Mouse Genome Overview
Information concerning the continuing improvement of the mouse genome.
The GRC is working hard to provide the best possible reference assembly for mouse. We do this by both generating multiple representations (alternate loci) for regions that are too complex to be represented by a single path. Additionally, we are releasing regional fixes known as patches. This allows users who are interested in a specific locus to get an improved representation without affecting users who need chromosome coordinate stability.
Getting Data
- GRCm38 (Latest Major release from the GRC): FTP
- Alignments of MGSCv37 to GRCm38: GRC FTP
- MGSCv37: FTP
Next assembly update
The GRC will start the patch process for mouse. Quarterly announcements will be made about patch status.
GRCm38
- Release data: 23 Jan 2012
- Release type: major
- Release notes: Major update made the to last MGSC release. All chromosome coordinates have changed. There is now some representation of the PAR regions on the X and Y chromosomes. Additionally, we had to drop the Spretus alternate assembly unit to conform to GenBank guidelines.
- Assembly accession: GCA_000001635.2/GCF_000001635.20
| NAME | Chr | Start | Stop |
|---|---|---|---|
| PAR | Y | 90745845 | 91644698 |
| PAR | X | 169969759 | 170931299 |
| Sequence IDs | Assembly Unit | Region Name | Chr | Start | Stop | Patch Type |
|---|---|---|---|---|---|---|
| GL455989.1 | NT_095534.1 | BALB/c | Hbb_cluster | 7 | 103811478 | 103860690 | na |
| GL455990.1 | NT_039593.1 | A/J | Naip2_Naip5 | 13 | 100075065 | 100330017 | na |
| GL455991.1 | NT_039192.2 | 129S6/SvEvTac | Ren2 | 1 | 133239136 | 133489442 | na |
| GL455992.2 | NT_039194.5 | 129S6/SvEvTac | Ifi_cluster | 1 | 173701136 | 174051183 | na |
| GL455993.1 | NT_039198.1 | 129S6/SvEvTac | region4 | 1 | 78413759 | 78687489 | na |
| GL455994.1 | NT_039291.1 | 129S6/SvEvTac | Prame_region_1 | 4 | 144179444 | 144348902 | na |
| GL455995.1 | NT_039334.1 | 129S6/SvEvTac | region45 | 5 | 150872255 | 151123781 | na |
| GL455996.1 | NT_039469.1 | 129S6/SvEvTac | region54 | 8 | 41292834 | 41482533 | na |
| GL455997.1 | NT_039470.1 | 129S6/SvEvTac | Large | 8 | 73065642 | 73319050 | na |
| GL455998.1 | NT_078683.1 | 129S6/SvEvTac | olfactory_region_1 | 11 | 58613181 | 58787285 | na |
| GL455999.2 | NT_039594.3 | 129S6/SvEvTac | Ipo11 | 13 | 106801073 | 106932896 | na |
| GL456000.1 | NT_039622.1 | 129S6/SvEvTac | region19 | 15 | 80502872 | 80672368 | na |
| GL456001.2 | NT_039634.4 | 129S6/SvEvTac | DownSynCrit_region_1 | 16 | 94114272 | 95747459 | na |
| GL456002.2 | NT_039666.2 | 129S6/SvEvTac | MHC | 17 | 33681276 | 38548659 | na |
