Minimal Strain Sets Explaining All Diagnostic Classes (Number of Markers Explained):
Solution 1: C57BL/6J and C57BL/6NCrl
C57BL/6J: 128 / 176 (72.7%)
C57BL/6NCrl: 12 / 35 (34.3%)
Solution 2: B6N-Tyr/BrdCrCrl and C57BL/6J
C57BL/6J: 123 / 169 (72.8%)
B6N-Tyr/BrdCrCrl or C57BL/6J: 5 / 7 (71.4%)
B6N-Tyr/BrdCrCrl: 12 / 35 (34.3%)
Strain Reproducibility
Strain Reproducibility Samples: YA4452
Inbreeding Level: 77.2%
Y Chromosome: Donor
Congenicity Level: 51.9%
Donor Contribution in Linked Interval: 0.0Mb
The genome of this strain is not reproducible because there are regions that are still segregating (at least 22.8%) 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
77.4% of the genome is distinguishable between two substrains contributing to the primary background. Of this:
Level of inbreeding: 70.5%
C57BL/6J Contributes: 85.2%
C57BL/6NCrl Contributes: 14.8%
The genome of this strain is not reproducible because there are regions that are still segregating (29.5%) 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 (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 one XY sample YA4452 at the time of importation. The results of the analysis are inconsistent with the SDS, see special considerations section. There is positive evidence of C57BL/6J
and C57BL/6NCrl substrains. There is no evidence of additional backgrounds. The mitochondrial genome is consistent with both substrains (identical by descent). However, the Y chromosome is C57BL6/NCrl and has not been backcrossed to a male from C57BL6/J. The region containing the allele of interest has the expected C57BL6/J background and the sample is homozygous at the locus. None of the constructs detectable by MiniMUGA are present.
The genome of the MMRRC:67182 strain is 100 % inbred at the strain level. 29.5% of the genome is segregating for the two substrains (C57BL/6J and C57BL/6NCrl) that contribute to the strain background. The contribution of C57BL6/J is 85.2%. The contribution of C57BL/6NCrl is 14.8%.
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.
Special Considerations
The Y chromosome does not match the substrain background listed in the SDS (C57BL6/J).
Based on this report, a request has been made to update the strain name from C57BL/6J-Reltem1Jpsi/Mmnc
to C57BL/6-Reltem1Jpsi/Mmnc (March 30, 2023).