707799 ALT 46,440
region29 chr2:102983310-103388989 ALT 410,905
region31 chr3:47447005-47679964 ALT 243,366
region4 chr1:78413759-78687489 ALT 272,653
region40 chr4:67057602-67195172 ALT 138,473
region44 chr5:90653128-90826761 ALT 180,394
region45 chr5:150872255-151123781 ALT 262,166
region46 chr6:50779502-50919227 ALT 145,152
region47 chr6:82734575-83039841 ALT 312,568
region49 chr6:120377222-121015201 ALT 636,141
region51 chr7:27743215-27826849 ALT 91,251
region54 chr8:41292834-41482533 ALT 183,135
region57 chrX:72166181-72363206 ALT 194,271
region60 chr11:48799134-49141362 ALT, NOVEL 648,905
region61 chr11:58115562-58302084 ALT 186,379
region65 chr15:79892564-79986558 ALT 89,177
region70 chr18:60125920-60496981 ALT 231,969
region71 chr4:143214657-143582942 FIX 368,286
region72 chr7:3000001-3475222 FIX 473,738
region73 chrY:45842743-46337667 FIX 544,189
region74 chrY:66019703-66188541 FIX 221,588
region75 chr5:15457667-15635395 FIX 205,713
region76 chrY:49216909-49556418 FIX 331,480
region77 chrX:37690395-37986547 FIX 203,377
region78 chr17:54687402-55747384 FIX 1,059,955
region79 chr4:122217500-122473817 FIX 316,842
region80 chr3:15760691-15949398 FIX 214,957
region81 chr10:58205866-58311233 FIX 129,865
region82 chr15:3050001-3186530 FIX 166,012
region83 chr19:6183084-6688105 FIX 506,812
region84 chrX:60271962-60763715 FIX 490,000
region85 chrX:29000987-29562451 FIX 480,168
region86 chr1:178144751-178344759 FIX 200,008
region87 chr3:50686235-50904915 FIX 171,653
region88 chr4:121426261-122034165 FIX 583,977
region89 chr4:141987963-142697802 FIX 709,099
region90 chr10:7346541-7776389 FIX 355,613
region91 chr10:67228314-67653670 FIX 425,318
region92 chr11:7560598-7879512 FIX 318,915
region93 chr11:82933464-83353797 NOVEL 1,061,161
region94 chr14:24646407-24762340 FIX 66,290
region95 chr15:103658568-103917132 FIX 380,404
region96 chr17:7391520-7693199 FIX 253,113
region97 chr17:47916958-48583287 FIX 662,433
region98 chr18:76466242-76775534 FIX 263,917
region99 chrX:111104003-111543375 FIX 305,464
vomeronasal_region_1 chr6:89851149-90290463 ALT 198,515
Spanned gaps are found within scaffolds and there is some evidence suggesting linkage between the two sequences flanking the gap. Unspanned gaps are found between scaffolds and there is no evidence of linkage.
Spanned gaps Unspanned gaps
Chromosome   All scaffolds Placed scaffolds Unplaced scaffolds All scaffolds Placed scaffolds Unplaced scaffolds
1 34 34 0 11 11 0
2 17 17 0 11 11 0
3 5 5 0 7 7 0
4 44 35 9 8 8 0
5 19 19 0 15 15 0
6 1 1 0 9 9 0
7 25 25 0 8 8 0
8 6 6 0 8 8 0
9 26 26 0 10 10 0
10 24 24 0 7 7 0
11 1 1 0 6 6 0
12 1 1 0 5 5 0
13 3 3 0 8 8 0
14 8 8 0 5 5 0
15 5 5 0 7 7 0
16 1 1 0 5 5 0
17 33 33 0 6 6 0
18 1 1 0 6 6 0
19 2 2 0 5 5 0
X 99 72 27 25 25 0
Y 13 13 0 19 19 0
Un 75 na 75 0 na 0
Genome 443 332 111 191 191 0
