Supplementary Table 2: SNPs, previously shown to differ between DBA/1J and DBA/2J which were not supported by the DBA/1J and DBA/2J WGS data.

chr	coord		DBA/1J	DBA/2J
chr1	15806008	A	A
chr1	35578242	C	C
chr1	68587169	T	T
chr1	99682297	C	C
chr1	117023295	A	A
chr1	136955003	T	T
chr1	139555301	A	A
chr1	157285402	A	A
chr1	181456458	A	A
chr2	8021039		A	A
chr2	8241375		G	G
chr2	33526197	T	T
chr2	59876431	C	C
chr2	76213734	T	T
chr2	130064838	C	C
chr2	130366791	G	G
chr2	143878004	G	G
chr2	155311905	A	A
chr3	11823164	A	A
chr3	14626460	C	C
chr3	15417199	G	G
chr3	16109338	G	G
chr3	16141120	A	A
chr3	16433768	C	C
chr3	22323972	T	T
chr3	35665906	T	T
chr3	36116262	G	G
chr3	64390984	C	C
chr3	111173173	G	G
chr3	142060957	T	T
chr3	142680197	C	C
chr3	146340708	C	C
chr3	148570361	A	A
chr3	150164332	T	T
chr3	151165610	A	A
chr3	153986324	A	A
chr4	47187660	A	A
chr4	77706930	T	T
chr4	111547706	C	C
chr4	116414397	C	C
chr4	128217267	C	C
chr4	129529392	T	T
chr4	131463180	A	A
chr4	132434960	A	A
chr4	132560396	T	T
chr4	132836231	T	T
chr4	136909537	C	C
chr4	143580253	T	T
chr4	143627924	C	C
chr4	145955149	A	A
chr4	147331222	A	A
chr4	150745317	G	G
chr5	4478848	A	A
chr5	72711395	C	C
chr5	123008965	T	T
chr6	17560439	C	C
chr6	32072366	T	T
chr6	69534605	A	A
chr6	104522138	T	T
chr6	104726177	A	A
chr6	105185994	A	A
chr6	107957944	T	T
chr6	108074179	T	T
chr6	108148275	C	C
chr6	108538737	A	A
chr6	109882116	A	A
chr6	109890319	T	T
chr6	110113153	A	A
chr6	131402700	G	G
chr7	10685695	G	G
chr7	12184970	C	C
chr7	29596968	T	T
chr7	120243931	A	A
chr8	15370679	C	C
chr8	61522748	G	G
chr8	61861700	C	C
chr9	33466064	C	C
chr9	34072233	A	A
chr9	35728188	G	G
chr9	36285419	G	G
chr9	37503221	T	T
chr9	38139237	A	A
chr9	42228772	T	T
chr9	49272778	A	A
chr9	79132745	C	C
chr9	102535685	T	T
chr10	113962287	A	A
chr10	114333272	A	A
chr10	121284345	A	A
chr10	122887544	A	A
chr11	35769567	T	T
chr11	36700111	T	T
chr11	37780244	A	A
chr11	38387643	T	T
chr11	38500008	T	T
chr11	39423048	A	A
chr11	39939563	A	A
chr11	40881296	C	C
chr11	42640093	A	A
chr11	51035224	T	T
chr11	115532431	T	T
chr12	16477192	T	T
chr12	17684579	T	T
chr12	19106086	C	C
chr12	23263385	G	G
chr12	43647067	A	A
chr12	58258154	T	T
chr12	59185037	A	A
chr12	83658495	G	G
chr12	91741626	T	T
chr12	97341612	A	A
chr13	27783938	A	A
chr13	106691796	T	T
chr13	111386024	A	A
chr13	114257557	T	T
chr13	115255157	C	C
chr14	40964119	G	G
chr14	54951737	T	T
chr14	103031633	C	C
chr14	110076956	A	A
chr14	110192904	A	A
chr14	110470043	C	C
chr14	111167655	T	T
chr14	111636353	T	T
chr14	111719135	A	A
chr14	116058454	A	A
chr15	45794732	C	C
chr15	54490202	G	G
chr15	97327488	T	T
chr16	8032105	T	T
chr16	54693956	A	A
chr16	75063011	C	C
chr16	75791675	T	T
chr16	83421483	T	T
chr16	84284644	A	A
chr16	91331136	C	C
chr16	91559209	C	C
chr16	93132964	A	A
chr16	94385029	A	A
chr17	32579676	T	T
chr17	35276713	G	G
chr17	41770264	T	T
chr17	42319468	A	A
chr17	62183129	G	G
chr18	15323634	A	A
chr18	61741622	A	A
chr19	27952804	T	T
chrX	35241421	T	T
chrX	38919922	C	C
chrX	63291324	T	T
chrX	66761276	T	T
chrX	80160887	G	G
chrX	82765489	G	G
chrX	139465557	A	A