| GL456003.2 | NT_039739.2 | 129S6/SvEvTac | Odz1 | X | 42891057 | 43298842 | na |
| GL456004.1 | NT_099024.1 | 129S6/SvEvTac | Xlr_region_1 | X | 73003651 | 73121964 | na |
| GL456005.1 | NT_039195.1 | 129X1/SvJ | Ifi_cluster | 1 | 173701136 | 174051183 | na |
| GL456006.1 | NT_039248.1 | 129S1/SvImJ | NOD_mouse_Idd3.1 | 3 | 36806723 | 37563603 | na |
| GL456007.1 | NT_039256.1 | 129S1/SvImJ | NOD_mouse_Idd3.1 | 3 | 36806723 | 37563603 | na |
| GL456008.1 | NT_080257.1 | 129S1/SvImJ | Tdpoz_cluster | 3 | 93583858 | 93685263 | na |
| GL456009.1 | NT_109318.2 | UNKNOWN | Padi_cluster | 4 | 140721097 | 140961448 | na |
| GL456010.1 | NT_039296.1 | 129X1/SvJ | olfactory_region_2 | 4 | 43762692 | 43857014 | na |
| GL456011.1 | NT_109599.1 | 129S1/SvImJ | region44 | 5 | 90653128 | 90826761 | na |
| GL456012.2 | NT_039372.2 | 129X1/SvJ | region47 | 6 | 82734575 | 83039841 | na |
| GL456013.1 | NT_039443.1 | 129S2/SvPas | olfactory_region_3 | 7 | 106888710 | 106927250 | na |
| GL456014.1 | NT_078572.1 | 129S1/SvImJ | region51 | 7 | 27743215 | 27826849 | na |
| GL456015.1 | NT_078651.1 | UNKNOWN | Grm1 | 10 | 10861646 | 10927384 | na |
| GL456016.1 | NT_039525.1 | 129X1/SvJ | Mapt | 11 | 104203258 | 104362532 | na |
| GL456017.2 | NT_114985.3 | 129S1/SvImJ | Igh | 12 | 113067904 | 114458697 | na |
| GL456019.1 | NT_039614.1 | 129S1/SvImJ | Tcra_Tcrd | 14 | 52352473 | 54229076 | na |
| GL456020.1 | NT_096797.1 | 129X1/SvJ | region17 | 14 | 51863012 | 51973562 | na |
| GL456021.2 | NT_039661.4 | 129S6/SvEvTac | MHC | 17 | 33681276 | 38548659 | na |
| GL456022.2 | NT_039662.3 | 129X1/SvJ | MHC | 17 | 33681276 | 38548659 | na |
| GL456024.2 | NT_039223.3 | 129S1/SvImJ | region29 | 2 | 102983310 | 103388989 | na |
| GL456025.1 | NT_039373.1 | 129S1/SvImJ | region46 | 6 | 50779502 | 50919227 | na |
| GL456026.2 | NT_039382.4 | 129S1/SvImJ | region49 | 6 | 120377222 | 121015201 | na |
| GL456028.2 | NT_039630.5 | 129X1/SvJ | DiGeorge | 16 | 17742495 | 19065968 | na |
| GL456031.1 | NT_111920.1 | 129S1/SvImJ | Xic | X | 103589284 | 103841870 | na |
| GL456032.1 | NT_039744.2 | 129S1/SvImJ | region57 | X | 72166181 | 72363206 | na |
| GL456033.2 | NT_039747.4 | 129S1/SvImJ | Xlr_region_2 | X | 73185425 | 73263090 | na |
| GL456042.2 | NT_114257.4 | NOD/MrkTac | NOD_mouse_Idd18.1 | 3 | 109116720 | 109807685 | na |
| GL456044.2 | NT_166287.2 | NOD/MrkTac | NOD_mouse_Idd18.2 | 3 | 103590378 | 104055839 | na |
| GL456045.2 | NT_039247.2 | NOD/MrkTac | NOD_mouse_Idd3.1 | 3 | 36806723 | 37563603 | na |
| GL456048.1 | NT_039252.1 | NOD/MrkTac | NOD_mouse_Idd3.1 | 3 | 36806723 | 37563603 | na |
| GL456049.2 | NT_039257.4 | NOD/MrkTac | region31 | 3 | 47447005 | 47679964 | na |
