Supplementary Figure Legends

Figure 1. Whole genome coverage (1kb windows) of 2 MA strains without aneuploidy.

Figure 2. Whole genome coverage (1kb windows) of 4 MA strains with aneuploidy.


Supplementary Materials 1 Fixed Differences Between MA Ancestor and S288C

Chromosome	Position	S288C	MA Ancestor	Notes
2	7912	GA	G	Indel
2	172242	T	TA	Indel
2	197708	TGG	T	Indel
3	91567	T	TG	Indel
3	307455	T	TT	Indel
3	307463	C	CAT	Indel
3	307751	CACTA	C	Indel
4	381512	AG	A	Indel
4	1150910	A	AG	Indel
4	1305680	TG	T	Indel
5	42844	G	GTA	Indel
5	63589	AG	A	Indel
5	462232	GA	G	Indel
7	368551	G	GA	Indel
7	423701	AT	A	Indel
7	430869	A	AAGC	Indel
7	433681	CTA	C	Indel
7	434600	GA	G	Indel
7	436559	G	GGA	Indel
7	529602	TTCA	T	Indel
7	531506	CACAAATGGAA	C	Indel
7	575820	TAG	T	Indel
7	584200	A	AT	Indel
7	643888	AC	A	Indel
7	648165	CT	C	Indel
8	93346	TATTATGAGGCAG	T	Indel
8	395169	CTGT	C	Indel
8	423045	T	TAGTCTAAC	Indel
8	450838	A	AT	Indel
9	332900	TA	T	Indel
10	62701	T	TG	Indel
10	521978	AAT	A	Indel
11	260061	C	CT	Indel
11	260957	A	AC	Indel
11	630488	TA	T	Indel
12	187137	AT	A	Indel
12	322222	T	TC	Indel
12	345332	C	CATT	Indel
12	350810	CCAGGTTCGTCGTTTTCATTAT	C	Indel
12	602909	T	TATAG	Indel
12	669715	GGAA	G	Indel
12	760762	GCC	G	Indel
12	764195	AT	A	Indel
12	766106	CA	C	Indel
13	23878	A	AGAGAG	Indel
13	167431	GA	G	Indel
13	167952	T	TA	Indel
13	169808	GA	G	Indel
13	196231	CTACAA	C	Indel
13	352374	AT	A	Indel
13	433352	CGTATCGATT	C	Indel
13	434643	TT	T	Indel
13	434661	A	AA	Indel
14	7478	A	AT	Indel
14	312328	AACG	A	Indel
15	301214	A	AAATAG	Indel
15	307922	CT	C	Indel
15	343649	GA	G	Indel
15	347482	AT	A	Indel
15	479892	TGAA	T	Indel
15	493440	CA	C	Indel
15	560701	G	GA	Indel
16	502842	CA	C	Indel
1	25340	C	A
1	27129	C	G
1	141030	T	A
2	12117	C	T
2	15518	A	G
2	16392	A	G
2	159797	C	T
2	159891	A	C
2	159926	C	A
2	160143	T	G
2	160403	G	T
2	160810	T	G
2	161065	G	A
2	166703	G	A
2	167924	A	T
2	168065	T	C
2	168194	G	A
2	168731	A	G
2	168747	A	G
2	168775	A	T
2	169496	G	C
2	169566	G	T
2	169589	A	G
2	169601	A	G
2	169621	C	T
2	171612	G	C
2	172028	G	C
2	172038	T	A
2	172113	T	C
2	172223	A	G
2	172245	C	T
2	172262	A	G
2	172302	A	G
2	172307	T	C
2	177622	G	A
2	178351	C	T
2	179248	A	G
2	179257	C	T
2	179290	C	G
2	179410	T	C
2	179872	T	C
2	180070	T	G
2	180255	G	T
2	180379	A	G
2	180607	G	A
2	181033	T	C
2	181034	G	T
2	181425	A	C
2	181635	C	T
2	181647	T	C
2	182128	T	C
2	182137	G	T
2	182323	C	G
2	182436	T	C
2	182892	G	A
2	182901	C	T
2	183084	A	C
2	184932	A	C
2	184941	T	A
2	185762	T	C
2	185891	T	A
2	185922	A	G
2	185954	A	G
2	185979	T	A
2	186008	T	G
2	186049	T	A
2	186067	A	G
2	186778	A	G
2	186915	T	C
2	187153	G	A
2	187157	G	A
2	187873	T	C
2	188734	T	C
2	188743	G	A
2	189263	T	C
2	189739	G	C
2	197372	T	C
2	197440	G	A
2	197464	T	C
2	197474	G	C
2	197588	C	G
2	471963	C	T
3	37395	G	A
3	37525	A	G
3	37664	A	G
3	38178	A	G
3	38503	T	C
3	38664	A	G
3	39123	A	T
3	39265	T	C
3	39326	T	G
3	39967	A	G
3	40008	G	A
3	40089	G	A
3	40109	C	A
3	40144	C	T
3	40197	T	A
3	61544	G	A
3	61630	A	G
3	62434	A	G
3	63578	C	A
3	63878	C	G
3	64304	C	T
3	65087	G	C
3	68070	T	G
3	163059	T	C
3	193600	C	T
3	193828	G	A
3	194198	C	T
3	196972	A	G
3	198110	C	A
3	203936	T	A
3	301736	A	G
3	302896	G	C
3	302979	G	A
3	303798	G	A
3	304102	A	G
3	304825	G	C
3	307149	A	T
3	307443	T	C
3	307465	C	T
3	307477	T	C
3	307489	C	T
3	307696	C	T
3	307768	A	C
3	307772	C	T
3	310319	G	C
3	314456	C	T
4	203927	C	A
4	210356	G	A
4	306463	C	T
4	307974	C	T
4	307984	T	C
4	308212	A	C
4	308238	A	G
4	366637	A	G
4	376028	T	A
4	376661	T	A
4	377123	A	G
4	377176	T	C
4	377486	T	G
4	377936	C	T
4	378086	T	C
4	378664	T	C
4	379556	T	C
4	380035	G	A
4	380086	A	G
4	380668	C	T
4	380743	A	G
4	380924	T	C
4	381444	G	C
4	381458	C	G
4	381481	A	G
4	381576	T	C
4	382330	C	T
4	382655	T	C
4	382829	C	T
4	382830	C	T
4	383065	G	A
4	383227	C	T
4	383229	C	T
4	383443	G	A
4	383454	C	T
4	383478	T	C
4	383572	C	A
4	383684	T	G
4	383874	A	G
4	384257	T	C
4	385740	G	A
4	385961	G	A
4	385972	C	T
4	386094	T	A
4	386135	T	C
4	388038	A	T
4	388221	G	T
4	388305	A	G
4	388440	A	G
4	391712	T	C
4	392128	C	G
4	392938	C	A
4	393651	T	C
4	394249	C	T
4	394339	T	C
4	394385	G	A
4	394555	C	T
4	394798	A	C
4	394876	C	T
4	395381	C	T
4	395767	A	T
4	395957	C	A
4	396862	T	C
4	397012	C	T
4	398297	C	A
4	398518	T	C
4	398523	T	G
4	398655	G	C
4	398669	A	G
4	398697	A	G
4	398734	T	C
4	398862	C	T
4	398875	A	C
4	398907	T	C
4	399007	C	T
4	399193	A	G
4	399202	C	T
4	399900	C	T
4	400242	A	T
4	400395	G	A
4	400404	G	C
4	403061	G	A
4	404304	C	T
4	404690	A	G
4	404730	A	C
4	404818	G	A
4	404981	T	C
4	638865	G	A
4	671537	G	A
4	1021281	G	A
4	1047299	G	C
4	1073253	C	T
4	1265985	G	T
4	1280001	G	A
4	1342500	G	A
4	1369395	G	A
4	1402305	C	T