Region Location Sequence types Scaffolds Spanned gaps Unspanned gaps
4933416I08Rik chrX:53444973-53687352 FIX 1 0 0
Ahnak2 chr12:112701299-112815832 FIX 1 0 0
Airn chr17:12729292-12861171 ALT 1 0 0
Anxa13 chr15:57983529-58517868 FIX 1 1 0
Atg4a chrX:140784762-141363409 FIX 1 0 0
Auts2 chr5:131326290-132550462 FIX 1 0 0
Baalc chr15:38582635-39142852 FIX 1 0 0
Dgkk chrX:6763452-7054396 FIX 1 0 0
DiGeorge chr16:17742495-19065968 ALT, FIX 7 0 0
Dnah12 chr14:26629355-26911986 FIX 1 0 0
DownSynCrit_region_1 chr16:94114272-95747459 ALT 1 0 0
DownSynCrit_region_2 chr16:95846204-96221063 ALT 1 0 0
DownSynCrit_region_3 chr16:97054368-97223607 ALT 1 0 0
Efcab7 chr4:99625547-100035456 FIX 1 0 0
Grm1 chr10:10861646-10927384 ALT 1 0 0
Hbb_cluster chr7:103811478-103860690 ALT 1 0 0
Ide chr19:37204249-37492988 FIX 1 0 0
Ifi_cluster chr1:173701136-174051183 ALT 3 0 0
Igh chr12:113067904-114458697 ALT 3 1 0
Impact chr18:11238883-11458280 ALT, FIX 2 0 0
Intu chr3:40505691-40944643 FIX 1 0 0
Ipo11 chr13:106801073-106932896 ALT 1 0 0
Jakmip3 chr7:138934711-139370933 FIX 1 0 0
Large chr8:73065642-73319050 ALT 1 0 0
MHC chr17:33681276-38548659 ALT 8 2 0
Mapt chr11:104203258-104362532 ALT 1 0 0
Meg3 chr12:109373903-109689534 FIX 1 0 0
Muc2 chr7:141683154-141786694 FIX 1 0 0
Mup_region_1 chr4:61778759-62041201 ALT 1 0 0
Mup_region_2 chr4:62045255-62237529 ALT 1 0 0
Mup_region_3 chr4:59870283-60154907 ALT 1 0 0
Mup_region_4 chr4:60250666-61586638 ALT, FIX 4 0 0
NOD_mouse_Idd10.1 chr3:99953865-101307585 ALT 1 2 0
NOD_mouse_Idd16.1 chr17:27313323-29215977 ALT 1 0 0
NOD_mouse_Idd18.1 chr3:109116720-109807685 ALT 1 0 0
NOD_mouse_Idd18.2 chr3:103590378-104055839 ALT 1 0 0
NOD_mouse_Idd3.1 chr3:36806723-37563603 ALT 4 0 0
NOD_mouse_Idd4.1 chr11:69895472-71336724 ALT, NOVEL 4 0 0
NOD_mouse_Idd4.2 chr11:72908911-74370562 ALT 1 0 0
NOD_mouse_Idd4.2Q chr11:86869779-89954755 ALT, FIX 2 0 0
NOD_mouse_Idd5.1 chr1:60640809-63588262 ALT, NOVEL 2 3 0
NOD_mouse_Idd5.3 chr1:65597865-69265254 ALT 1 1 0
NOD_mouse_Idd5.4 chr1:130311064-130653047 ALT 1 0 0
NOD_mouse_Idd6.1+2 chr6:143536594-149568188 ALT 1 6 0
NOD_mouse_Idd6.3 chr6:129636567-130656471 ALT 1 3 0
NOD_mouse_Idd9.1 chr4:128397119-131686709 ALT, FIX 3 4 0
NOD_mouse_Idd9.1M chr4:135021547-135237421 ALT 1 0 0
NOD_mouse_Idd9.2_Idd9.3 chr4:146068508-151320022 ALT, FIX 3 6 0
Nadk2 chr15:9054779-9266110 FIX 1 0 0
Naip2_Naip5 chr13:100075065-100330017 ALT 2 0 0
Nlrp4g chr9:124268539-124479149 FIX 1 12 0
Odz1 chrX:42891057-43298842 ALT 1 0 0
Padi_cluster chr4:140721097-140961448 ALT 1 2 0
Prame_region_1 chr4:144179444-144348902 ALT 1 0 0
Pstpip2 chr18:77623953-78117342 FIX 1 0 0
Ptpmt1 chr2:90853948-91049681 FIX 1 0 0
Rab3a_Ifi30 chr8:70673831-70845694 FIX 1 0 0
Ren2 chr1:133239136-133489442 ALT 1 0 0
Rims1 chr1:22159855-22877939 FIX 1 0 0
Serpin_region_1 chr12:103722705-103922810 ALT 1 0 0
Sftpb chr6:72296717-72451483 FIX 1 0 0