| GL456050.1 | NT_080256.1 | NOD/MrkTac | na | Un | not aligned | not aligned | na |
| GL456053.2 | NT_166299.2 | NOD/MrkTac | NOD_mouse_Idd9.2_Idd9.3 | 4 | 146068508 | 151320022 | na |
| GL456054.2 | NT_166305.2 | NOD/ShiLtJ | NOD_mouse_Idd6.1+2 | 6 | 143536594 | 149568188 | na |
| GL456060.2 | NT_166317.2 | NOD/MrkTac | NOD_mouse_Idd4.2 | 11 | 72908911 | 74370562 | na |
| GL456064.1 | NT_039292.1 | UNKNOWN | region40 | 4 | 67057602 | 67195172 | na |
| GL456065.1 | NT_039367.1 | 129X1/SvJ | vomeronasal_region_1 | 6 | 89851149 | 90290463 | na |
| GL456068.1 | NT_096355.1 | BALB/c | Igh | 12 | 113067904 | 114458697 | na |
| GL456069.1 | NT_097336.1 | UNKNOWN | Airn | 17 | 12729292 | 12861171 | na |
| GL456070.1 | NT_165784.1 | RIII | Impact | 18 | 11308625 | 11318460 | na |
| GL456071.1 | NT_166396.1 | CAST/Ei | na | Y | not aligned | not aligned | na |
| GL456072.1 | NT_166398.1 | CAST/Ei | na | Y | not aligned | not aligned | na |
| GL456073.1 | NT_166399.1 | CAST/Ei | na | Y | not aligned | not aligned | na |
| GL456074.1 | NT_114988.1 | 129S1/SvImJ | Serpin_region_1 | 12 | 103722705 | 103922810 | na |
| GL456075.1 | NT_166293.1 | 129S7/SvEvBrd-Hprt-b-m2 | Mup_region_1 | 4 | 61778759 | 62041201 | na |
| GL456076.1 | NT_166294.1 | 129S7/SvEvBrd-Hprt-b-m2 | Mup_region_2 | 4 | 62045255 | 62237529 | na |
| GL456077.1 | NT_166295.1 | 129S7/SvEvBrd-Hprt-b-m2 | Mup_region_4 | 4 | 60374393 | 61285346 | na |
| GL456078.1 | NT_166322.1 | 129S7/SvEvBrd-Hprt-b-m2 | Igh | 12 | 113067904 | 114458697 | na |
| GL456079.1 | NT_039697.1 | 129P2/OlaHsd | region28 | 19 | 5679043 | 5707799 | na |
| GL456080.1 | NT_166394.1 | AKR/J | na | Y | not aligned | not aligned | na |
| GL456081.1 | NT_166397.1 | AKR/J | na | Y | not aligned | not aligned | na |
| GL456082.1 | NT_166400.1 | AKR/J | na | Y | not aligned | not aligned | na |
| GL456349.1 | NT_166433.1 | RIII | Tcl1_region_1 | 12 | 105147714 | 105196166 | na |
| JH584264.1 | NT_187002.1 | NOD/ShiLtJ | NOD_mouse_Idd6.3 | 6 | 129636567 | 130656471 | na |
| JH584265.1 | NT_187003.1 | NOD/ShiLtJ | NOD_mouse_Idd4.2Q | 11 | 86869779 | 89954755 | na |
| JH584266.1 | NT_187004.1 | NOD/ShiLtJ | MHC | 17 | 33681276 | 38548659 | na |
| JH584267.1 | NT_187005.1 | NOD/ShiLtJ | NOD_mouse_Idd16.1 | 17 | 27313323 | 29215977 | na |
| JH584268.1 | NT_186999.1 | 129S7/SvEvBrd-Hprt-b-m2 | Mup_region_4 | 4 | 60374393 | 61285346 | na |
| JH584269.1 | NT_187000.1 | 129S7/SvEvBrd-Hprt-b-m2 | Mup_region_3 | 4 | 59870283 | 60154907 | na |
| JH584270.1 | NT_187001.1 | 129S7/SvEvBrd-Hprt-b-m2 | region65 | 15 | 79892564 | 79986558 | na |
| JH584305.1 | NT_187006.1 | 129S1/SvImJ | Naip2_Naip5 | 13 | 100075065 | 100330017 | na |