4	1433710	A	T
5	29278	C	T
5	40520	C	T
5	40623	A	G
5	40988	A	G
5	41039	G	A
5	41432	C	G
5	41545	T	C
5	41687	A	C
5	41711	C	G
5	42216	A	C
5	42217	C	T
5	43074	T	C
5	43242	C	T
5	43485	C	T
5	43494	A	G
5	43578	A	G
5	43659	G	A
5	43744	C	T
5	43746	A	G
5	43838	A	G
5	43959	G	A
5	44568	T	C
5	44601	T	G
5	44613	T	C
5	44763	A	G
5	44999	C	G
5	45208	T	C
5	45816	A	G
5	45963	T	C
5	46022	C	T
5	46030	C	G
5	46838	G	A
5	46866	T	C
5	46910	A	G
5	46989	T	C
5	47089	T	C
5	47317	A	G
5	49068	T	A
5	49109	C	T
5	49397	T	C
5	51579	A	G
5	51706	T	G
5	51780	A	G
5	51822	C	T
5	56129	A	C
5	57707	G	A
5	60057	A	G
5	60147	G	C
5	60162	C	T
5	61667	A	G
5	61799	G	A
5	62026	G	A
5	63253	A	C
5	63498	G	C
5	63676	C	T
5	63726	A	C
5	63847	A	C
5	63934	C	T
5	64295	T	C
5	64403	C	T
5	64421	A	T
5	65418	G	A
5	65424	C	T
5	65622	A	G
5	65697	G	C
5	65944	C	T
5	66141	T	C
5	66168	G	A
5	66258	G	A
5	66738	A	G
5	66817	G	T
5	67018	G	C
5	67311	T	C
5	67758	G	A
5	67770	T	C
5	68268	A	G
5	68547	G	A
5	68643	A	G
5	68702	C	G
5	68714	C	G
5	68718	T	G
5	68794	G	A
5	68798	T	G
5	68910	T	C
5	68945	G	T
5	68996	G	A
5	69083	T	C
5	69202	T	G
5	69209	A	C
5	69229	C	T
5	69251	C	T
5	69310	C	T
5	69459	C	T
5	69468	T	C
5	69568	T	G
5	69584	C	T
5	69592	G	C
5	69766	A	G
5	69939	A	G
5	70003	A	G
5	70005	A	G
5	70113	T	C
5	70335	A	C
5	70822	A	C
5	70852	T	C
5	70912	A	G
5	70954	A	G
5	70969	A	C
5	70986	C	T
5	71054	G	A
5	71062	C	T
5	71182	G	C
5	71197	T	C
5	71279	A	G
5	71422	A	C
5	71593	A	G
5	71842	T	G
5	72112	G	A
5	72295	T	C
5	72326	A	G
5	72483	A	C
5	72502	T	C
5	72990	T	G
5	73131	G	A
5	73250	T	A
5	76382	A	G
5	109375	C	T
5	154531	T	A
5	160010	T	C
5	297012	G	A
5	462222	C	G
5	462226	G	A
5	462249	A	G
5	462471	T	C
5	462614	A	G
5	462755	C	T
5	462850	C	T
5	464494	G	A
5	467553	T	C
5	468178	A	G
5	468183	C	G
5	468194	T	C
5	468269	C	T
5	468307	G	T
5	468390	C	T
5	468645	T	C
5	468777	A	T
6	229067	C	T
6	229320	G	A
6	229517	T	C
6	229520	A	G
6	229790	G	A
6	229838	T	A
6	230250	A	G
6	231775	A	G
6	231831	A	G
6	232697	T	C
6	233456	C	T
6	238493	G	A
6	239478	G	A
6	239639	C	G
6	239696	A	G
6	239986	G	A
6	241183	C	T
6	242843	C	G
6	257096	T	C
6	258551	C	A
6	259052	A	G
7	76882	T	C
7	334658	C	T
7	335241	C	T
7	367741	G	A
7	368041	T	G
7	368341	C	T
7	369600	A	G
7	369922	G	A
7	370647	A	G
7	370737	C	G
7	371244	C	T
7	371263	G	A
7	371265	A	G
7	371335	G	A
7	371489	T	G
7	371528	A	G
7	371640	T	C
7	372033	G	C
7	372223	T	G
7	372417	G	A
7	372605	A	T
7	372717	G	A
7	373580	T	C
7	373624	C	T
7	373646	C	T
7	373781	A	G
7	373940	C	G
7	373957	A	T
7	373958	C	T
7	374354	A	G
7	374582	T	C
7	374962	C	G
7	374973	G	A
7	375001	G	A
7	375227	A	T
7	375494	G	T
7	375538	G	C
7	376314	G	A
7	376364	A	G
7	376883	A	T
7	377024	C	T
7	377048	C	T
7	377049	C	T
7	378078	C	A
7	380141	C	T
7	380177	A	T
7	381438	A	G
7	381441	C	T
7	381517	C	G
7	381897	G	A
7	382144	A	C
7	382476	A	G
7	383010	G	A
7	383402	A	C
7	383573	G	T
7	383584	T	C
7	383893	A	G
7	383977	T	C
7	384196	C	A
7	384239	T	C
7	384425	T	C
7	384641	C	A
7	384678	G	A
7	385495	A	C
7	385519	T	C
7	385522	G	T
7	385525	A	G
7	385531	C	T
7	385540	A	G
7	385542	T	C
7	385555	C	A
7	385570	T	C
7	385619	C	T
7	385714	C	T
7	386557	A	C
7	386581	G	A
7	386593	C	T
7	386596	C	T
7	386599	C	T
7	386608	G	A
7	386978	C	G
7	386979	G	C
7	387977	T	C
7	389105	G	A
7	390472	C	G
7	390484	A	T
7	391186	T	C
7	391249	G	A
7	391279	A	G
7	395239	A	G
7	395241	C	G
7	395359	C	T
7	395608	G	T
7	395717	G	C
7	396269	A	G
7	396452	A	G
7	396575	T	C
7	396581	C	T
7	397322	A	G
7	397325	T	C
7	397586	T	C
7	398081	A	G
7	398572	G	A
7	401475	A	G
7	405892	T	C
7	406503	C	T
7	406558	G	C
7	407307	A	G
7	408003	C	T
7	408708	G	A
7	408709	A	C
7	408716	C	G
7	409654	G	A
7	409886	C	G
7	410080	G	A
7	410294	A	G
7	410420	C	T
7	410453	T	C
7	410531	G	A
7	411573	G	A
7	411574	C	T
7	411689	G	A
7	411698	A	G
7	411737	C	T
7	411842	T	C
7	411857	G	A
7	411962	A	G
7	412161	T	G
7	412167	A	T
7	412395	A	C
7	412398	G	T
7	412850	A	G
7	412992	C	T
7	413040	C	G
7	413298	C	T
7	413440	C	T
7	413612	C	G
7	413660	T	G
7	413728	C	G
7	413797	C	T
7	414265	G	A
7	414479	C	T
7	414527	C	T
7	414653	G	A
7	414724	C	T
7	414752	T	C
7	415307	G	A
7	415371	G	T
7	417363	G	A
7	417671	A	G
7	418253	G	A
7	418292	A	T
7	421036	C	T
7	421865	A	G
7	421889	T	C
7	421943	A	G
7	421962	G	A
7	422059	T	G
7	422613	G	A
7	422836	T	A
7	422862	T	A
7	423339	C	T
7	423906	G	A
7	424327	A	T
7	424338	A	G
7	424620	C	T
7	424652	A	C
7	424942	A	T
7	424971	T	A
7	425181	C	G
7	425227	G	C
7	425322	A	G
7	425446	A	C
7	425755	G	A
7	425869	G	A
7	426136	C	T
7	426148	A	G
7	426538	G	T
7	426675	T	C
7	427600	A	G
7	427741	G	A
7	428152	A	G
7	428325	C	G
7	428363	G	A
7	428397	T	C
7	428441	T	G
7	428542	C	G
7	428698	A	T
7	428728	T	A
7	428729	T	C
7	429150	G	C
7	430810	T	C
7	430867	G	A
7	431116	T	C
7	431867	A	G