Sgms2 chr3:131299856-131505512 FIX 1 0 0
Slc1a1 chr19:28892559-28918752 ALT 1 0 0
Slc26a6 chr9:108784955-108953239 FIX 1 0 0
Spata5l1 chr2:122566305-122720961 FIX 1 0 0
Tcl1_region_1 chr12:105147714-105196166 ALT 1 0 0
Tcra_Tcrd chr14:52352473-54229076 ALT 1 0 0
Tdpoz_cluster chr3:93583858-93685263 ALT 1 0 0
Tmem134 chr19:4013986-4260737 FIX 1 0 0
Traf5 chr1:191793213-192106925 FIX 1 1 0
Trerf1 chr17:47094952-47423636 FIX 1 0 0
Xic chrX:103589284-103841870 ALT 1 0 0
Xlr_region_1 chrX:73003651-73121964 ALT 1 0 0
Xlr_region_2 chrX:73185425-73263090 ALT 1 0 0
olfactory_region_1 chr11:58613181-58787285 ALT 1 0 0
olfactory_region_2 chr4:43762692-43857014 ALT 1 0 0
olfactory_region_3 chr7:106888710-106927250 ALT 1 0 0
region17 chr14:51863012-51973562 ALT 1 0 0
region19 chr15:80502872-80672368 ALT 1 0 0
region28 chr19:5679043-5707799 ALT 1 0 0
region29 chr2:102983310-103388989 ALT 1 0 0
region31 chr3:47447005-47679964 ALT 1 0 0
region4 chr1:78413759-78687489 ALT 1 0 0
region40 chr4:67057602-67195172 ALT 1 0 0
region44 chr5:90653128-90826761 ALT 1 0 0
region45 chr5:150872255-151123781 ALT 1 0 0
region46 chr6:50779502-50919227 ALT 1 0 0
region47 chr6:82734575-83039841 ALT 1 0 0
region49 chr6:120377222-121015201 ALT 1 0 0
region51 chr7:27743215-27826849 ALT 1 0 0
region54 chr8:41292834-41482533 ALT 1 0 0
region57 chrX:72166181-72363206 ALT 1 0 0
region60 chr11:48799134-49141362 ALT, NOVEL 3 0 0
region61 chr11:58115562-58302084 ALT 1 0 0
region65 chr15:79892564-79986558 ALT 1 0 0
region70 chr18:60125920-60496981 ALT 1 0 0
region71 chr4:143214657-143582942 FIX 1 0 0
region72 chr7:3000001-3475222 FIX 1 0 0
region73 chrY:45842743-46337667 FIX 1 0 0
region74 chrY:66019703-66188541 FIX 1 0 0
region75 chr5:15457667-15635395 FIX 1 0 0
region76 chrY:49216909-49556418 FIX 1 0 0
region77 chrX:37690395-37986547 FIX 1 0 0
region78 chr17:54687402-55747384 FIX 1 0 0
region79 chr4:122217500-122473817 FIX 1 0 0
region80 chr3:15760691-15949398 FIX 1 0 0
region81 chr10:58205866-58311233 FIX 1 0 0
region82 chr15:3050001-3186530 FIX 1 0 0
region83 chr19:6183084-6688105 FIX 1 0 0
region84 chrX:60271962-60763715 FIX 1 0 0
region85 chrX:29000987-29562451 FIX 2 0 0
region86 chr1:178144751-178344759 FIX 1 0 0
region87 chr3:50686235-50904915 FIX 1 0 0
region88 chr4:121426261-122034165 FIX 1 0 0
region89 chr4:141987963-142697802 FIX 1 0 0
region90 chr10:7346541-7776389 FIX 1 0 0
region91 chr10:67228314-67653670 FIX 1 3 0
region92 chr11:7560598-7879512 FIX 1 0 0
region93 chr11:82933464-83353797 NOVEL 3 0 0
region94 chr14:24646407-24762340 FIX 1 0 0
region95 chr15:103658568-103917132 FIX 1 0 0
region96 chr17:7391520-7693199 FIX 1 0 0
region97 chr17:47916958-48583287 FIX 1 0 0
region98 chr18:76466242-76775534 FIX 1 0 0
region99 chrX:111104003-111543375 FIX 1 0 0
vomeronasal_region_1 chr6:89851149-90290463 ALT 1 0 0
Scaffold counts.
