Mouse Genome Assembly GRCm38.p3
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 |
|---|---|---|---|
| Airn | chr17:12729292-12861171 | ALT | 138,490 |
| DiGeorge | chr16:17742495-19065968 | ALT, FIX | 1,810,596 |
| 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 |
| Grm1 | chr10:10861646-10927384 | ALT | 77,891 |
| Hbb_cluster | chr7:103811478-103860690 | ALT | 55,856 |
| Ifi_cluster | chr1:173701136-174051183 | ALT | 495,160 |
| Igh | chr12:113067904-114458697 | ALT | 1,874,038 |
| Impact | chr18:11238883-11458280 | ALT, FIX | 438,003 |
| Ipo11 | chr13:106801073-106932896 | ALT | 138,435 |
| 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 |
| 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 | chr4:60374393-61285346 | ALT | 152,971 |
| 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 | chr11:69895472-71298870 | ALT | 1,550,185 |
| 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 | chr6:129636567-130660308 | ALT, FIX | 2,379,737 |
| NOD_mouse_Idd9.1 | chr4:128397119-131686709 | ALT | 3,050,841 |
| NOD_mouse_Idd9.1M | chr4:135021547-135237421 | ALT | 215,601 |
| NOD_mouse_Idd9.2_Idd9.3 | chr4:146068508-151320022 | ALT | 4,830,966 |
| 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 |
| Ren2 | chr1:133239136-133489442 | ALT | 281,255 |
| Serpin_region_1 | chr12:103722705-103922810 | ALT | 84,250 |
| Sftpb | chr6:72296717-72451483 | FIX | 154,766 |
| Slc1a1 | chr19:28892559-28918752 | ALT | 25,407 |
| 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 |
| 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 | 247,497 |
| 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:37804742-37986547 | FIX | 182,256 |
| region78 | chr17:54687402-55747384 | FIX | 1,059,955 |
| 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 |
|---|---|---|---|
| Airn | chr17:12729292-12861171 | ALT | 138,490 |
| DiGeorge | chr16:17742495-19065968 | ALT, FIX | 261,336 |
| 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 |
| Grm1 | chr10:10861646-10927384 | ALT | 77,891 |
| Hbb_cluster | chr7:103811478-103860690 | ALT | 55,856 |
| Ifi_cluster | chr1:173701136-174051183 | ALT | 154,284 |
| Igh | chr12:113067904-114458697 | ALT | 1,714,434 |
| Impact | chr18:11238883-11458280 | ALT, FIX | 352,455 |
| Ipo11 | chr13:106801073-106932896 | ALT | 138,435 |
| 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 |
| 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 | chr4:60374393-61285346 | ALT | 83,218 |
| 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 | chr11:69895472-71298870 | ALT | 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 | chr6:129636567-130660308 | ALT, FIX | 1,759,414 |
| NOD_mouse_Idd9.1 | chr4:128397119-131686709 | ALT | 3,050,841 |
| NOD_mouse_Idd9.1M | chr4:135021547-135237421 | ALT | 215,601 |
| NOD_mouse_Idd9.2_Idd9.3 | chr4:146068508-151320022 | ALT | 3,205,425 |
| 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 |
| Ren2 | chr1:133239136-133489442 | ALT | 281,255 |
| Serpin_region_1 | chr12:103722705-103922810 | ALT | 84,250 |
| Sftpb | chr6:72296717-72451483 | FIX | 154,766 |
| Slc1a1 | chr19:28892559-28918752 | ALT | 25,407 |
| 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 |
| 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 | 247,497 |
| 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:37804742-37986547 | FIX | 182,256 |
| region78 | chr17:54687402-55747384 | FIX | 1,059,955 |
| 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 |
|---|---|---|---|
| Airn | chr17:12729292-12861171 | ALT | 138,490 |
| DiGeorge | chr16:17742495-19065968 | ALT, FIX | 1,810,596 |
| 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 |
| Grm1 | chr10:10861646-10927384 | ALT | 77,891 |
| Hbb_cluster | chr7:103811478-103860690 | ALT | 55,856 |
| Ifi_cluster | chr1:173701136-174051183 | ALT | 495,160 |
| Igh | chr12:113067904-114458697 | ALT | 1,872,699 |
| Impact | chr18:11238883-11458280 | ALT, FIX | 438,003 |
| Ipo11 | chr13:106801073-106932896 | ALT | 138,435 |
| 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 |
| 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 | chr4:60374393-61285346 | ALT | 152,971 |
| 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 | chr11:69895472-71298870 | ALT | 1,550,185 |
| 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 | chr6:129636567-130660308 | ALT, FIX | 2,179,737 |
| NOD_mouse_Idd9.1 | chr4:128397119-131686709 | ALT | 2,950,841 |
| NOD_mouse_Idd9.1M | chr4:135021547-135237421 | ALT | 215,601 |
| NOD_mouse_Idd9.2_Idd9.3 | chr4:146068508-151320022 | ALT | 4,580,966 |