7	432654	G	A
7	432913	C	A
7	432925	A	T
7	432934	A	G
7	433212	G	A
7	433234	A	G
7	433416	T	A
7	434259	T	C
7	434380	G	T
7	434403	A	G
7	434442	A	G
7	434447	A	G
7	434580	G	A
7	434603	T	C
7	434630	A	G
7	434654	G	A
7	434720	A	C
7	434752	C	G
7	434758	C	A
7	434905	G	A
7	435041	G	C
7	435126	T	C
7	435682	T	C
7	436601	C	T
7	436605	T	C
7	436774	T	C
7	438009	G	T
7	438031	A	G
7	438069	A	T
7	438333	G	T
7	438567	T	C
7	438674	A	G
7	438728	A	T
7	438750	C	A
7	438803	T	A
7	439277	C	T
7	440693	T	A
7	441362	T	C
7	442557	G	T
7	445967	C	T
7	446000	T	C
7	446059	T	C
7	446068	C	T
7	446382	A	G
7	446904	A	G
7	446910	G	A
7	447534	G	A
7	447761	G	C
7	447987	A	G
7	448106	T	C
7	448116	G	A
7	448538	T	C
7	449525	C	T
7	450623	C	G
7	451307	A	G
7	451921	T	C
7	452296	A	C
7	452571	A	G
7	452796	C	T
7	453315	G	C
7	453554	A	G
7	455013	G	A
7	457721	G	A
7	459620	G	A
7	460218	C	G
7	460330	T	C
7	461146	A	G
7	461302	G	A
7	461875	G	A
7	463837	A	G
7	467387	T	C
7	467473	A	G
7	469537	G	A
7	473951	G	T
7	476076	A	G
7	476182	A	C
7	485256	A	G
7	485293	T	C
7	485421	A	G
7	485424	T	C
7	490539	C	G
7	493773	T	C
7	525947	A	G
7	526684	T	C
7	527159	A	G
7	527390	T	G
7	527396	T	C
7	527439	C	G
7	527673	C	T
7	528447	A	C
7	528489	C	T
7	528501	T	C
7	528596	A	T
7	528828	C	T
7	528861	A	G
7	529248	T	C
7	529347	A	T
7	529378	G	A
7	529383	A	G
7	529630	A	G
7	529644	A	T
7	529824	C	G
7	530308	A	G
7	530805	A	T
7	531322	G	A
7	531431	G	A
7	531684	A	T
7	531741	A	C
7	534162	A	G
7	541809	C	T
7	543805	G	A
7	546126	C	T
7	546392	G	A
7	546403	A	G
7	546446	G	T
7	546714	A	G
7	549148	T	C
7	551329	G	T
7	551439	A	G
7	554539	C	T
7	554830	G	A
7	554853	T	C
7	556902	C	T
7	557736	G	A
7	561645	G	A
7	561747	G	T
7	561780	A	G
7	561784	G	A
7	575955	C	T
7	576078	A	G
7	576519	T	C
7	576592	A	G
7	576820	C	G
7	577533	A	C
7	577801	A	G
7	577881	A	G
7	577893	G	A
7	578083	T	A
7	578218	T	A
7	578231	G	A
7	578265	G	A
7	578356	G	A
7	578379	G	A
7	578422	A	G
7	578448	G	A
7	578512	C	T
7	578520	C	A
7	579120	T	C
7	579190	A	C
7	579227	G	A
7	579280	G	A
7	579473	A	G
7	579474	G	C
7	579508	A	G
7	579785	T	A
7	579795	A	G
7	579802	G	T
7	579827	T	C
7	579860	A	T
7	579915	C	T
7	580060	G	A
7	580103	G	A
7	580178	G	T
7	580283	G	A
7	580425	C	G
7	580852	A	G
7	581134	G	C
7	581206	A	G
7	581386	T	G
7	581392	A	G
7	581814	A	G
7	583389	A	T
7	583808	G	A
7	583953	G	A
7	584037	G	A
7	584220	C	T
7	584298	T	C
7	584388	G	C
7	584683	C	G
7	584900	A	G
7	584916	G	A
7	585274	T	C
7	598162	C	T
7	620815	A	G
7	622738	C	T
7	622800	C	A
7	628050	G	T
7	628417	T	C
7	628549	C	T
7	628627	C	T
7	628640	A	C
7	628754	T	C
7	628958	T	A
7	629998	C	T
7	630128	A	G
7	630261	T	A
7	630340	C	G
7	635431	G	A
7	637449	C	T
7	637458	A	G
7	638787	T	C
7	638835	C	T
7	638846	A	T
7	638935	A	G
7	639017	C	T
7	639331	T	C
7	639460	C	T
7	639715	T	C
7	639762	T	A
7	639768	C	T
7	640786	T	C
7	640992	C	G
7	641220	T	C
7	642042	A	G
7	642145	G	A
7	642162	G	A
7	642168	A	G
7	642227	A	C
7	642373	T	C
7	642480	A	G
7	642577	C	T
7	642606	A	T
7	642633	C	T
7	642723	T	C
7	642915	T	C
7	643548	G	C
7	643560	T	C
7	643620	T	G
7	643727	A	G
7	643743	A	G
7	644097	A	T
7	645955	C	T
7	645958	G	T
7	646047	T	C
7	646177	T	C
7	646871	A	G
7	647261	A	G
7	647350	C	G
7	647545	C	T
7	647660	T	C
7	648077	T	G
7	648107	T	C
7	648788	T	C
7	649667	A	G
7	649985	C	T
7	650252	A	G
7	651108	A	G
7	651370	G	A
7	651434	A	G
7	651771	G	T
7	654010	A	G
7	654308	A	T
7	654783	T	C
7	656248	T	G
7	656413	G	T
7	657546	T	C
7	659437	T	C
7	660120	G	A
7	668528	C	T
7	672625	C	G
7	672695	G	A
7	673934	T	C
7	674123	G	A
7	674153	C	A
7	674888	T	C
7	675020	T	C
7	675722	T	A
7	676517	G	A
7	677274	T	C
7	677484	G	A
7	678429	C	T
7	678454	T	A
7	678805	G	A
7	678853	T	C
7	678864	T	C
7	679471	C	T
7	679705	T	C
7	679731	C	A
7	679750	A	G
7	680542	T	C
7	680929	T	C
7	680935	A	G
7	681411	T	C
7	681706	C	T
7	681775	C	T
7	684022	A	G
7	687872	C	T
7	688726	C	T
7	688768	T	C
7	689389	G	A
7	689452	G	A
7	689454	A	G
7	689803	C	T
7	689812	A	G
7	689896	C	T
7	689948	T	C
7	690039	G	C
7	690131	C	T
7	691114	G	A
7	691862	T	C
7	701026	T	G
7	702776	C	T
7	702790	A	C
7	702791	C	T
7	988274	C	T
8	84663	C	G
8	84686	A	G
8	84687	T	C
8	84699	A	G
8	84708	G	A
8	84777	A	C
8	84820	A	G
8	84829	T	C
8	84910	T	C
8	84920	C	T
8	85001	T	C
8	85218	C	G
8	92232	C	T
8	92608	G	A
8	92658	A	G
8	92677	T	A
8	92692	T	G
8	92694	G	A
8	92759	A	C
8	92914	C	A
8	92927	G	T
8	92971	T	C
8	92978	C	G
8	95092	A	G
8	95107	G	A
8	95292	G	A
8	95322	C	T
8	95481	C	A
8	95871	G	A
8	96126	A	G
8	96393	C	T
8	96628	C	T
8	96654	T	A
8	96942	G	C
8	120946	T	C
8	122053	C	T
8	191072	T	C
8	192080	C	T
8	207134	G	A
8	380512	T	C
8	380673	A	G
8	380685	A	G
8	381790	T	C
8	382788	T	C
8	382813	C	T
8	382878	T	C
8	382967	G	A
8	383024	G	A
8	383029	A	G
8	383035	G	A
8	383037	C	T
8	383055	C	A
