Table 2.

Genetic variants in laboratory populations

	Variants sites	Variants	Variant type			Predicted impact			Alt/Alt homozygous % (mean ± SD)	Genotype qual (mean ± SD)
			SNPs	Indels	Mixeda	High	Low	Moderate
RatCollection	15,804,627	19,987,273	12,661,110	7,313,702	12,461	18,646	262,685	125,523	97.9 ± 1.4	70.1 ± 21.2
HS progenitors	12,418,243	16,438,302	9,947,112	6,479,485	11,705	6,980	205,316	94,659	98.5 ± 0.3	71.4 ± 22.0
FXLE/LEXFb	9,183,562	13,070,345	7,036,182	6,023,391	10,772	13,988	143,623	66,186	96.8 ± 2.4	72.3 ± 21.0
HXB/BXHb	7,520,223	11,256,227	5,705,592	5,541,195	9,440	10,121	115,081	53,819	97.9 ± 1.2	72.2 ± 22.8
SS/SR	7,171,447	10,522,763	5,544,220	4,969,398	9,145	8,606	111,658	51,149	98.0 ± 0.9	72.3 ± 21.8
LL/LN/LH	6,923,575	10,112,755	5,433,556	4,670,291	8,908	4,142	111,040	52,364	98.5 ± 0.3	73.2 ± 21.4

The RatCollection includes 163 rats (88 strains and 32 substrains, with some biological replicates). The HRDP contains the HXB/BXH and FXLE/LEXF panels as well as 30 or so classic inbreds. Our analysis includes ∼80% of the HRDP. The variants were jointly called using Deepvariant and GLNexus. Variant impact was annotated using SnpEff.

^aVariants that are combinations of insertions, deletions, or SNPs.

^bIncluding parental strains.