Chromosome All scaffolds Placed scaffolds Unplaced scaffolds
1 13 8 5
2 7 7 0
3 4 4 0
4 9 3 6
5 17 12 5
6 4 4 0
7 6 5 1
8 5 5 0
9 7 7 0
10 3 3 0
11 2 2 0
12 2 2 0
13 5 5 0
14 2 2 0
15 3 3 0
16 2 2 0
17 3 3 0
18 3 3 0
19 2 2 0
X 21 20 1
Y 20 16 4
Un 22 na 22
Genome 162 118 44
Region Location Sequence types Scaffold length
4933416I08Rik chrX:53444973-53687352 FIX 1
Ahnak2 chr12:112701299-112815832 FIX 1
Airn chr17:12729292-12861171 ALT 1
Anxa13 chr15:57983529-58517868 FIX 1
Atg4a chrX:140784762-141363409 FIX 1
Auts2 chr5:131326290-132550462 FIX 1
Baalc chr15:38582635-39142852 FIX 1
Dgkk chrX:6763452-7054396 FIX 1
DiGeorge chr16:17742495-19065968 ALT, FIX 7
Dnah12 chr14:26629355-26911986 FIX 1
DownSynCrit_region_1 chr16:94114272-95747459 ALT 1
DownSynCrit_region_2 chr16:95846204-96221063 ALT 1
DownSynCrit_region_3 chr16:97054368-97223607 ALT 1
Efcab7 chr4:99625547-100035456 FIX 1
Grm1 chr10:10861646-10927384 ALT 1
Hbb_cluster chr7:103811478-103860690 ALT 1
Ide chr19:37204249-37492988 FIX 1
Ifi_cluster chr1:173701136-174051183 ALT 3
Igh chr12:113067904-114458697 ALT 3
Impact chr18:11238883-11458280 ALT, FIX 2
Intu chr3:40505691-40944643 FIX 1
Ipo11 chr13:106801073-106932896 ALT 1
Jakmip3 chr7:138934711-139370933 FIX 1
Large chr8:73065642-73319050 ALT 1
MHC chr17:33681276-38548659 ALT 8
Mapt chr11:104203258-104362532 ALT 1
Meg3 chr12:109373903-109689534 FIX 1
Muc2 chr7:141683154-141786694 FIX 1
Mup_region_1 chr4:61778759-62041201 ALT 1
Mup_region_2 chr4:62045255-62237529 ALT 1
Mup_region_3 chr4:59870283-60154907 ALT 1
Mup_region_4 chr4:60250666-61586638 ALT, FIX 4
NOD_mouse_Idd10.1 chr3:99953865-101307585 ALT 1
NOD_mouse_Idd16.1 chr17:27313323-29215977 ALT 1
NOD_mouse_Idd18.1 chr3:109116720-109807685 ALT 1
NOD_mouse_Idd18.2 chr3:103590378-104055839 ALT 1
NOD_mouse_Idd3.1 chr3:36806723-37563603 ALT 4
NOD_mouse_Idd4.1 chr11:69895472-71336724 ALT, NOVEL 4
NOD_mouse_Idd4.2 chr11:72908911-74370562 ALT 1
NOD_mouse_Idd4.2Q chr11:86869779-89954755 ALT, FIX 2
NOD_mouse_Idd5.1 chr1:60640809-63588262 ALT, NOVEL 2
NOD_mouse_Idd5.3 chr1:65597865-69265254 ALT 1
NOD_mouse_Idd5.4 chr1:130311064-130653047 ALT 1
NOD_mouse_Idd6.1+2 chr6:143536594-149568188 ALT 1
NOD_mouse_Idd6.3 chr6:129636567-130656471 ALT 1
NOD_mouse_Idd9.1 chr4:128397119-131686709 ALT, FIX 3
NOD_mouse_Idd9.1M chr4:135021547-135237421 ALT 1
NOD_mouse_Idd9.2_Idd9.3 chr4:146068508-151320022 ALT, FIX 3
Nadk2 chr15:9054779-9266110 FIX 1
Naip2_Naip5 chr13:100075065-100330017 ALT 2
Nlrp4g chr9:124268539-124479149 FIX 1
Odz1 chrX:42891057-43298842 ALT 1
Padi_cluster chr4:140721097-140961448 ALT 1
Prame_region_1 chr4:144179444-144348902 ALT 1
Pstpip2 chr18:77623953-78117342 FIX 1
Ptpmt1 chr2:90853948-91049681 FIX 1
Rab3a_Ifi30 chr8:70673831-70845694 FIX 1
Ren2 chr1:133239136-133489442 ALT 1
Rims1 chr1:22159855-22877939 FIX 1
Serpin_region_1 chr12:103722705-103922810 ALT 1
Sftpb chr6:72296717-72451483 FIX 1
Sgms2 chr3:131299856-131505512 FIX 1
Slc1a1 chr19:28892559-28918752 ALT 1
Slc26a6 chr9:108784955-108953239 FIX 1