| 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 |
| Ren2 | chr1:133239136-133489442 | ALT | 281,255 |
| Serpin_region_1 | chr12:103722705-103922810 | ALT | 84,250 |
| Sftpb | chr6:72296717-72451483 | FIX | 154,766 |
| Slc1a1 | chr19:28892559-28918752 | ALT | 25,407 |
| 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 |
| 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 | 247,497 |
| 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:37804742-37986547 | FIX | 182,256 |
| region78 | chr17:54687402-55747384 | FIX | 1,059,955 |
| 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 |
|---|---|---|---|---|---|
| Airn | chr17:12729292-12861171 | ALT | 1 | 0 | 0 |
| DiGeorge | chr16:17742495-19065968 | ALT, FIX | 7 | 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 |
| Grm1 | chr10:10861646-10927384 | ALT | 1 | 0 | 0 |
| Hbb_cluster | chr7:103811478-103860690 | ALT | 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 |
| Ipo11 | chr13:106801073-106932896 | ALT | 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 |
| 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 | chr4:60374393-61285346 | ALT | 2 | 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 | chr11:69895472-71298870 | ALT | 1 | 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 | chr6:129636567-130660308 | ALT, FIX | 2 | 4 | 0 |
| NOD_mouse_Idd9.1 | chr4:128397119-131686709 | ALT | 1 | 2 | 0 |
| NOD_mouse_Idd9.1M | chr4:135021547-135237421 | ALT | 1 | 0 | 0 |
| NOD_mouse_Idd9.2_Idd9.3 | chr4:146068508-151320022 | ALT | 2 | 5 | 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 |
| Ren2 | chr1:133239136-133489442 | ALT | 1 | 0 | 0 |
| Serpin_region_1 | chr12:103722705-103922810 | ALT | 1 | 0 | 0 |
| Sftpb | chr6:72296717-72451483 | FIX | 1 | 0 | 0 |
| Slc1a1 | chr19:28892559-28918752 | ALT | 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 |
| 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 | 1 | 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:37804742-37986547 | FIX | 1 | 0 | 0 |
| region78 | chr17:54687402-55747384 | 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 |
|---|---|---|---|
| Airn | chr17:12729292-12861171 | ALT | 1 |
| DiGeorge | chr16:17742495-19065968 | ALT, FIX | 7 |
| DownSynCrit_region_1 | chr16:94114272-95747459 | ALT | 1 |
| DownSynCrit_region_2 | chr16:95846204-96221063 | ALT | 1 |
| DownSynCrit_region_3 | chr16:97054368-97223607 | ALT | 1 |
| Grm1 | chr10:10861646-10927384 | ALT | 1 |
| Hbb_cluster | chr7:103811478-103860690 | ALT | 1 |
| Ifi_cluster | chr1:173701136-174051183 | ALT | 3 |
| Igh | chr12:113067904-114458697 | ALT | 3 |
| Impact | chr18:11238883-11458280 | ALT, FIX | 2 |
| Ipo11 | chr13:106801073-106932896 | ALT | 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 |
| 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 | chr4:60374393-61285346 | ALT | 2 |
| 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 | chr11:69895472-71298870 | ALT | 1 |
| 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 | chr6:129636567-130660308 | ALT, FIX | 2 |
| NOD_mouse_Idd9.1 | chr4:128397119-131686709 | ALT | 1 |
| NOD_mouse_Idd9.1M | chr4:135021547-135237421 | ALT | 1 |
| NOD_mouse_Idd9.2_Idd9.3 | chr4:146068508-151320022 | ALT | 2 |
| 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 |
| Ren2 | chr1:133239136-133489442 | ALT | 1 |
| Serpin_region_1 | chr12:103722705-103922810 | ALT | 1 |
| Sftpb | chr6:72296717-72451483 | FIX | 1 |
| Slc1a1 | chr19:28892559-28918752 | ALT | 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 |
| 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 | 1 |
| 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:37804742-37986547 | FIX | 1 |
| region78 | chr17:54687402-55747384 | FIX | 1 |
| vomeronasal_region_1 | chr6:89851149-90290463 | ALT | 1 |
| General | |
|---|---|
| Assembly name | GRCm38.p3 |
| Release date | 2014-03-21 |
| Assembly type | haploid-with-alt-loci |
| Release type | patch |
| Assembly units | 17 |
| Total bases | 2,800,055,571 |
| Total non-N bases | 2,720,699,037 |
| Primary assembly N50 | 54,517,951 |
| Regions | |
|---|---|
| Total regions | 84 |
| Regions with alternate loci | 70 |
| Regions with FIX patches | 16 |
| Regions with NOVEL patches | 1 |
| Regions as PAR | 2 |
| Alternate loci and patches | |
|---|---|
| Alternate loci | 99 |
| Alternate loci aligned to primary assembly | 92 |
| FIX patches | 16 |
| FIX patches aligned to primary assembly | 16 |
| NOVEL patches | 1 |
| NOVEL patches aligned to primary assembly | 1 |