MiniMUGA Sample Report

MiniMUGA Sample Report - V2

Sample ID

129S;B6-Gt(ROSA)26Sortm4(ACTB-tdTomato,-EGFP)Luo Rb1tm3Tyj Rbl2tm2Tyj Trp53tm1Brn/Mmucd_M_5343

Neogen ID

KM9602

MMRRC Strain ID

43692

MMRRC Strain Name

STOCK Gt(ROSA)26Sor^{tm4(ACTB-tdTomato,-EGFP)Luo} Rb1^tm3Tyj Rbl2^tm2Tyj Trp53^tm1Brn/Mmucd

Summary

The genotype of this sample is of excellent quality. It is male and outbred, and likely a mix of 129S4/SvJaeJ and multiple C57BL/6 substrains. Clustering of unexplained markers is evidence of an additional background strain.

Diagnostic SNPs indicate the presence of the background strain groups 129S, C57BL/6 and the substrains C57BL/6J, FVB/NJ.

NOTE: There is a discrepancy between the diganostic background analysis (C57BL/6J, FVB/NJ) and the primary and secondary background analysis (C57BL/6NCrl, multiple C57BL/6 substrains, C57BL/6NTac, C57BL/6ByJ, C57BL/6J, C57BL/6NJ, C57BL/6JEiJ, C57BL/6JBomTac, C57BL/6NHsd, C57BL/6JOlaHsd, B6N-Tyr/BrdCrCrl, C57BL/6NRj, 129S4/SvJaeJ). This is uncommon and should be investigated further.

The sample contains the following genetic constructs: Bovine growth hormone poly A signal sequence, "Greenish" Fluorescent Protein (EGFP, EYFP, ECFP), hCMV enhancer version a, hCMV enhancer version b, "Reddish" fluorescent protein (tdTomato, mCherry)

Genotyping Quality

Excellent (6 N calls)
All reported results are dependent on genotyping quality.

Chromosomal Sex

Inbreeding Estimate

Outbred (336 H calls at autosomal, X, and PAR chromosome markers)

Inbreeding and
Genotyping Quality
(Plot)

Constructs Detected

BlastR	bpA	Cas9	chlor	Cre	DTA	g_FP	hCMV_a	hCMV_b	hTK_pr	iCre	IRES	Luc	r_FP	rtTA	SV40	tTA
-	+	-	-	-	-	+	+	+	-	-	-	-	+	-	-	-

Primary Background
(Autosomes,
X Chromosome)

Strain	Total	Consistent	Inconsistent	Heterozygous	Excluded
129S4/SvJaeJ	9719	7737 (80.7%)	1513 (15.8%)	335 (3.5%)	134

Secondary Background
(Autosomes,
X Chromosome)

Strain	Total	Explained	Unexplained	Excluded
multiple C57BL/6 substrains	1848 Clustered	1587 (16.6%) 1521 Clustered	210 (2.2%) 179 Clustered	51 (0.5%)

Y Chromosome

Y Haplogroup 6 - 98.4% Consistent
Includes 129S4/SvJaeJ and 11 other strains

MT Chromosome

MT Haplogroup 1 - 100.0% Consistent

Background Ideogram

Backgrounds Detected
(Diagnostic Alleles)

	Diagnostic Alleles Observed
Substrain	Homozygous	Heterozygous	Potential	% Observed
C57BL/6J	27	8	156	22.4%
FVB/NJ	1	2	79	3.8%
Strain Group	Homozygous	Heterozygous	Potential	% Observed
129S (129S1/SvImJ, 129S2/SvHsd, 129S2/SvPasOrlRj, 129S4/SvJaeJ, 129S6/SvEvTac)	4	1	17	29.4%
C57BL/6 (B6N-Tyr/BrdCrCrl, C57BL/6J, C57BL/6JBomTac, C57BL/6JEiJ, C57BL/6JOlaHsd, C57BL/6NJ, C57BL/6NTac)	2	1	21	14.3%

Refined Analysis

Background	Informative Markers	Informative Markers %	Genomic Region %
129S4/SvJaeJ	1277	41.5%	40.3%
multiple C57BL/6 substrains	1312	42.7%	47.8%
Heterozygous	275	8.9%	7.1%
Unexplained Homozygous	168	5.5%	3.8%
Unexplained Heterozygous	42	1.4%	1.0%
Total	3074	100.0%	100.0%

Refined Ideogram

Notes

This sample is outbred and contains more than two strains. A potential solution was generated based on the SDS decription and the presence of diagnostics. bpA, g_FP, hCMV_a and b, and r_FP constructs were detected.