Spata5l1 chr2:122566305-122720961 FIX 1
Tcl1_region_1 chr12:105147714-105196166 ALT 1
Tcra_Tcrd chr14:52352473-54229076 ALT 1
Tdpoz_cluster chr3:93583858-93685263 ALT 1
Tmem134 chr19:4013986-4260737 FIX 1
Traf5 chr1:191793213-192106925 FIX 1
Trerf1 chr17:47094952-47423636 FIX 1
Xic chrX:103589284-103841870 ALT 1
Xlr_region_1 chrX:73003651-73121964 ALT 1
Xlr_region_2 chrX:73185425-73263090 ALT 1
olfactory_region_1 chr11:58613181-58787285 ALT 1
olfactory_region_2 chr4:43762692-43857014 ALT 1
olfactory_region_3 chr7:106888710-106927250 ALT 1
region17 chr14:51863012-51973562 ALT 1
region19 chr15:80502872-80672368 ALT 1
region28 chr19:5679043-5707799 ALT 1
region29 chr2:102983310-103388989 ALT 1
region31 chr3:47447005-47679964 ALT 1
region4 chr1:78413759-78687489 ALT 1
region40 chr4:67057602-67195172 ALT 1
region44 chr5:90653128-90826761 ALT 1
region45 chr5:150872255-151123781 ALT 1
region46 chr6:50779502-50919227 ALT 1
region47 chr6:82734575-83039841 ALT 1
region49 chr6:120377222-121015201 ALT 1
region51 chr7:27743215-27826849 ALT 1
region54 chr8:41292834-41482533 ALT 1
region57 chrX:72166181-72363206 ALT 1
region60 chr11:48799134-49141362 ALT, NOVEL 3
region61 chr11:58115562-58302084 ALT 1
region65 chr15:79892564-79986558 ALT 1
region70 chr18:60125920-60496981 ALT 1
region71 chr4:143214657-143582942 FIX 1
region72 chr7:3000001-3475222 FIX 1
region73 chrY:45842743-46337667 FIX 1
region74 chrY:66019703-66188541 FIX 1
region75 chr5:15457667-15635395 FIX 1
region76 chrY:49216909-49556418 FIX 1
region77 chrX:37690395-37986547 FIX 1
region78 chr17:54687402-55747384 FIX 1
region79 chr4:122217500-122473817 FIX 1
region80 chr3:15760691-15949398 FIX 1
region81 chr10:58205866-58311233 FIX 1
region82 chr15:3050001-3186530 FIX 1
region83 chr19:6183084-6688105 FIX 1
region84 chrX:60271962-60763715 FIX 1
region85 chrX:29000987-29562451 FIX 2
region86 chr1:178144751-178344759 FIX 1
region87 chr3:50686235-50904915 FIX 1
region88 chr4:121426261-122034165 FIX 1
region89 chr4:141987963-142697802 FIX 1
region90 chr10:7346541-7776389 FIX 1
region91 chr10:67228314-67653670 FIX 1
region92 chr11:7560598-7879512 FIX 1
region93 chr11:82933464-83353797 NOVEL 3
region94 chr14:24646407-24762340 FIX 1
region95 chr15:103658568-103917132 FIX 1
region96 chr17:7391520-7693199 FIX 1
region97 chr17:47916958-48583287 FIX 1
region98 chr18:76466242-76775534 FIX 1
region99 chrX:111104003-111543375 FIX 1
vomeronasal_region_1 chr6:89851149-90290463 ALT 1
General
Assembly nameGRCm38.p6
Release date2017-09-15
Assembly typehaploid-with-alt-loci
Release typepatch
Assembly units17
Total bases2,818,974,548
Total non-N bases2,739,538,976
Primary assembly N5054,517,951
Regions
Total regions129
Regions with alternate loci70
Regions with FIX patches65
Regions with NOVEL patches9
Regions as PAR2
Alternate loci and patches
Alternate loci99
Alternate loci aligned to primary assembly92
FIX patches65
FIX patches aligned to primary assembly64
NOVEL patches9
NOVEL patches aligned to primary assembly9