MiniMUGA Sample Report - Initial Version
MMRRC Strain Name B6.129P2-Gabrqtm1Dgen/Mmnc
MMRRC Strain ID 11620
Sample ID EJ9304
Genotyping Quality Excellent (3 N calls)
All reported results are dependent on genotyping quality.
Chromosomal Sex XY
2022-11-08T02:49:10.700756 image/svg+xml Matplotlib v3.5.1, https://matplotlib.org/
Genome Analysis
Background Zygosity Informative
Markers
Informative
Markers %
Genome %
C57BL/6J and C57BL/6NCrl Homozygous 2651 96.9% 98.4%
129P2/OlaHsd Homozygous 34 1.2% 1.1%
C57BL/6J and C57BL/6NCrl X 129P2/OlaHsd Heterozygous 52 1.9% 0.5%
Total 2737 100.0% 100.0%
* Please see substrain reproducibility section
Constructs Detected
BlastR
bpA
Cas9
chlor
cHS4
Cre
DTA
Flp
g_FP
hCMV_a
hCMV_b
hTK_pr
iCre
IRES
Luc
r_FP
rtTA
SV40
tTA
- - - - - - - - - - - - - + - - - - -
Backgrounds Detected
(Diagnostic Alleles)
  Diagnostic Alleles Observed
Diagnostic Class Homozygous Heterozygous Potential % Observed
C57BL/6J, C57BL/6JRj 61 69 142 91.5%
C57BL/6J, C57BL/6JEiJ, C57BL/6JRj 8 12 21 95.2%
B6N-Tyr<c-Brd>/BrdCrCrl, C57BL/6J, C57BL/6JRj 3 2 5 100.0%
B6N-Tyr<c-Brd>/BrdCrCrl, C57BL/6NCrl 0 4 20 20.0%
B6N-Tyr<c-Brd>/BrdCrCrl, C57BL/6NCrl, C57BL/6NRj 0 4 10 40.0%
C57BL/6J 1 2 4 75.0%
B6N-Tyr<c-Brd>/BrdCrCrl, C57BL/6J, C57BL/6JBomTac, C57BL/6JEiJ, C57BL/6JOlaHsd, C57BL/6JRj 1 1 2 100.0%
B6N-Tyr<c-Brd>/BrdCrCrl, C57BL/6J, C57BL/6JEiJ, C57BL/6JRj 1 0 1 100.0%
C57BL/6J, C57BL/6JEiJ, C57BL/6JOlaHsd, C57BL/6JRj 1 0 1 100.0%
B6N-Tyr<c-Brd>/BrdCrCrl, C57BL/6ByJ, C57BL/6NCrl, C57BL/6NRj 0 1 1 100.0%
B6N-Tyr<c-Brd>/BrdCrCrl, C57BL/6NCrl, C57BL/6NHsd, C57BL/6NJ, C57BL/6NRj, C57BL/6NTac 0 1 2 50.0%
C57BL/6J, C57BL/6JBomTac, C57BL/6JEiJ, C57BL/6JOlaHsd, C57BL/6JRj 0 1 1 100.0%

Minimal Strain Sets Explaining All Diagnostic Classes (Number of Markers Explained):
  • Solution 1: C57BL/6J and C57BL/6NCrl
    • C57BL/6J: 163 / 177 (92.1%)
    • C57BL/6NCrl: 10 / 33 (30.3%)
  • Solution 2: C57BL/6J and B6N-Tyr/BrdCrCrl
    • C57BL/6J: 155 / 169 (91.7%)
    • B6N-Tyr/BrdCrCrl or C57BL/6J: 8 / 8 (100.0%)
    • B6N-Tyr/BrdCrCrl: 10 / 33 (30.3%)
Strain Reproducibility Strain Reproducibility Samples: TU1546, EJ9304
Inbreeding Level: 98.6%
Y Chromosome: Host
Congenicity Level: 99.5%
Donor Contribution in Linked Interval: 28.1Mb

The genome of this strain is not reproducible because there are regions that are still segregating (at least 1.4%) 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 97.4% of the genome is distinguishable between two substrains contributing to the primary background. Of this:
  • Level of inbreeding: 28.1%
  • C57BL/6J Contributes: 60.4%
  • C57BL/6NCrl Contributes: 39.6%
The genome of this strain is not reproducible because there are regions that are still segregating (71.9%) 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 (TU1546, EJ9304) at the time of importation and the conclusions are consistent in all samples. The results of the analysis are fully congruent with the SDS and EJ9304 is the representative sample selected for the report. The primary (host) background is C57BL/6. There is positive evidence for the presence of the C57BL/6J and C57BL/6NCrl substrains. The secondary (donor) background is consistent with 129P2/OlaHsd, which is indicated in the submission and the SDS as the donor strain. The mitochondrial genome is consistent with both the host and donor backgrounds (identical by descent). The Y chromosome is consistent with at least one backcross to a male from the host background. The region containing the allele of interest has the expected donor background (129P2/OlaHsd). Both samples are hemizygous for the donor background at the locus. The following construct(s) are detected in all samples: IRES.

The genome of MMRRC:011620 mice is 98.6 % inbred and 99.5% congenic at the strain level. 1.4% of the genome is segregating for the secondary (donor) background. 71.9% of the genome is segregating for the two substrains (C57BL/6J and C57BL/6NCrl) that contribute to the primary (host) background. The contribution of C57BL/6J is 60.4%. The contribution of C57BL/6NCrl is 39.6%.

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.
Diplotype Intervals
Report generated on 2022-11-08 02:49