UNC Systems Genetics

Here we provide genotype probability files for each Collaborative Cross strain, as well as individual CC and founder strain animals for both mouse genome builds 37 and 38.  Mice were genotyped on the MegaMUGA array, and SNP intensities were used to calculate the probability of genome region descent from each of the 8 founder strains.  These results are presented as files showing the probability of being each of 36 genotype calls (8 homozygous strain calls, as well as 28 heterozygous calls) at each genome marker on the array.  We also present consensus genotype probabilities for each CC strain.  These files are identical in format to the individual genotype probability files, but are a weighted consensus of the individual genotype probability of the most recent common ancestors in that strain (animals who are obligate ancestors of all distributed animals within that strain).  This weighting ensures that rare founder genotype probabilities are accounted for and preserved in CC strain characterization.

October, 2017

We recently discovered inconsistencies on CC haplotype probability file in build 38 compared to build 37. The two errors are as follows: On chromosome 5, there are two markers (SAbGeoEUCOMM001 SAbGeoEUCOMM002) that should not be given genome position. On chromosome 13, there is a problem with the last set of approximately 80 markers that result in an inconsistent pattern of founder haplotype reconstruction. (Beginning near UNC23486670 CH13:118447298 to UNC23498758 CH13:119480991)

We recommend that for now build 37 be used until further notice. Alternatively, it is possible to continue to use build 38 by masking markers in these two regions. We will correct this issue as soon as possible in the next few weeks and release an updated version of CC haplotype probabilities in build 38.

Collaborative Cross Lines
CC Strain MRCAs   CC Strain MRCAs
 CC001/Unc  OR13140f3012
   CC002/Unc  OR15156f3011
 CC003/Unc  OR13067f3006
   CC004/TauUnc  IL16188f3006
 CC005/TauUnc  IL16211f3008
   CC006/TauUnc  IL16750f3254
 CC007/Unc  OR13421f3004
   CC008/GeniUnc  AU8036f212
 CC009/Unc  OR5489f255
   CC010/GeniUnc  AU8018f203
 CC011/Unc  OR3252f494
   CC012/GeniUnc  AU8005f212
 CC013/GeniUnc  AU8010f215
   CC014/Unc  OR3415m650
 CC015/Unc  OR3154f550
   CC016/GeniUnc  AU8024f207
 CC017/Unc  OR3032f285
   CC018/Unc  OR3609f296
 CC019/TauUnc  IL16513f3732
   CC020/GeniUnc  AU8054f201
 CC021/Unc  OR1566f850
   CC022/GeniUnc  AU8046f201
 CC023/GeniUnc  AU8043f201
   CC024/GeniUnc  AU8004f217
 CC025/GeniUnc  AU8008f202
   CC026/GeniUnc  AU8026f201
 CC027/GeniUnc  AU8027f225
   CC028/GeniUnc  AU8016f214
 CC029/Unc  OR3564f256
   CC030/GeniUnc  AU8034f204
 CC031/GeniUnc  AU8031f204
   CC032/GeniUnc  AU8002f201
 CC033/GeniUnc  AU8033f205
   CC034/Unc  OR5080f275
 CC035/Unc  OR5035f470
   CC036/Unc  OR477f205
 CC037/TauUnc  IL16072f201
   CC038/GeniUnc  AU8049f201
 CC039/Unc  OR15155f3022
   CC040/TauUnc  IL16557f3182
 CC041/TauUnc  IL16441f3016
   CC042/GeniUnc  AU18042f3008
 CC043/GeniUnc  AU8021m201
   CC044/Unc  OR4410f821
 CC045/GeniUnc  AU8045f478
   CC046/Unc  OR5346f536
 CC047/Unc  OR5612f822
   CC048/Unc  OR5248f341
 CC049/TauUnc  IL16296f3633
   CC050/Unc  OR867f470
 CC051/TauUnc  IL16912f3442
   CC052/GeniUnc  AU8052f203
 CC053/Unc  OR773f391
   CC054/GeniUnc  AU8050f201
 CC055/TauUnc  IL16680f3193
   CC056/GeniUnc  AU8056f201
 CC057/Unc  OR3393f309
   CC058/Unc  OR5358f444
 CC059/TauUnc  IL16012f3351
   CC060/Unc  OR3460f438
 CC061/GeniUnc  AU8048f217
   CC062/Unc  OR5306f366
 CC063/Unc  OR5391f372
   CC065/Unc  OR5119f395
 CC068/TauUnc  IL16768f3613
   CC070/TauUnc  IL16034f3284
 CC071/TauUnc  IL16785f3094
   CC072/TauUnc  IL16521f3006
 CC073/Unc  OR1515f472
   CC074/Unc  OR3015f165
 CC075/Unc  OR3260f415
   CC076/Unc  OR5343f411
 CC078/Tau  IL6126f559
   CC079/Tau  IL6411f871
 CC080/Tau  IL6573f895
   CC081/Unc  OR3269f269
 CC082/Unc  OR3172M434
   CC083/Unc  OR15090m3095
 OR559  OR559f221