8	383077	T	A
8	383114	A	C
8	383160	G	A
8	383194	G	A
8	383825	T	C
8	384317	T	C
8	386000	C	T
8	387439	T	C
8	387771	G	A
8	387812	T	C
8	387848	A	G
8	388103	T	C
8	388130	G	A
8	388214	G	C
8	388271	C	T
8	388791	C	A
8	388948	G	T
8	388949	G	T
8	390446	G	A
8	390561	T	C
8	390900	C	T
8	391205	T	A
8	391307	G	A
8	391559	G	A
8	391599	C	T
8	393725	A	G
8	393734	T	C
8	394179	A	G
8	394728	A	G
8	394731	G	A
8	394959	G	A
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8	395164	T	C
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8	395310	C	A
8	395453	T	C
8	396288	A	T
8	396423	C	T
8	396474	T	C
8	396631	A	G
8	397561	C	T
8	397787	A	G
8	397848	G	A
8	398618	C	T
8	398985	G	A
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8	399484	T	G
8	399595	A	T
8	399862	A	G
8	400069	A	G
8	400618	C	T
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8	401408	C	T
8	401484	G	A
8	402478	T	C
8	402964	C	T
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8	403151	C	A
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8	408482	A	G
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8	410162	T	C
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8	415310	T	C
8	415439	G	A
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8	417907	A	G
8	421507	T	C
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8	422992	A	G
8	423389	T	C
8	423669	G	A
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8	424239	C	T
8	424817	G	A
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8	426290	T	A
8	427588	C	T
8	428194	T	C
8	428738	G	A
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8	430583	T	C
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8	435329	T	C
8	435482	A	G
8	436433	A	G
8	436457	A	G
8	436613	T	C
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8	437014	G	T
8	437680	G	A
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8	439062	C	T
8	439450	T	C
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8	440150	G	A
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8	440255	T	C
8	440682	C	T
8	441833	A	G
8	442603	T	C
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8	443404	A	G
8	443899	C	G
8	444367	A	G
8	444691	G	A
8	444788	C	T
8	444841	T	A
8	444931	T	C
8	445169	T	C
8	447036	A	T
8	447550	G	A
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8	449954	G	A
8	449957	A	G
8	450131	G	A
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8	451932	C	T
8	452163	A	G
8	452436	T	C
9	269954	C	T
9	308815	C	A
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9	310160	T	C
9	310171	A	G
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9	310412	G	C
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9	311108	T	C
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9	311545	A	G
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9	312474	A	G
9	312591	A	T
9	312613	A	T
9	318694	T	A
9	323727	C	A
9	323976	A	G
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9	328196	C	T
9	328585	T	C
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9	332541	A	G
9	332714	G	A
9	332903	C	T
9	332947	C	A
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9	333667	G	A
9	333801	A	G
9	333942	T	C
10	97478	G	A
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10	272847	T	C
10	273266	T	C
10	275952	G	A
10	277623	T	C
10	277760	C	T
10	279703	G	A
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10	281003	T	C
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10	285461	C	G
10	288319	A	G
10	288468	A	T
10	288609	G	A
10	290553	G	A
10	290872	T	C
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10	292038	G	A
10	292616	T	C
10	292713	A	G
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10	294951	T	G
10	296106	A	T
10	296872	T	A
10	297043	T	C
10	297732	T	G
10	297976	C	T
10	392346	G	A
10	484997	A	G
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10	485447	G	A
10	486166	A	G
10	486193	C	T
10	486703	T	C
10	486724	A	G
10	487716	T	G
10	487992	A	G
10	488152	A	G
10	488230	T	C
10	488782	T	C
10	489978	C	G
10	491340	C	T
10	491395	C	T
10	492486	A	C
10	492678	T	C
10	493119	C	T
10	494940	A	G
10	494949	C	A
10	494994	C	G
10	495112	T	A
10	495458	G	A
10	496029	T	C
10	497589	A	G
10	497615	T	C
10	497765	C	T
10	497879	A	G
10	497985	G	C
10	498149	A	G
10	498362	C	T
10	498452	G	T
10	500159	G	A
10	500192	A	G
10	502139	G	C
10	502260	G	T
10	502798	T	C
10	502945	C	T
10	503779	A	G
10	503880	G	C
10	504074	G	A
10	504158	A	G
10	504709	T	C
10	505510	G	A
10	505992	G	A
10	506929	C	T
10	507730	A	G
10	507782	G	A
10	508366	C	G
10	508525	G	A
10	508529	A	C
10	508627	T	C
10	508859	C	T
10	509110	G	A
10	509235	C	T
10	509746	C	T
10	510871	G	A
10	510914	G	A
10	511529	C	T
10	513874	A	G
10	514320	A	G