| JH584306.1 | NT_187007.1 | 129S1/SvImJ | DiGeorge | 16 | 17742495 | 19065968 | na |
| JH584307.1 | NT_187008.1 | 129S1/SvImJ | DiGeorge | 16 | 17742495 | 19065968 | na |
| JH584308.1 | NT_187010.1 | 129S1/SvImJ | MHC | 17 | 33681276 | 38548659 | na |
| JH584309.1 | NT_187011.1 | 129S1/SvImJ | MHC | 17 | 33681276 | 38548659 | na |
| JH584310.1 | NT_187012.1 | 129S6/SvEvTac | DiGeorge | 16 | 17742495 | 19065968 | na |
| JH584311.1 | NT_187013.1 | 129S6/SvEvTac | DiGeorge | 16 | 17742495 | 19065968 | na |
| JH584312.1 | NT_187014.1 | 129S6/SvEvTac | DiGeorge | 16 | 17742495 | 19065968 | na |
| JH584313.1 | NT_187015.1 | 129S6/SvEvTac | DownSynCrit_region_2 | 16 | 95846204 | 96221063 | na |
| JH584314.1 | NT_187016.1 | 129S6/SvEvTac | DownSynCrit_region_3 | 16 | 97054368 | 97223607 | na |
| JH584315.1 | NT_187017.1 | 129X1/SvJ | Ifi_cluster | 1 | 173701136 | 174051183 | na |
| JH584316.1 | NT_187028.1 | CAST/Ei | region60 | 11 | 48799134 | 49141362 | na |
| JH584317.1 | NT_187029.1 | CAST/Ei | region61 | 11 | 58115562 | 58302084 | na |
| JH584318.1 | NT_187030.1 | CAST/Ei | region70 | 18 | 60125920 | 60496981 | na |
| JH584319.1 | NT_187018.1 | UNKNOWN | Slc1a1 | 19 | 28892559 | 28918752 | na |
| JH584320.1 | NT_187019.1 | NOD/MrkTac | NOD_mouse_Idd5.1 | 1 | 60640809 | 63588262 | na |
| JH584321.1 | NT_187020.1 | NOD/MrkTac | NOD_mouse_Idd5.3 | 1 | 65597865 | 69265254 | na |
| JH584322.1 | NT_187021.1 | NOD/MrkTac | NOD_mouse_Idd5.4 | 1 | 130311064 | 130653047 | na |
| JH584323.1 | NT_187022.1 | NOD/MrkTac | NOD_mouse_Idd10.1 | 3 | 99953865 | 101307585 | na |
| JH584324.1 | NT_187023.1 | NOD/MrkTac | NOD_mouse_Idd9.1 | 4 | 128397119 | 131686709 | na |
| JH584325.1 | NT_187024.1 | NOD/MrkTac | NOD_mouse_Idd9.1M | 4 | 135021547 | 135237421 | na |
| JH584326.1 | NT_187025.1 | NOD/MrkTac | NOD_mouse_Idd9.2_Idd9.3 | 4 | 146068508 | 151320022 | na |
| JH584327.1 | NT_187026.1 | NOD/MrkTac | NOD_mouse_Idd4.1 | 11 | 69895472 | 71298870 | na |
| JH584328.1 | NT_187027.1 | NOD/MrkTac | MHC | 17 | 33681276 | 38548659 | na |
| JH590470.1 | NT_187009.1 | 129S1/SvImJ | MHC | 17 | 33681276 | 38548659 | na |
MGSCv37
- Release data: 10 Jul 2007
- Release type: major
- Release notes: Last assembly released by the MGSC. The GRC has updated the assembly structure so that it resembles human. This means the alternate loci (sequence from other strains) have been aligned to the chromosome and put into a chromosome context. Some alternate loci that were very similar to C57BL/6J were dropped, but no changes were made to the C57BL/6J part of the assemlby. This assembly was also submitted to GenBank.
