MiniMUGA Sample Report

MiniMUGA Sample Report - V2

Sample ID

MMRRC_B6;SJL-Nos2+ Tg(APPSWE)2576Kha Tg(PSEN1)1Zhe/Mmnc_M24067

Neogen ID

UB0400

MMRRC Strain ID

11170

MMRRC Strain Name

STOCK Nos2⁺ Tg(APPSWE)2576Kha Tg(Thy1-PSEN1*A246E)16-3Sqn/Mmnc

Summary

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

Diagnostic SNPs indicate the presence of the background strain groups C57BL/6 and the substrains C57BL/6J.

No genetic constructs were detected in this sample.

Genotyping Quality

Excellent (15 N calls)
All reported results are dependent on genotyping quality.

Chromosomal Sex

Inbreeding Estimate

Outbred (1223 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
multiple C57BL/6 substrains	8911	6476 (76.3%)	886 (10.4%)	1130 (13.3%)	419

Secondary Background
(Autosomes,
X Chromosome)

Strain	Total	Explained	Unexplained	Excluded
SJL/J	2016 Clustered	2008 (23.6%) 2008 Clustered	4 (0.0%) 3 Clustered	4 (0.0%)

Y Chromosome

Y Haplogroup 12 - 100.0% Consistent
Includes B6N-Tyr/BrdCrCrl, C57BL/6ByJ, C57BL/6NCrl, C57BL/6NHsd, C57BL/6NJ, C57BL/6NRj, C57BL/6NTac and 14 other strains

MT Chromosome

MT Haplogroup 1 - 100.0% Consistent
Includes B6N-Tyr/BrdCrCrl, C57BL/6ByJ, C57BL/6J, C57BL/6JBomTac, C57BL/6JEiJ, C57BL/6JOlaHsd, C57BL/6NCrl, C57BL/6NHsd, C57BL/6NJ, C57BL/6NRj, C57BL/6NTac, SJL/J and 150 other strains

Background Ideogram

Backgrounds Detected
(Diagnostic Alleles)

	Diagnostic Alleles Observed
Substrain	Homozygous	Heterozygous	Potential	% Observed
C57BL/6J	15	73	156	56.4%
Strain Group	Homozygous	Heterozygous	Potential	% Observed
C57BL/6 (B6N-Tyr/BrdCrCrl, C57BL/6J, C57BL/6JBomTac, C57BL/6JEiJ, C57BL/6JOlaHsd)	1	3	21	19.0%

Refined Analysis

Background	Informative Markers	Informative Markers %	Genomic Region %
multiple C57BL/6 substrains	614	23.4%	27.1%
SJL/J	886	33.7%	30.2%
Heterozygous	1122	42.7%	42.5%
Unexplained Homozygous	0	0.0%	0.0%
Unexplained Heterozygous	4	0.2%	0.2%
Total	2626	100.0%	100.0%

Refined Ideogram

Notes

Sample is outbred. The report agrees with strain nomenclature and the SDS. The sample is mostly explained by SJL and B6 but there is evidence of a small contribution of a third strain, possibly 129S7.