10	514422	T	C
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10	515450	C	T
10	516370	T	G
10	516436	G	A
10	516605	G	A
10	516609	C	G
10	516694	A	G
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10	516707	C	T
10	516847	T	C
10	517094	A	G
10	517900	T	C
10	517926	G	C
10	520853	C	T
10	520988	T	C
10	521432	G	A
10	521645	T	G
10	522284	T	C
10	522481	C	G
10	522484	C	T
10	522503	G	A
10	522608	T	C
10	522848	T	C
10	523142	C	T
10	523349	G	A
10	523373	C	T
10	524213	T	C
10	524254	A	C
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10	524370	T	C
10	524384	T	C
10	524404	G	A
10	524412	C	T
10	524435	C	T
10	576458	T	C
10	576551	C	T
10	576835	C	A
10	577387	A	G
10	577591	C	T
10	577732	G	A
10	588031	C	T
10	622799	A	G
10	622874	G	A
10	623040	T	C
10	623184	C	G
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10	623380	G	A
10	623961	C	T
10	624129	G	A
10	624402	A	G
10	624405	T	C
10	627942	G	A
10	627948	G	A
10	628044	T	C
10	628048	G	A
10	628623	T	C
10	628891	C	T
10	629035	G	A
10	629082	A	G
10	629091	T	C
10	629098	G	C
10	630149	A	T
10	630373	A	G
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10	630494	C	T
10	630716	C	T
10	630728	A	C
10	631978	A	G
10	645822	A	C
10	646018	A	C
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10	646496	T	C
10	646622	T	C
10	646793	C	A
10	647196	C	T
10	647307	T	G
10	648431	T	C
10	648461	G	A
10	649802	T	G
10	650201	T	C
10	651638	T	C
10	652362	T	C
10	653755	T	C
10	653843	A	G
10	655251	T	C
10	655475	C	T
10	656567	C	T
10	657858	A	G
10	658223	A	C
10	658561	G	A
10	659016	C	T
10	659384	T	A
10	659425	T	C
10	660402	A	G
10	660487	A	G
10	660546	C	T
10	660786	G	A
10	661626	T	C
10	662248	A	G
10	662262	T	C
10	662293	G	A
10	662347	G	T
10	662479	A	G
10	663082	A	G
10	663083	A	G
10	663098	A	G
10	663253	G	C
10	663261	T	G
10	663511	T	C
10	663564	A	G
10	663590	A	C
10	663968	T	A
10	663993	A	T
10	664024	C	T
10	664087	G	A
10	664236	C	T
10	664330	T	C
10	664516	T	C
10	664569	G	C
10	664824	A	G
10	664854	C	T
10	665027	T	C
10	665076	C	T
10	665087	T	G
10	666046	T	C
10	666422	C	T
10	666427	G	A
10	666523	T	C
10	666742	T	G
10	671070	G	A
10	671429	C	T
10	672566	C	T
10	673954	A	G
10	679537	G	T
10	681606	T	C
10	682740	T	C
10	682752	A	G
10	682784	A	T
10	683975	T	C
10	684785	T	C
10	685862	T	C
10	685982	T	C
10	690730	C	A
10	690731	A	T
10	690963	G	T
10	691035	T	A
10	691354	T	C
10	691681	T	C
10	691772	C	T
10	692082	A	G
10	692544	T	G
10	693120	C	T
10	693187	T	C
10	700864	T	A
10	701165	T	G
10	701241	T	A
10	701326	C	T
10	701478	C	T
10	701906	T	C
10	701912	G	A
10	701944	C	G
10	702420	T	C
10	702597	C	A
10	702874	G	A
10	703226	G	A
10	703327	G	A
10	703332	T	C
10	703339	A	G
10	703431	C	A
10	703467	C	A
10	703814	C	T
10	703858	G	A
10	703893	C	T
10	704056	G	A
10	704310	C	T
10	704419	A	G
10	704425	G	A
10	704426	C	A
10	704499	G	A
10	704535	G	A
10	704699	G	A
10	704768	C	G
10	704987	G	A
10	704992	T	C
10	704998	C	T
10	705014	T	C
10	706135	G	A
10	706547	A	G
10	706608	A	T
10	707018	G	A
10	707070	C	T
10	707089	G	A
10	707205	T	C
10	707333	C	T
10	708844	A	G
10	708946	T	C
10	709369	C	T
10	709489	A	G
10	709498	C	G
10	709864	C	T
10	710013	A	G
10	710105	A	G
10	718630	G	A
10	719442	A	T
10	720758	T	C
11	68015	G	A
11	258873	A	G
11	259465	T	C
11	259468	T	C
11	259516	T	C
11	259792	G	A
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11	260129	T	C
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11	260245	A	C
11	260628	T	C
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11	261359	T	C
11	262136	C	A
11	262375	C	G
11	262447	T	C
11	263019	A	C
11	263873	A	G
11	264213	G	A
11	264216	A	G
11	264611	T	G
11	264824	T	C
11	264974	C	T
11	265405	G	C
11	270096	T	C
11	270178	G	C
11	270231	A	G
11	272740	A	C
11	272747	T	G
11	273028	A	G
11	276020	T	C
11	276092	G	A
11	276098	G	A
11	276123	C	T
11	276368	C	T
11	276446	G	A
11	276842	A	G
11	276922	T	A
11	277106	T	C
11	555881	A	C
12	93501	G	A
12	291384	A	G
12	291386	A	G
12	291459	T	C
12	292618	G	C
12	294637	G	A
12	295045	C	T
12	295063	A	G
12	295222	C	T
12	295250	T	C
12	295292	C	T
12	295360	C	T
12	296854	T	A
12	297011	A	T
12	297445	G	C
12	297969	G	C
12	298893	C	T
12	299037	A	G
12	299174	A	G
12	299315	G	T
12	299526	A	C
12	299532	A	G
12	300946	A	G
12	301291	G	A
12	301570	G	A
12	302139	T	C
12	302144	T	C
12	302154	C	T
12	302196	C	G
12	302440	A	G
12	302717	C	T
12	302719	A	G
12	302764	A	T
12	303487	C	A
12	303795	A	G
12	304035	A	G
12	304128	C	T
12	304243	G	A
12	304381	A	G
12	304435	A	G
12	305296	C	T
12	305324	G	A
12	305360	A	T
12	305835	A	G
12	306910	T	C
12	308322	G	A
12	308379	C	T
12	308630	G	A
12	308703	T	C
12	308802	C	T
12	310443	T	C
12	310626	C	T
12	310695	C	T
12	310980	A	G
12	310983	T	C
12	311181	G	A
12	311493	C	T
