REAGENT or RESOURCE	SOURCE	IDENTIFIER
Experimental models: Cell lines
Mouse cell line: C57BL/6J Upf2-KO ES cells	Laboratory of Miles Wilkinson	N/A
Mouse cell line: C57BL/6J Upf2-WT ES cells	Laboratory of Miles Wilkinson	N/A
Experimental models: Organisms/strains
Mouse: C57BL/6NTac	Taconic	Model No: B6
Mouse: C57BL/6NJ	The Jackson Laboratory	Stock No: 005304
Mouse: C57BL/6NHsd	Harlan	Order code: 044
Mouse: C57BL/6NCrl	Charles River	Strain code: 027
Mouse: C57BL/6JEiJ	The Jackson Laboratory	Stock No: 000924
Mouse: C57BL/6JBomTac	Taconic	Model No: B6JBom
Mouse: C57BL/6J	The Jackson Laboratory	Stock No: 000664
Mouse: C57BL/6ByJ	The Jackson Laboratory	Stock No: 001139
Mouse: B6N-TyrC/BrdCrCrl	Charles River	Strain code: 493
Mouse: C57BL/10SnJ	The Jackson Laboratory	Stock No: 000666
Mouse: C57BL/10ScSnJ	The Jackson Laboratory	Stock No: 000476
Mouse: C57BL/10ScNHsd	Taconic	Model No: 046
Mouse: C57BL/10ScCr	The Jackson Laboratory	Stock No: 003752
Mouse: C57BL/10J	The Jackson Laboratory	Stock No: 000665
Software and algorithms
HiSat2 v.2.1.0	Kim et. al. 2019	http://daehwankimlab.github.io/hisat2/
HTSeq	Anders et. al. 2015	https://htseq.readthedocs.io/en/master/overview.html
SpeedSeq	Chiang et. al. 2015	https://github.com/hall-lab/speedseq
STAR v2.7.9a	Dobin et. al. 2013	https://github.com/alexdobin/STAR
GATK v4.2.2.0	Van der Auwera GA and O'Connor BD. 2020	https://gatk.broadinstitute.org/hc/en-us
Plink v1.9	Purcell et. al. 2007	https://www.cog-genomics.org/plink/
edgeR	Robinson et. al. 2010	https://bioconductor.org/packages/release/bioc/html/edgeR.html
HipSTR v0.6	Willems et. al. 2017	https://hipstr-tool.github.io/HipSTR/
LUMPY	Layer et. al. 2014	https://github.com/arq5x/lumpy-sv
CNVnator	Abyzov et. al. 2011	https://github.com/abyzovlab/CNVnator
Mosdepth	Pedersen and Quinlan 2018	https://github.com/brentp/mosdepth
Limix v3.0.4	Lippert et. al. 2014	https://horta-limix.readthedocs.io/en/api/installation.html
Variant Effect Predictor (VEP)	McLaren et. al. 2016	https://m.ensembl.org/info/docs/tools/vep/script/vep_download.html
sashimi_plot: used in Figure 3D	Katz et. al. 2010	https://miso.readthedocs.io/en/fastmiso/sashimi.html
R v4.1.1	R Core Team 2021	https://www.r-project.org
Custom codes required to generate figures and perform analyses in this paper	This paper	https://zenodo.org/record/5716285
Deposited data
RNAseq and WGS short read data	This paper	SRA: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA705216/
Data required to run our custom codes and reproduce the figures and results	This paper	Mendeley: https://doi.org/10.17632/39sw8xcrmv.2
Processed data generated in this paper	This paper	Mendeley: https://doi.org/10.17632/k6tkmm6m5h.3