- Assembly accession: GCA_000001635.1/GCF_000001635.18
| Sequence IDs | Assembly Unit | Region Name | Chr | Start | Stop | Patch Type |
|---|---|---|---|---|---|---|
| GL455989.1 | NT_095534.1 | Balb/c | Hbb_cluster | 7 | 110959995 | 111009204 | na |
| GL455990.1 | NT_039593.1 | A/J | Naip2_Naip5 | 13 | 100922006 | 101021810 | na |
| GL455991.1 | NT_039192.2 | 129/SvEvTac | Ren2 | 1 | 135135713 | 135386019 | na |
| GL455992.1 | NT_039194.4 | 129/SvEvTac | Ifi_cluster | 1 | 175631261 | 175981314 | na |
| GL455993.1 | NT_039198.1 | 129/SvEvTac | region4 | 1 | 78410334 | 78684064 | na |
| GL455994.1 | NT_039291.1 | 129/SvEvTac | na | 4 | not aligned | not aligned | na |
| GL455995.1 | NT_039334.1 | 129/SvEvTac | region45 | 5 | 151674830 | 151925798 | na |
| GL455996.1 | NT_039469.1 | 129/SvEvTac | region54 | 8 | 42378188 | 42567887 | na |
| GL455997.1 | NT_039470.1 | 129/SvEvTac | Large | 8 | 75589541 | 75842949 | na |
| GL455998.1 | NT_078683.1 | 129/SvEvTac | olfactory_region_1 | 11 | 58426683 | 58600787 | na |
| GL455999.1 | NT_039594.2 | 129/SvEvTac | Ipo11 | 13 | 107591153 | 107722976 | na |
| GL456000.1 | NT_039622.1 | 129/SvEvTac | region19 | 15 | 80333302 | 80502798 | na |
| GL456001.1 | NT_039634.3 | 129/SvEvTac | DownSynCrit | 16 | 94114517 | 95701295 | na |
| GL456002.1 | NT_039666.1 | 129/SvEvTac | MHC_region_2 | 17 | 36230820 | 38050373 | na |
| GL456003.1 | NT_039739.1 | 129/SvEvTac | Odz1 | X | 40330809 | 40652019 | na |
| GL456004.1 | NT_099024.1 | 129/SvEvTac | Xlr_region_1 | X | 70248990 | 70367303 | na |
| GL456005.1 | NT_039195.1 | 129/SvJ | Ifi_cluster | 1 | 175631261 | 175981314 | na |
| GL456006.1 | NT_039248.1 | 129/SvJ | region30 | 3 | 36705645 | 37462525 | na |
| GL456007.1 | NT_039256.1 | 129/SvJ | region30 | 3 | 36705645 | 37462525 | na |
| GL456008.1 | NT_080257.1 | 129/SvJ | na | 3 | not aligned | not aligned | na |
| GL456009.1 | NT_109318.2 | 129/SvJ | Padi_cluster | 4 | 140277012 | 140517363 | na |
| GL456010.1 | NT_039296.1 | 129/SvJ | olfactory_region_2 | 4 | 43775564 | 43869886 | na |
| GL456011.1 | NT_109599.1 | 129/SvJ | region44 | 5 | 91082154 | 91255787 | na |
| GL456012.1 | NT_039372.1 | 129/SvJ | region47 | 6 | 82834040 | 82989835 | na |
| GL456013.1 | NT_039443.1 | 129/SvJ | olfactory_region_3 | 7 | 114032224 | 114070764 | na |
| GL456014.1 | NT_078572.1 | 129/SvJ | region51 | 7 | 28528234 | 28611868 | na |
| GL456015.1 | NT_078651.1 | 129/SvJ | Grm1 | 10 | 10581444 | 10647182 | na |
| GL456016.1 | NT_039525.1 | 129/SvJ | Mapt | 11 | 104064572 | 104223846 | na |
| GL456017.1 | NT_114985.2 | 129/SvJ | Igh | 12 | 105978478 | 115696908 | na |