12	312972	T	C
12	312984	T	A
12	313107	T	G
12	313195	G	A
12	313374	T	C
12	316628	T	C
12	316874	T	C
12	318348	A	G
12	318498	A	G
12	319560	G	A
12	319635	A	G
12	320465	C	T
12	320691	G	A
12	320799	C	T
12	321057	T	G
12	321084	C	T
12	321555	C	T
12	321772	T	C
12	322181	G	A
12	322198	C	T
12	322259	C	T
12	322263	C	G
12	322264	T	C
12	322494	A	G
12	322740	G	A
12	322753	A	G
12	322903	G	A
12	323467	G	A
12	323543	T	C
12	323570	T	A
12	324449	C	T
12	324470	G	A
12	324662	A	G
12	324710	A	G
12	326975	C	T
12	327075	G	A
12	328246	T	C
12	328306	C	A
12	328498	C	T
12	328525	A	G
12	328528	A	G
12	329551	G	C
12	329556	A	T
12	329557	T	C
12	329680	G	A
12	334170	A	G
12	334208	G	A
12	334635	A	G
12	335245	G	C
12	338988	C	T
12	339159	A	G
12	339318	C	T
12	340119	C	T
12	340365	A	G
12	340551	A	C
12	340584	T	C
12	340602	A	G
12	340616	A	G
12	340695	T	C
12	340821	T	C
12	341507	C	A
12	341678	G	A
12	341688	T	A
12	341926	T	G
12	341974	T	C
12	342190	A	G
12	342295	T	C
12	342331	T	C
12	342421	C	T
12	342448	T	C
12	342508	C	T
12	342533	G	A
12	343120	G	A
12	343396	C	T
12	344475	C	T
12	344847	T	C
12	344859	C	T
12	345102	T	C
12	345204	T	C
12	345249	A	G
12	345286	T	C
12	345295	C	T
12	345397	T	C
12	346533	C	G
12	346553	C	T
12	346554	C	T
12	346565	C	A
12	346884	T	G
12	347086	T	C
12	347194	C	T
12	347536	T	G
12	347880	G	A
12	347911	C	T
12	348136	A	G
12	349585	A	G
12	349651	A	G
12	349899	G	A
12	350013	T	C
12	350281	T	C
12	350793	C	T
12	350795	G	A
12	350799	C	T
12	350896	G	A
12	351004	A	G
12	351127	C	T
12	351600	G	C
12	351683	A	G
12	352492	C	T
12	352942	C	T
12	353555	G	T
12	354979	A	G
12	355027	C	T
12	355082	C	T
12	355284	G	A
12	356647	A	G
12	357508	C	G
12	357535	A	G
12	357577	C	T
12	357639	C	T
12	357640	A	G
12	357940	T	C
12	358096	C	T
12	358302	A	G
12	358692	C	T
12	359296	T	C
12	360439	C	G
12	360526	A	G
12	360772	A	G
12	360970	G	A
12	361819	A	G
12	361865	A	G
12	362782	G	A
12	363207	G	A
12	364096	T	C
12	364406	T	C
12	364410	C	T
12	364505	A	G
12	364537	A	G
12	364596	T	A
12	364787	G	T
12	366194	T	C
12	367545	T	C
12	368770	C	T
12	368772	C	T
12	369062	G	A
12	369632	A	G
12	370629	C	G
12	371874	T	A
12	372213	C	G
12	372265	T	C
12	372291	C	T
12	372303	C	T
12	372524	C	T
12	372738	A	G
12	374970	A	T
12	375089	G	C
12	375126	T	C
12	375154	A	G
12	375438	T	C
12	375556	T	C
12	375574	T	G
12	375697	G	A
12	375724	C	T
12	375813	G	A
12	376012	C	T
12	376222	C	T
12	376303	G	A
12	376900	A	G
12	376993	C	G
12	377350	A	C
12	377477	C	T
12	377512	C	T
12	377522	G	T
12	377564	T	C
12	377594	T	C
12	377619	T	G
12	377629	A	G
12	377691	A	G
12	377739	A	G
12	378020	A	C
12	378221	G	C
12	378260	T	C
12	378437	A	G
12	379144	A	G
12	379786	G	C
12	379794	A	G
12	379874	T	G
12	379914	A	G
12	380028	G	A
12	380114	A	G
12	380294	G	A
12	380306	C	G
12	381370	G	C
12	381754	C	T
12	382560	T	C
12	382590	T	C
12	382614	C	T
12	383695	G	A
12	383932	T	C
12	384348	G	A
12	384511	G	A
12	386266	A	G
12	386351	G	A
12	386700	G	A
12	387140	A	G
12	387438	A	G
12	387636	C	G
12	388273	T	C
12	388456	C	T
12	528749	T	A
12	577073	G	A
12	577535	C	T
12	577607	C	G
12	580245	T	C
12	581598	A	G
12	582374	C	T
12	583188	C	A
12	583193	A	C
12	583195	A	C
12	583697	T	C
12	583763	T	G
12	584675	G	A
12	585608	T	G
12	586054	A	G
12	586124	G	A
12	586255	T	C
12	586284	C	T
12	586954	G	A
12	587297	G	A
12	587519	T	C
12	588163	C	T
12	589339	T	C
12	592315	A	G
12	592353	G	A
12	600445	T	G
12	600547	C	T
12	600676	A	G
12	601307	A	G
12	601489	A	G
12	601888	A	G
12	601934	C	T
12	602186	A	G
12	602932	A	G
12	603075	G	T
12	603216	A	T
12	603313	C	G
12	603319	A	G
12	603325	C	T
12	603566	A	G
12	603584	T	A
12	603646	T	A
12	603667	T	C
12	603907	C	A
12	604223	C	T
12	658158	G	C
12	658599	G	T
12	659350	C	T
12	659470	A	T
12	660046	T	C
12	660194	A	G
12	660357	C	T
12	660371	C	T
12	660472	G	A
12	660622	A	T
12	660916	A	G
12	661444	G	A
12	661750	C	T
12	661864	T	C
12	661927	A	G
12	662311	T	C
12	662318	G	T
12	662353	G	A
12	662494	C	G
12	662515	G	A
12	662627	T	C
12	662864	A	T
12	663017	T	C
12	663332	G	A
12	663368	A	G
12	663890	T	C
12	664157	A	G
12	664658	G	A
12	665159	G	A
12	665216	G	A
12	665756	T	G
12	666395	T	C
12	666935	A	G
12	667631	T	A
12	667773	C	T
12	667877	T	C
12	668207	G	C
12	668241	G	A
12	668244	C	T
12	668550	G	A
12	669897	C	A
12	669990	T	A
12	669994	G	A
12	670009	T	A
12	670061	C	G
12	670460	C	G
12	671669	G	A
12	671703	A	G
12	671956	A	C
12	672242	G	A
12	672265	A	G
12	672293	A	G
12	672355	G	C
12	672394	C	T
12	673274	T	C
12	674152	A	G
12	676885	G	A
12	676925	G	C
12	676937	T	C
12	677005	A	G
12	677164	A	G
12	677323	A	G
12	677675	G	A
12	677699	T	G
12	677814	T	C
12	677900	T	C
12	677991	G	A
12	678096	T	C
12	678531	C	T
12	678619	C	T
12	678645	T	C
12	679276	C	T
12	679600	C	T
12	680159	C	T
12	680346	T	C
