Minimal Strain Sets Explaining All Diagnostic Classes (Number of Markers Explained):
Solution 1: C57BL/6J and C57BL/6NCrl
C57BL/6J: 161 / 167 (96.4%)
C57BL/6NCrl: 25 / 33 (75.8%)
Strain Reproducibility
Strain Reproducibility Samples: IA1539
Inbreeding Level: 95.7%
Y Chromosome: N/A
Congenicity Level: 97.0%
Donor Contribution in Linked Interval: 37.0Mb
The genome of this strain is not reproducible because there are regions that are still segregating (at least 4.3%) 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
52.1% of the genome is distinguishable between two substrains contributing to the primary background. Of this:
Level of inbreeding: 3.8%
C57BL/6J Contributes: 51.3%
C57BL/6NCrl Contributes: 47.4%
The genome of this strain is not reproducible because there are regions that are still segregating (96.2%) 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 XX sample IA1539 (XX) at the time of importation and the results of the analysis are congruent with the SDS. The primary (host) background is C57BL/6. There is positive evidence of, C57BL/6J and C57BL/6N substrains. The secondary (donor) background is consistent with 129P2, which is indicated in the submission and the SDS as the donor strain. The mitochondrial genome is consistent with both the host and donor background (identical by descent). The background of the Y chromosome was not assessed because only an XX sample was genotyped. The region containing the allele of interest has the expected donor background (129P2). The sample is heterozygous for the donor background at the locus. The IRES construct is detected in the sample.
The genome of the MMRRC: 11632 strain is 95.7 % inbred and 97% congenic at the strain level. 4.3% of the genome is segregating for the secondary (donor) background. 96.2% of the genome is segregating for the two substrains (C57BL/6J and C57BL/6N) that contribute to the primary (host) background. The contribution of C57BL/6J is 51.3%. The contribution of C57BL/6N is 47.4%.
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.
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.