Minimal Strain Sets Explaining All Diagnostic Classes (Number of Markers Explained):
Solution 1: C57BL/6J and C57BL/6NTac
C57BL/6J: 152 / 167 (91.0%)
C57BL/6NTac: 5 / 28 (17.9%)
Solution 2: C57BL/6J and C57BL/6NRj
C57BL/6J: 152 / 167 (91.0%)
C57BL/6NRj: 5 / 28 (17.9%)
Strain Reproducibility
Strain Reproducibility Samples: WA9288, JK5682
Inbreeding Level: 100.0%
Y Chromosome: Host
Congenicity Level: 100.0%
Donor Contribution in Linked Interval: 0.3Mb
Substrain Reproducibility
97.0% of the genome is distinguishable between two substrains contributing to the primary background. Of this:
Level of inbreeding: 87.7%
C57BL/6J Contributes: 87.9%
C57BL/6NTac Contributes: 12.1%
The genome of this strain is not reproducible because there are regions that are still segregating (12.3%) at the substrain level.
The estimation of contribution of substrains depends on the number of samples genotyped.
The impact of this on the published phenotype(s) is unknown.
Ideogram 1 Ideogram 2
Notes
Genetic QC analysis (GQC) was performed on representative samples from the donor submission and provides a baseline reference. Regardless of the material ordered (live mice, sperm, embryos, resuscitated animals), the provided material is guaranteed to contain the primary genetic alteration of interest; however, the composition of the genetic background may vary (See Reproducibility sections of the report for details). The impact of genetic background on previously reported phenotypes has not been evaluated.
GQC analysis was done on two XY samples, WA9288 and JK5682, at the time of importation and the conclusions are consistent in all samples. The results of the analysis are congruent with the SDS and WA9288 is the representative sample selected for the report. The primary (host) background is C57BL/6 and there is positive evidence of the C57BL/6J and C57BL/6N substrains. The mitochondrial genome is consistent with the C57BL/6 background and the Y chromosome is consistent with at least one backcross to C57BL/6J. Both samples are homozygous for the C57BL/6N background at the locus. The following constructs are detected in all samples: IRES, r_FP?.
The genome of MMRRC:046280 mice is 87% inbred at the substrain level. 13% of the genome is segregating for the two substrains,C57BL/6J and C57BL/6N. The contribution of C57BL/6J is 86.3%. The contribution of C57BL/6N is 13.7%.
The estimated inbreeding, congenicity, and the relative strain/substrain contribution depend on the number of samples genotyped. The genomes of strains that are not fully inbred are not completely reproducible.
ATTENTION: MiniMUGA has detected a potential unexpected construct (r_FP) that may interfere with the experimental design/rigor and reproducibility. It is recommended to genotype to ensure that r_FP is not present.
Based on this report, a request has been made to update the strain name from C57BL/6J-Rgs21tm1.1Dski/Mmnc to C57BL/6-Rgs21tm1.1Dski/Mmnc
Special Considerations
MiniMUGA has detected a potential unexpected construct (r_FP) that may interfere with the experimental design/rigor and reproducibility. It is recommended to genotype to ensure that r_FP is not present.
Based on this report, a request has been made to update the strain name from C57BL/6J-Rgs21tm1.1Dski/Mmnc to C57BL/6-Rgs21tm1.1Dski/Mmnc
WARNINGS
This sample likely has more than 2 genetic backgrounds (unexplained regions and/or fractured ideogram). The strain selected for secondary background may be incorrect. The estimation of the contribution of primary and secondary background are likely incorrect. This can potentially be addressed with input from the user.