MiniMUGA Sample Report - Initial Version
MMRRC Strain Name B6(129S4)-Prdx6tm4.1Abf/Mmnc
MMRRC Strain ID 42293
Sample ID PV8351
Genotyping Quality Excellent (0 N calls)
All reported results are dependent on genotyping quality.
Chromosomal Sex XY
2023-12-12T19:31:28.982023 image/svg+xml Matplotlib v3.5.3, https://matplotlib.org/
Genome Analysis
Background Zygosity Informative
Markers		 Informative
Markers %		 Genome %
C57BL/6J and C57BL/6NCrl N/A 2757 99.4% 99.6%
129S4/SvJaeJ Homozygous 1 0.0% 0.0%
C57BL/6J and C57BL/6NCrl X 129S4/SvJaeJ Heterozygous 16 0.6% 0.4%
Total 2774 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 100 23 132 93.2%
C57BL/6J, C57BL/6JEiJ, C57BL/6JRj 13 5 21 85.7%
B6N-Tyr<c-Brd>/BrdCrCrl, C57BL/6J, C57BL/6JRj 4 1 5 100.0%
B6N-Tyr<c-Brd>/BrdCrCrl, C57BL/6J, C57BL/6JBomTac, C57BL/6JEiJ, C57BL/6JOlaHsd, C57BL/6JRj 2 0 2 100.0%
C57BL/6J 1 1 3 66.7%
B6N-Tyr<c-Brd>/BrdCrCrl, C57BL/6J, C57BL/6JEiJ, C57BL/6JRj 1 0 1 100.0%
B6N-Tyr<c-Brd>/BrdCrCrl, C57BL/6NCrl 1 0 19 5.3%
B6N-Tyr<c-Brd>/BrdCrCrl, C57BL/6NCrl, C57BL/6NRj 0 2 10 20.0%
C57BL/6J, C57BL/6JBomTac, C57BL/6JEiJ, C57BL/6JOlaHsd, C57BL/6JRj 1 0 2 50.0%
C57BL/6J, C57BL/6JEiJ, C57BL/6JOlaHsd, C57BL/6JRj 1 0 1 100.0%

Minimal Strain Sets Explaining All Diagnostic Classes (Number of Markers Explained):
  • Solution 1: C57BL/6J and C57BL/6NCrl
    • C57BL/6J: 153 / 167 (91.6%)
    • C57BL/6NCrl: 3 / 29 (10.3%)
  • Solution 2: B6N-Tyr/BrdCrCrl and C57BL/6J
    • C57BL/6J: 145 / 159 (91.2%)
    • B6N-Tyr/BrdCrCrl or C57BL/6J: 8 / 8 (100.0%)
    • B6N-Tyr/BrdCrCrl: 3 / 29 (10.3%)
Strain Reproducibility Strain Reproducibility Samples: PV8351, DS2217
Inbreeding Level: 99.6%
Y Chromosome: Donor
Congenicity Level: 99.5%
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 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 99.2% of the genome is distinguishable between two substrains contributing to the primary background. Of this:
  • Level of inbreeding: 75.5%
  • C57BL/6J Contributes: 82.2%
  • C57BL/6NCrl Contributes: 17.4%
The genome of this strain is not reproducible because there are regions that are still segregating (24.5%) 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
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 PV8351and DS2217 at the time of importation and the conclusions are consistent in all samples. The results of the analysis are congruent with the SDS and PV8351 is the representative sample selected for the report. The primary (host and donor) background is C57BL/6 and there is positive evidence of C57BL/6J and C57BL/6N substrains. The secondary (but not donor) background is consistent with 129S4. The mitochondrial genome is consistent with at least one backcross to a female from the host background. The Y chromosome is inconsistent with at least one backcross to a male from the primary/host background. The region containing the allele of interest is C57BL/6Ncrl, which is consistent with the strain background of the ES cells( C57BL/6 derived EAP ES cells). Both sample(s) are homozygous for the donor background at the locus. None of the constructs detectable by MiniMUGA are present.

The genome of the MMRRC: 42293 strain is 99.6% inbred and 99.5% congenic at the strain level. 0.5% of the genome is segregating for the secondary background. The Y chromosome matches the secondary background; therefore, this is not a true congenic strain. 24.5% 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 82.2%. The contribution of C57BL/6NCrl is 17.4%.

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.

SPECIAL CONSIDERATIONS Y chromosome does not match the host (primary) background. Users should do at least one backcross through a male C57BL/6 to eliminate the discordant Y chromosome.
Diplotype Intervals
Report generated on 2023-12-12 19:31