| GL456018.1 | NT_039572.1 | 129/SvJ | Igh | 12 | 105978478 | 115696908 | na |
| GL456019.1 | NT_039614.1 | 129/SvJ | Tcra_Tcrd | 14 | 52971974 | 54848751 | na |
| GL456020.1 | NT_096797.1 | 129/SvJ | region17 | 14 | 52482687 | 52593237 | na |
| GL456021.1 | NT_039661.3 | 129/SvJ | MHC_region_2 | 17 | 36230820 | 38050373 | na |
| GL456022.1 | NT_039662.2 | 129/SvJ | MHC_region_1 | 17 | 33888191 | 35744546 | na |
| GL456023.1 | NT_039663.1 | 129/SvJ | MHC_region_1 | 17 | 33888191 | 35744546 | na |
| GL456024.1 | NT_039223.2 | 129/Sv | region29 | 2 | 102863803 | 103229146 | na |
| GL456025.1 | NT_039373.1 | 129/Sv | region46 | 6 | 50729501 | 50869226 | na |
| GL456026.1 | NT_039382.3 | 129/Sv | region49 | 6 | 120327240 | 120965219 | na |
| GL456027.1 | NT_039613.3 | 129/Sv | Fhit | 14 | 11148176 | 11650860 | na |
| GL456028.1 | NT_039630.4 | 129/Sv | DiGeorge | 16 | 17742588 | 19066061 | na |
| GL456029.1 | NT_039664.1 | 129/Sv | na | 17 | not aligned | not aligned | na |
| GL456030.1 | NT_039665.1 | 129/Sv | MHC_region_2 | 17 | 36230820 | 38050373 | na |
| GL456031.1 | NT_111920.1 | 129/Sv | Xic | X | 100784623 | 101037209 | na |
| GL456032.1 | NT_039744.2 | 129/Sv | region57 | X | 69411520 | 69608545 | na |
| GL456033.1 | NT_039747.3 | 129/Sv | Xlr_region_2 | X | 70430764 | 70508135 | na |
| GL456034.1 | NT_166393.1 | Spret/Ei | na | Y | not aligned | not aligned | na |
| GL456035.1 | NT_166395.1 | Spret/Ei | na | Y | not aligned | not aligned | na |
| GL456036.1 | NT_165757.1 | NOD | region1 | 1 | 60697653 | 61195514 | na |
| GL456037.1 | NT_039197.1 | NOD | region2 | 1 | 61754170 | 61941338 | na |
| GL456038.1 | NT_039199.1 | NOD | region1 | 1 | 60697653 | 61195514 | na |
| GL456039.1 | NT_039200.1 | NOD | region1 | 1 | 60697653 | 61195514 | na |
| GL456040.1 | NT_039201.1 | NOD | region3 | 1 | 63440029 | 63634836 | na |
| GL456041.1 | NT_109311.1 | NOD | region32 | 3 | 99757788 | 99890338 | na |
| GL456042.1 | NT_114257.3 | NOD | region36 | 3 | 108919638 | 109610603 | na |
| GL456043.1 | NT_114258.1 | NOD | na | 3 | not aligned | not aligned | na |
| GL456044.1 | NT_166287.1 | NOD | region35 | 3 | 103394301 | 103719496 | na |
| GL456045.1 | NT_039247.1 | NOD | region30 | 3 | 36705645 | 37462525 | na |
| GL456046.1 | NT_039250.1 | NOD | region33 | 3 | 100124682 | 100629140 | na |
| GL456047.1 | NT_039251.2 | NOD | region34 | 3 | 100709803 | 101111508 | na |
| GL456048.1 | NT_039252.1 | NOD | region30 | 3 | 36705645 | 37462525 | na |
| GL456049.1 | NT_039257.3 | NOD | region31 | 3 | 47250927 | 47483886 | na |
| GL456050.1 | NT_080256.1 | NOD | na | 3 | not aligned | not aligned | na |
