MiniMUGA Sample Report - Initial Version
MMRRC Strain Name B6J(129S4)-Prdx6tm5.1Abf/Mmnc
MMRRC Strain ID 42283
Sample ID BU3027
Genotyping Quality Excellent (6 N calls)
All reported results are dependent on genotyping quality.
Chromosomal Sex XY
2023-03-30T14:15:10.146866 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 2678 99.8% 99.9%
C57BL/6J and C57BL/6NCrl X 129S4/SvJaeJ Heterozygous 5 0.2% 0.1%
Total 2683 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 60 29 139 64.0%
C57BL/6J, C57BL/6JEiJ, C57BL/6JRj 7 6 21 61.9%
B6N-Tyr<c-Brd>/BrdCrCrl, C57BL/6NCrl, C57BL/6NRj 5 2 11 63.6%
B6N-Tyr<c-Brd>/BrdCrCrl, C57BL/6NCrl 2 6 21 38.1%
B6N-Tyr<c-Brd>/BrdCrCrl, C57BL/6J, C57BL/6JRj 4 1 5 100.0%
C57BL/6J 1 1 6 33.3%
B6N-Tyr<c-Brd>/BrdCrCrl, C57BL/6J, C57BL/6JEiJ, C57BL/6JRj 1 0 1 100.0%
B6N-Tyr<c-Brd>/BrdCrCrl, C57BL/6NCrl, C57BL/6NHsd 1 0 1 100.0%
B6N-Tyr<c-Brd>/BrdCrCrl, C57BL/6NCrl, C57BL/6NHsd, C57BL/6NJ, C57BL/6NRj, C57BL/6NTac 1 0 3 33.3%
C57BL/6J, C57BL/6JEiJ, C57BL/6JOlaHsd, C57BL/6JRj 1 0 1 100.0%
B6N-Tyr<c-Brd>/BrdCrCrl, C57BL/6J, C57BL/6JBomTac, C57BL/6JEiJ, C57BL/6JOlaHsd, C57BL/6JRj 0 1 2 50.0%
C57BL/6J, C57BL/6JBomTac, C57BL/6JEiJ, C57BL/6JOlaHsd, C57BL/6JRj 0 1 2 50.0%

Minimal Strain Sets Explaining All Diagnostic Classes (Number of Markers Explained):
  • Solution 1: C57BL/6J and C57BL/6NCrl
    • C57BL/6J: 113 / 177 (63.8%)
    • C57BL/6NCrl: 17 / 36 (47.2%)
  • Solution 2: B6N-Tyr/BrdCrCrl and C57BL/6J
    • C57BL/6J: 106 / 169 (62.7%)
    • B6N-Tyr/BrdCrCrl: 17 / 36 (47.2%)
    • B6N-Tyr/BrdCrCrl or C57BL/6J: 7 / 8 (87.5%)
Strain Reproducibility Strain Reproducibility Samples: BU3027
Inbreeding Level: 99.9%
Y Chromosome: Donor
Congenicity Level: 99.9%
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 0.1%) 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 99.4% of the genome is distinguishable between two substrains contributing to the primary background. Of this:
  • Level of inbreeding: 73.9%
  • C57BL/6J Contributes: 57.9%
  • C57BL/6NCrl Contributes: 42.1%
The genome of this strain is not reproducible because there are regions that are still segregating (26.1%) 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 1) GQC analysis was done on two XY samples BU3027 and QH9545 at the time of importation and the conclusions are consistent in all samples. The results of the analysis are mostly congruent with the SDS (see special considerations section) and BU3027 is the representative sample selected for the report. The primary background is C57BL/6. There is positive evidence of C57BL/6J and C57BL/6NCrl substrains. The secondary background is consistent with 129S4, which is indicated in the submission and the SDS as the background of Flp mice used to remove the selection cassette. 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 host background. The region containing the allele of interest does not have the expected donor background (C57BL/6J). The SDS indicates the use EAP6 ES cells (C57BL/6J). However, there is evidence of C57BL/6NCrl throughout the genome and at the targeted locus so this may be incorrect. None of the constructs detectable by MiniMUGA are present.

The genome of the MMRRC: 42283 strain is 99.9 % inbred and 99.9% congenic at the strain level. 0.1% of the genome is segregating for the secondary (donor) background. 26.1% of the genome is segregating for the two substrains (C57BL/6J and C57BL/6NCrl) that contribute to the primary background. The contribution of C57BL6J is 57.9%. The contribution of C57BL/6NCrl is 42.1%.

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(129S4)-Prdx6tm5.1Abf/Mmnc to B6(129S4)-Prdx6tm5.1Abf/Mmnc (March 30, 2023).
Diplotype Intervals
Report generated on 2023-03-30 14:15