12	680364	C	T
12	680926	G	A
12	680974	A	G
12	681097	T	C
12	681851	A	G
12	682830	G	A
12	682839	C	A
12	684068	T	G
12	684785	G	A
12	685853	T	C
12	686000	C	T
12	686213	G	A
12	686785	G	A
12	686789	G	A
12	689157	C	T
12	689216	G	T
12	689502	G	C
12	689626	T	C
12	689719	G	A
12	689793	A	G
12	690766	C	T
12	690899	G	A
12	692970	C	T
12	693006	A	G
12	693579	A	G
12	695163	A	G
12	698705	T	C
12	698944	G	A
12	700764	C	T
12	701320	T	C
12	701704	T	C
12	701793	A	T
12	702363	G	A
12	702384	T	C
12	702786	T	C
12	702788	G	A
12	703275	T	G
12	703329	G	C
12	703527	C	T
12	703539	T	A
12	703572	G	A
12	703659	G	A
12	704656	G	A
12	704793	A	G
12	704929	C	T
12	706112	T	C
12	706747	G	A
12	706756	T	C
12	706780	A	G
12	706789	A	G
12	706807	G	A
12	707644	A	G
12	707758	T	A
12	708185	G	A
12	708755	G	T
12	708796	C	T
12	708814	A	T
12	708837	T	G
12	708840	G	A
12	708942	A	C
12	708955	C	T
12	709175	G	C
12	709384	A	G
12	709879	G	A
12	710056	T	C
12	710068	C	A
12	710283	T	G
12	710871	G	A
12	710894	C	G
12	711837	T	G
12	713420	C	G
12	713479	T	C
12	713543	A	C
12	713644	A	G
12	713693	G	C
12	713843	T	C
12	714002	G	A
12	714020	G	A
12	714062	A	G
12	714134	A	G
12	714158	A	G
12	714185	G	A
12	714200	C	T
12	714302	G	A
12	714320	G	T
12	714379	T	C
12	714407	A	G
12	714439	G	A
12	714546	G	A
12	714587	C	T
12	715595	A	G
12	715772	G	T
12	716177	C	T
12	716369	G	A
12	716594	T	C
12	716777	G	A
12	717181	T	C
12	718521	T	C
12	718821	T	C
12	718896	G	A
12	719036	T	C
12	719400	G	A
12	719436	T	C
12	719509	T	C
12	719618	A	G
12	719910	C	T
12	721257	G	A
12	721788	C	T
12	721984	G	A
12	722079	A	T
12	722344	C	G
12	722380	T	C
12	722447	T	C
12	722471	T	A
12	722593	T	C
12	722699	G	A
12	723252	G	A
12	723283	G	C
12	723290	A	G
12	723319	T	G
12	723329	A	G
12	723330	A	G
12	723342	C	T
12	723355	T	C
12	723463	T	C
12	723618	T	G
12	723739	T	C
12	724534	A	G
12	725538	C	T
12	725542	A	G
12	725578	T	C
12	725584	G	C
12	725693	A	T
12	725936	G	A
12	726161	C	G
12	726449	G	A
12	726580	A	G
12	729938	C	T
12	729962	T	C
12	730685	C	T
12	730719	C	A
12	730778	G	A
12	731012	C	T
12	734157	A	T
12	736154	G	A
12	736352	A	G
12	736586	G	A
12	736757	G	A
12	738097	G	C
12	738125	T	C
12	738353	A	G
12	738992	C	T
12	739051	T	C
12	739067	A	G
12	739624	T	C
12	740250	C	G
12	741197	T	C
12	741422	G	A
12	741983	G	A
12	743135	A	G
12	743183	G	A
12	743189	C	T
12	743204	A	G
12	744416	A	G
12	744446	T	C
12	744566	A	T
12	746036	G	A
12	747505	T	C
12	747982	C	T
12	748236	G	A
12	748416	A	T
12	748497	T	A
12	748572	A	G
12	749284	C	G
12	749673	G	C
12	749793	A	G
12	749934	A	G
12	750485	G	A
12	750621	C	T
12	753079	G	A
12	754651	G	A
12	754945	T	C
12	755191	A	G
12	755968	C	T
12	756553	T	G
12	756805	T	A
12	757020	C	T
12	757068	T	C
12	757090	A	G
12	757367	A	G
12	757576	C	A
12	757763	C	T
12	757817	C	G
12	758057	A	G
12	758099	T	C
12	758492	C	G
12	758524	C	T
12	758853	C	T
12	758959	A	G
12	759015	A	G
12	759162	A	G
12	759216	G	A
12	759268	A	G
12	759438	A	G
12	759458	A	C
12	759842	T	C
12	759860	T	C
12	759872	G	A
12	759887	G	A
12	759985	A	G
12	760502	C	A
12	760719	A	T
12	761014	T	A
12	761052	C	T
12	761145	C	T
12	761210	G	A
12	761214	C	T
12	761396	G	A
12	761425	C	T
12	762058	T	C
12	763412	T	C
12	763666	C	A
12	763742	C	T
12	764339	A	G
12	764398	A	G
12	764614	A	G
12	764623	T	C
12	764781	A	C
12	764796	T	A
12	765047	A	G
12	765566	A	G
12	765605	G	A
12	765881	A	C
12	765920	A	G
12	765921	C	T
12	765944	A	G
12	765971	A	G
12	765989	G	A
12	766006	C	T
12	766039	C	T
12	766116	A	T
12	768623	A	G
12	768836	T	C
12	769226	T	C
12	769460	C	G
12	769888	A	G
12	770182	T	C
12	770488	T	G
12	770630	G	A
12	770790	A	G
12	770842	A	T
12	770846	G	A
12	770890	T	A
12	775104	T	C
12	828903	C	T
13	10234	C	T
13	10239	T	C
13	10479	T	C
13	10737	C	T
13	10791	C	T
13	12215	T	C
13	12730	G	A
13	12902	T	G
13	13034	G	A
13	13064	A	G
13	14478	G	C
13	14530	G	C
13	14562	A	G
13	14580	A	G
13	14705	G	A
13	14781	C	A
13	14933	C	A
13	14934	G	T
13	15357	A	G
13	15621	T	C
13	16224	T	C
13	16287	G	A
13	16314	C	T
13	16338	G	A
13	16368	T	C
13	16406	G	A
13	16418	T	C
13	16434	A	G
13	16498	G	T
13	16764	G	A
13	17038	T	C
13	17247	C	T
13	17462	T	C
13	17648	T	C
13	17660	T	C
13	17663	A	C
13	17810	C	T
13	17843	T	A
13	17955	T	G
13	18546	C	T
13	18729	C	T
13	19498	A	G
13	20313	A	G
13	20392	A	G
13	20497	T	C
13	20971	T	C
13	21082	C	T
13	21105	T	C
13	21163	A	G
13	21175	A	G
13	21253	G	A
13	21331	G	A
13	21391	A	G
13	21496	A	G
13	21523	A	G
13	21525	A	T
13	21547	C	T
13	21607	T	C
13	21881	C	G
13	22495	G	A
13	22768	A	G
13	22888	G	A
13	22939	A	G
13	22987	T	C
13	23203	T	C
13	23573	C	T
13	23630	A	C
13	23707	G	A
13	23743	A	G
13	24034	C	T
13	24106	C	G
13	24134	A	T
13	24474	G	T
13	24556	T	G
13	24568	G	A
13	24592	T	C
13	24595	T	C
13	24637	A	G
13	24712	C	A
13	24775	C	T