| GL456051.1 | NT_166297.1 | NOD | region42 | 4 | 129673209 | 129813999 | na |
| GL456052.1 | NT_166298.1 | NOD | region41 | 4 | 129222696 | 129387052 | na |
| GL456053.1 | NT_166299.1 | NOD | na | 4 | not aligned | not aligned | na |
| GL456054.1 | NT_166305.1 | NOD | region50 | 6 | 144953971 | 145181710 | na |
| GL456055.1 | NT_110625.3 | NOD | region9 | 11 | 69708974 | 70768432 | na |
| GL456056.1 | NT_110626.2 | NOD | region9 | 11 | 69708974 | 70768432 | na |
| GL456057.1 | NT_114882.1 | NOD | region11 | 11 | 88404152 | 88462832 | na |
| GL456058.1 | NT_114883.1 | NOD | na | 11 | not aligned | not aligned | na |
| GL456059.1 | NT_165774.1 | NOD | region9 | 11 | 69708974 | 70768432 | na |
| GL456060.1 | NT_166317.1 | NOD | region10 | 11 | 72722413 | 72881612 | na |
| GL456061.1 | NT_165781.2 | NOD | region24 | 17 | 27792385 | 29352922 | na |
| GL456062.1 | NT_165782.2 | NOD | region24 | 17 | 27792385 | 29352922 | na |
| GL456063.1 | NT_166329.1 | NOD | region23 | 17 | 27450268 | 27705657 | na |
| GL456064.1 | NT_039292.1 | unknown strain | region40 | 4 | 66718636 | 66856206 | na |
| GL456065.1 | NT_039367.1 | unknown strain | vomeronasal_region_1 | 6 | 90040061 | 90240457 | na |
| GL456066.1 | NT_166319.1 | unknown strain | Igh | 12 | 105978478 | 115696908 | na |
| GL456067.1 | NT_166320.1 | unknown strain | Igh | 12 | 105978478 | 115696908 | na |
| GL456068.1 | NT_096355.1 | unknown strain | na | 12 | not aligned | not aligned | na |
| GL456069.1 | NT_097336.1 | unknown strain | Airn | 17 | 12922132 | 13054037 | na |
| GL456070.1 | NT_165784.1 | unknown strain | Impact | 18 | 11308623 | 11423912 | na |
| GL456071.1 | NT_166396.1 | Cast/Ei | na | Y | not aligned | not aligned | na |
| GL456072.1 | NT_166398.1 | Cast/Ei | na | Y | not aligned | not aligned | na |
| GL456073.1 | NT_166399.1 | Cast/Ei | na | Y | not aligned | not aligned | na |
| GL456074.1 | NT_114988.1 | 129/J | na | 12 | not aligned | not aligned | na |
| GL456075.1 | NT_166293.1 | 129S7/SvEv | Mup_region_1 | 4 | 60433222 | 61702235 | na |
| GL456076.1 | NT_166294.1 | 129S7/SvEv | Mup_region_2 | 4 | 61706289 | 61898563 | na |
| GL456077.1 | NT_166295.1 | 129S7/SvEv | na | 4 | not aligned | not aligned | na |
| GL456078.1 | NT_166322.1 | 129S7/SvEv | Igh | 12 | 105978478 | 115696908 | na |
| GL456079.1 | NT_039697.1 | 129P2/OlaHsd | region28 | 19 | 5679043 | 5707799 | na |
| GL456080.1 | NT_166394.1 | AKR/J | na | Y | not aligned | not aligned | na |
| GL456081.1 | NT_166397.1 | AKR/J | na | Y | not aligned | not aligned | na |
| GL456082.1 | NT_166400.1 | AKR/J | na | Y | not aligned | not aligned | na |
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