MiniMUGA Sample Report - new algorithm
MMRRC Strain Name B6J.129P2-Lpltm1Mae/Mmnc
MMRRC Strain ID 43619
Sample ID BN1426
Genotyping Quality Excellent (1 N calls)
All reported results are dependent on genotyping quality.
Chromosomal Sex XY
2023-07-28T21:14:41.755802 image/svg+xml Matplotlib v3.5.1, https://matplotlib.org/
Genome Analysis
Background Zygosity Informative
Markers		 Informative
Markers %		 Genome %
C57BL/6J and C57BL/6NHsd N/A 2846 99.7% 99.6%
C57BL/6J and C57BL/6NHsd X 129P2/OlaHsd Heterozygous 9 0.3% 0.4%
Total 2855 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 34 95 132 97.7%
C57BL/6J, C57BL/6JEiJ, C57BL/6JRj 8 13 21 100.0%
B6N-Tyr<c-Brd>/BrdCrCrl, C57BL/6J, C57BL/6JRj 3 2 5 100.0%
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/6NCrl, C57BL/6NHsd, C57BL/6NJ, C57BL/6NRj, C57BL/6NTac 0 2 2 100.0%
C57BL/6J 0 2 3 66.7%
C57BL/6NCrl, C57BL/6NHsd, C57BL/6NJ, C57BL/6NRj, C57BL/6NTac 0 2 2 100.0%
B6N-Tyr<c-Brd>/BrdCrCrl, C57BL/6J, C57BL/6JEiJ, C57BL/6JRj 0 1 1 100.0%
C57BL/6J, C57BL/6JBomTac, C57BL/6JEiJ, C57BL/6JOlaHsd, C57BL/6JRj 0 1 2 50.0%
C57BL/6J, C57BL/6JEiJ, C57BL/6JOlaHsd, C57BL/6JRj 0 1 1 100.0%
C57BL/6NHsd, C57BL/6NJ, C57BL/6NRj, C57BL/6NTac 0 1 1 100.0%

Minimal Strain Sets Explaining All Diagnostic Classes (Number of Markers Explained):
  • Solution 1: C57BL/6J and C57BL/6NHsd
    • C57BL/6J: 162 / 167 (97.0%)
    • C57BL/6NHsd: 5 / 5 (100.0%)
  • Solution 2: C57BL/6J and C57BL/6NJ
    • C57BL/6J: 162 / 167 (97.0%)
    • C57BL/6NJ: 5 / 5 (100.0%)
  • Solution 3: C57BL/6J and C57BL/6NTac
    • C57BL/6J: 162 / 167 (97.0%)
    • C57BL/6NTac: 5 / 5 (100.0%)
  • Solution 4: C57BL/6J and C57BL/6NRj
    • C57BL/6J: 162 / 167 (97.0%)
    • C57BL/6NRj: 5 / 5 (100.0%)
Strain Reproducibility Strain Reproducibility Samples: BN1426
Inbreeding Level: 99.6%
Y Chromosome: Donor
Congenicity Level: 100.0%
Donor Contribution in Linked Interval: 10.6Mb

The genome of this strain is not reproducible because there are regions that are still segregating (at least 0.4%) 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 98.6% of the genome is distinguishable between two substrains contributing to the primary background. Of this:
  • Level of inbreeding: 29.9%
  • C57BL/6J Contributes: 50.0%
  • C57BL/6NHsd Contributes: 50.0%
The genome of this strain is not reproducible because there are regions that are still segregating (70.1%) 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 (BN1426) at the time of importation. 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/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 background (identical by descent). The Y chromosome is inconsistent 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). The sample is heterozygous for the donor background at the locus. None of the constructs detectable by MiniMUGA are present.

The genome of the MMRRC: 43619 strain is 99.6 % inbred and 100% congenic at the strain level. 0.4.% of the genome is segregating for the secondary (donor) background. The level of congenicity estimated by miniMUGA is consistent with the number of backcross generations reported in the SDS. 70.1% 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 50%. The contribution of C57BL/6N is 50%.

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 host (primary) background

Based on this report, a request has been made to update the strain name from B6J.129P2-Lpltm1Mae/Mmnc to B6.129P2-Lpltm1Mae/Mmnc (May 23, 2023).
Diplotype Intervals
Report generated on 2023-07-28 21:14