Minimal Strain Sets Explaining All Diagnostic Classes (Number of Markers Explained):
Solution 1: C57BL/6J and 129S6/SvEvTac and C57BL/6NCrl
C57BL/6J: 117 / 170 (68.8%)
129S6/SvEvTac: 8 / 47 (17.0%)
C57BL/6NCrl: 3 / 5 (60.0%)
Solution 2: C57BL/6J and 129S6/SvEvTac and C57BL/6NJ
C57BL/6J: 117 / 170 (68.8%)
129S6/SvEvTac: 8 / 47 (17.0%)
C57BL/6NJ: 3 / 5 (60.0%)
Solution 3: C57BL/6J and 129S6/SvEvTac and C57BL/6NHsd
C57BL/6J: 117 / 170 (68.8%)
129S6/SvEvTac: 8 / 47 (17.0%)
C57BL/6NHsd: 3 / 5 (60.0%)
Solution 4: C57BL/6J and 129S6/SvEvTac and C57BL/6NTac
C57BL/6J: 117 / 170 (68.8%)
129S6/SvEvTac: 8 / 47 (17.0%)
C57BL/6NTac: 3 / 5 (60.0%)
Solution 5: C57BL/6JRj and 129S6/SvEvTac and C57BL/6NCrl
C57BL/6JRj: 117 / 170 (68.8%)
129S6/SvEvTac: 8 / 47 (17.0%)
C57BL/6NCrl: 3 / 5 (60.0%)
Solution 6: C57BL/6J and 129S6/SvEvTac and C57BL/6NRj
C57BL/6J: 117 / 170 (68.8%)
129S6/SvEvTac: 8 / 47 (17.0%)
C57BL/6NRj: 3 / 5 (60.0%)
Solution 7: C57BL/6JRj and 129S6/SvEvTac and C57BL/6NJ
C57BL/6JRj: 117 / 170 (68.8%)
129S6/SvEvTac: 8 / 47 (17.0%)
C57BL/6NJ: 3 / 5 (60.0%)
Solution 8: C57BL/6JRj and 129S6/SvEvTac and C57BL/6NHsd
C57BL/6JRj: 117 / 170 (68.8%)
129S6/SvEvTac: 8 / 47 (17.0%)
C57BL/6NHsd: 3 / 5 (60.0%)
Solution 9: C57BL/6JRj and 129S6/SvEvTac and C57BL/6NTac
C57BL/6JRj: 117 / 170 (68.8%)
129S6/SvEvTac: 8 / 47 (17.0%)
C57BL/6NTac: 3 / 5 (60.0%)
Solution 10: C57BL/6JRj and 129S6/SvEvTac and C57BL/6NRj
C57BL/6JRj: 117 / 170 (68.8%)
129S6/SvEvTac: 8 / 47 (17.0%)
C57BL/6NRj: 3 / 5 (60.0%)
Strain Reproducibility
Strain Reproducibility Samples: IE7920
Inbreeding Level: 91.7%
Y Chromosome: Host
Congenicity Level: 85.8%
Donor Contribution in Linked Interval: 84.6Mb
The genome of this strain is not reproducible because there are regions that are still segregating (at least 8.3%) at the strain level.
The estimation of contribution of primary and secondary background depends on the number of samples genotyped.
The impact of this on the published phenotype(s) is unknown.
Substrain Reproducibility
69.3% of the genome is distinguishable between two substrains contributing to the primary background. Of this:
Level of inbreeding: 71.7%
C57BL/6J Contributes: 81.1%
C57BL/6NCrl Contributes: 16.3%
The genome of this strain is not reproducible because there are regions that are still segregating (28.3%) 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
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. The impact of genetic background on previously reported phenotypes has not been evaluated.
GQC analysis was done on one XY sample, IE7920, at the time of importation. The results of the analysis are inconsistent with the SDS, see details below. The primary (host) background is C57BL/6. There is positive evidence of C57BL/6J and C57BL/6N substrains. The secondary (donor) background, 129Sv, is consistent with the F1(C57BL/6J x 129/Sv) ES cells indicated in the submission and the SDS and 129S6SvEv diagnostics are detected. However, there is an additional unknown strain present. The mitochondrial genome is consistent with at least one backcross to a female from the C57BL/6 background. The Y chromosome is consistent with at least one backcross to a male from the host/C57BL6J background. The sample is homozygous for the donor background at the locus. IRES and g_FP constructs are detected in the sample.
This sample 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.
Special Considerations
Based on this report (indicates more than one C57BL/6 substrain, and the presence of a 3rd unknown strain) a request has been made to update the strain name from B6J.129-Dlx1tm3.1Jlr/Mmucd to B6;129(Cg)-Dlx1tm3.1Jlr/Mmucd (2/17/23).
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.