Other Samples
 129S1/SvImJf0827  AU18042f3005  AU18042f3007  AU18042m3001
 AU18042m3002  AU18042m3003  AU8002m265  AU8002m586
 AU8004f204  AU8004f214  AU8004f215  AU8004m202
 AU8004m219  AU8005f249  AU8005m252  AU8005m354
 AU8008f201  AU8008m204  AU8008m247  AU8008m276
 AU8010f219  AU8010m227  AU8010m234  AU8016m256
 AU8018m235  AU8024m216  AU8026f205  AU8026f225
 AU8033f207  AU8033m209  AU8034m216  AU8036f201
 AU8036f203  AU8036f212  AU8036m205  AU8036m?
 AU8042f205  AU8042m201  AU8042m234  AU8043m219
 AU8049m?  AU8050f202  AU8050f203  AU8050m205
 AU8052f201  AU8052f202  AU8052f204  AU8052m206
 AU8052m208  AU8054f202  AU8054f203  AU8054f205
 AU8054f206  AU8054f207  AU8054m209  CC084/TauJUnc_F10
 CC084/TauJUnc_F11  CC084/TauJUnc_F12  CC084/TauJUnc_F5  CC084/TauJUnc_F6
 CC084/TauJUnc_F7  CC084/TauJUnc_F8  CC084/TauJUnc_F9  CC084/TauJUnc_M1
 CC084/TauJUnc_M2  CC084/TauJUnc_M3  CC084/TauJUnc_M4  IL16188f3209
 IL16188f3210  IL16188f3211  IL16188f3212  IL16188f3213
 IL16188m3206  IL16188m3207  IL16188m3208  IL16211m3048
 IL16441m3013  IL16521m3005  IL16521m3007  IL16521m3008
 IL16557f3053  IL16557f3152  IL16557m3050  IL16557m3149
 IL16750f3546  IL16750m3544  IL16912f3281  IL16912f3288
 IL16912f3441  IL16912f3444  IL16912f3470  IL16912m3278
 IL16912m3286  IL16912m3445  IL16912m3468  IL6126f559
 OR1237m224  OR13155f3004  OR13155f3005  OR13155m3001
 OR13155m3002  OR13155m3003  OR13421f3028  OR15090f3002
 OR15090f3004  OR15090f3005  OR15090m3001  OR15090m3003
 OR15119f3003  OR15119m3001  OR15119m3002  OR15155f3007
 OR15155f3020  OR15155m3001  OR15156m3224  OR1566f797
 OR1566m795  OR16012u?  OR3032f278  OR3032f290
 OR3032m280  OR3067m352  OR3119f179  OR3119f186
 OR3119f193  OR3119m174  OR3119m182  OR3119m194
 OR3154f731  OR3154m655  OR3154m851  OR3172f253
 OR3172f255  OR3172f?(m224)  OR3172m254  OR3172m256
 OR3172m?(f223)  OR3252m1213  OR3269f129  OR3269m125
 OR3393f221  OR3393f222  OR3393f238  OR3393f245
 OR3393m177  OR3393m224  OR3393m240  OR3393m246
 OR3415f555  OR3415f557  OR3415m552  OR3460f319
 OR3460m323  OR3564f188  OR3564m191  OR3575f275
 OR3575m276  OR3609f364  OR3609f386  OR3609m339
 OR3609m365  OR3640f249  OR3640m250  OR4410f643
 OR4410m644  OR5035f359  OR5035f360  OR5035f361
 OR5035m364  OR5035m365  OR5080f299  OR5080m373
 OR5119f456  OR5119m458  OR5119m478  OR5211f272
 OR5211m263  OR5248f261  OR5248m213  OR5346f311
 OR5346m314  OR5358f307  OR5358f308  OR5358f309
 OR5358f313  OR5358f411  OR5358m266  OR5358m288
 OR5358m315  OR5358m383  OR5391f342  OR5391f352
 OR5391m353  OR5489f501  OR5489f576  OR5489f577
 OR5489m398  OR5489m398  OR5489m575  OR5530f220
 OR5530m221  OR559m683  OR559m723  OR559m737
 OR773f219  OR773f393  OR773f394  OR773f410
 OR773f411  OR773f412  OR773m221  OR773m395
 OR773m396  OR773m397  OR773m413  OR867m1121

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