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.