MiniMUGA Sample Report

MiniMUGA Sample Report - V2

Sample ID

MMRRC_SJL.B6-Tg(Nkx2-2*-EGFP)2Mtse/Mmnc_M9666

Neogen ID

WF3120

MMRRC Strain ID

37361

MMRRC Strain Name

SJL.B6-Tg(Nkx2-2*,-EGFP)2Mtse/Mmnc

Summary

The genotype of this sample is of excellent quality. It is male and outbred, and likely a mix of SJL/J 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 C57BL/6 and the substrains C57BL/6J.

The sample contains the following genetic constructs: Bovine growth hormone poly A signal sequence, Chloramphenicol acetyltransferase, Cre recombinase, "Greenish" Fluorescent Protein (EGFP, EYFP, ECFP)

Genotyping Quality

Excellent (19 N calls)
All reported results are dependent on genotyping quality.

Chromosomal Sex

Inbreeding Estimate

Outbred (1411 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
SJL/J	8911	6539 (74.6%)	832 (9.5%)	1399 (16.0%)	141

Secondary Background
(Autosomes,
X Chromosome)

Strain	Total	Explained	Unexplained	Excluded
multiple C57BL/6 substrains	2231 Clustered	1704 (19.4%) 1704 Clustered	444 (5.1%) 441 Clustered	83 (0.9%)

Y Chromosome

Y Haplogroup 1 - 98.4% Consistent
Includes SJL/J and 38 other strains

MT Chromosome

MT Haplogroup 1 - 100.0% Consistent
Includes SJL/J and 161 other strains

Background Ideogram

Backgrounds Detected
(Diagnostic Alleles)

	Diagnostic Alleles Observed
Substrain	Homozygous	Heterozygous	Potential	% Observed
C57BL/6J	14	58	156	46.2%
Strain Group	Homozygous	Heterozygous	Potential	% Observed
C57BL/6 (B6N-Tyr/BrdCrCrl, C57BL/6J, C57BL/6JBomTac, C57BL/6JEiJ, C57BL/6JOlaHsd, C57BL/6NJ, C57BL/6NRj, C57BL/6NTac)	2	4	21	28.6%

Refined Analysis

Background	Informative Markers	Informative Markers %	Genomic Region %
SJL/J	919	30.0%	29.7%
multiple C57BL/6 substrains	746	24.3%	26.0%
Heterozygous	958	31.2%	30.0%
Unexplained Homozygous	69	2.2%	2.1%
Unexplained Heterozygous	375	12.2%	12.2%
Total	3067	100.0%	100.0%

Refined Ideogram

Notes

The report indicates that this sample is outbred which contradicts the strain description that the strain was backcrossed 40G on SJL. A third strain in addition to SJL and C57BL/6 is detected. The sample contains bpA, chlor, g_FP and Cre contructs. The cre construct is not indicated in the SDS.