13	24787	A	G
13	24997	T	C
13	25021	C	A
13	25025	A	G
13	25114	T	A
13	25168	G	A
13	25294	A	G
13	26166	A	G
13	26434	G	A
13	26922	A	C
13	28623	T	C
13	28695	C	T
13	28764	A	T
13	29616	T	A
13	29721	C	T
13	29826	C	T
13	29994	T	G
13	30379	T	A
13	30523	C	T
13	30827	A	G
13	30836	G	A
13	31110	C	T
13	31154	A	G
13	31428	C	T
13	33899	A	G
13	34473	T	G
13	34722	T	C
13	35559	C	G
13	35592	T	C
13	36081	A	G
13	36176	C	T
13	36261	G	A
13	36440	T	C
13	36544	T	C
13	37053	T	C
13	38034	T	A
13	38146	T	C
13	38372	A	T
13	39077	G	A
13	39858	T	C
13	40370	C	A
13	40376	C	A
13	40487	T	C
13	40511	G	A
13	40689	C	G
13	41051	G	T
13	42835	G	A
13	43165	A	G
13	43624	T	G
13	45053	T	C
13	45364	A	C
13	45908	T	C
13	46211	C	T
13	46228	G	A
13	46331	A	G
13	47907	A	G
13	48814	A	G
13	48846	A	G
13	49008	A	T
13	50514	T	A
13	50831	C	T
13	50890	C	A
13	50955	T	G
13	51256	C	T
13	51358	G	T
13	51433	G	A
13	51596	A	G
13	51951	T	A
13	52335	G	A
13	52926	C	A
13	53026	A	G
13	53052	T	C
13	53073	A	G
13	53227	G	C
13	53276	C	G
13	53532	G	A
13	53537	T	C
13	53544	G	C
13	53642	A	G
13	53825	C	A
13	53841	A	G
13	54136	T	C
13	54916	A	G
13	55344	C	T
13	55558	A	G
13	55582	A	G
13	56231	A	G
13	57144	G	A
13	58847	T	G
13	59037	C	G
13	59135	C	T
13	60420	G	C
13	62513	A	C
13	62630	G	T
13	63905	C	T
13	64972	C	A
13	68826	T	C
13	69109	C	G
13	69113	A	G
13	70163	A	G
13	70356	C	T
13	71137	A	G
13	71382	T	C
13	71390	A	C
13	71397	T	C
13	71867	A	T
13	72351	C	A
13	73368	G	A
13	73993	C	T
13	74014	C	T
13	74436	C	T
13	74632	C	T
13	74704	A	G
13	75133	G	A
13	75304	T	C
13	76194	A	C
13	77030	G	A
13	77482	C	T
13	77676	C	G
13	77679	C	T
13	77739	G	C
13	77796	C	A
13	77879	T	G
13	78097	A	G
13	78101	T	C
13	78103	A	G
13	78125	C	T
13	78446	T	A
13	78710	A	C
13	78749	T	A
13	78777	T	C
13	78836	A	G
13	78839	G	A
13	79783	T	C
13	79948	T	C
13	80160	C	T
13	80220	G	A
13	80403	T	C
13	82027	A	G
13	82308	T	A
13	83404	G	A
13	83417	C	A
13	83860	T	C
13	83964	G	A
13	84058	C	T
13	84059	G	T
13	84233	T	C
13	84712	C	T
13	84896	A	C
13	86512	G	A
13	87318	T	C
13	87357	A	G
13	87360	T	C
13	89649	T	A
13	89691	A	G
13	89860	C	T
13	89876	C	T
13	90833	G	C
13	91086	A	G
13	91149	G	A
13	91448	A	G
13	91485	G	A
13	91527	A	G
13	91532	T	C
13	91587	G	A
13	91597	G	A
13	91667	A	G
13	91733	G	C
13	91890	A	G
13	91960	G	C
13	92531	G	A
13	93032	G	T
13	93961	A	G
13	93980	T	C
13	94572	T	C
13	94695	C	T
13	94898	G	C
13	94977	A	G
13	95216	C	T
13	96505	G	A
13	98939	A	G
13	99367	C	A
13	99579	G	A
13	99676	G	A
13	99717	G	A
13	100003	A	G
13	100054	A	G
13	100097	A	G
13	100208	T	G
13	100457	G	A
13	100551	C	T
13	100562	T	A
13	101469	A	T
13	101716	T	C
13	102269	A	G
13	102752	A	G
13	105255	T	C
13	105355	A	G
13	105406	G	A
13	105409	T	C
13	106249	A	G
13	110807	T	C
13	111621	T	C
13	113119	T	C
13	114304	T	C
13	114535	C	T
13	114553	C	T
13	115183	A	G
13	116112	A	G
13	116448	T	C
13	167959	T	C
13	168947	T	G
13	170004	T	A
13	170099	T	A
13	170932	T	C
13	171523	A	G
13	171785	T	C
13	171896	A	C
13	172523	C	A
13	172685	T	C
13	173678	C	T
13	173711	A	G
13	174980	T	A
13	175074	G	C
13	175777	A	G
13	176006	C	T
13	176260	C	T
13	176730	T	C
13	177392	T	C
13	177745	G	T
13	177928	C	T
13	178128	A	G
13	178207	G	T
13	178920	A	G
13	179054	C	T
13	179112	T	A
13	190481	C	T
13	190550	T	C
13	191318	C	T
13	191452	T	C
13	191551	G	A
13	191574	G	A
13	192291	G	A
13	192396	C	T
13	192414	A	G
13	192432	T	C
13	192436	T	C
13	193709	C	A
13	194164	C	T
13	195227	A	G
13	195282	A	G
13	195330	C	A
13	195393	A	G
13	195417	T	C
13	195423	C	T
13	195860	A	T
13	195984	T	A
13	196123	A	G
13	202269	C	T
13	202482	A	G
13	207364	A	G
13	208048	G	A
13	208108	C	T
13	208201	A	G
13	209449	C	G
13	209680	G	A
13	209924	C	T
13	210532	G	T
13	210609	G	A
13	210688	G	A
13	210877	G	C
13	210889	A	G
13	210922	T	A
13	211049	T	C
13	211216	G	A
13	211462	T	C
13	212592	C	G
13	212732	A	G
13	212836	G	A
13	212859	T	C
13	213947	C	T
13	213972	G	A
13	214086	C	T
13	214378	A	G
13	215391	A	G
13	215595	T	C
13	215788	C	A
13	215820	C	A
13	216100	A	G
13	216105	G	A
13	216689	T	C
13	216942	A	T
13	217030	T	G
13	217557	A	C
13	217558	T	C
13	217640	G	A
13	217641	G	A
13	218127	A	G
13	218501	C	T
13	218615	C	T
13	218882	T	C
13	219311	T	C
13	219326	G	A
13	219608	T	C
13	219620	A	G
13	219807	A	G
13	219863	T	C
13	220308	A	G
13	221642	T	C
13	221882	G	A
13	244001	G	C
13	249505	G	A
13	325905	T	A
13	356409	G	C
13	362992	G	A
13	363840	C	T
13	363895	A	G
13	364294	C	G
13	364324	T	C
13	364548	A	G
13	365054	C	T
13	365359	C	T
13	365365	T	A
13	365455	G	A
13	365505	G	C
13	365551	C	T
13	365580	G	A
13	365788	T	A
13	366043	T	C
13	366121	A	G
13	366559	T	C
13	366629	C	G
13	366707	A	G
13	366795	C	T
13	366806	T	C
13	367501	A	G
13	367522	G	T
13	367942	A	T
13	369062	A	C
13	369419	T	C
13	371525	G	A
13	371527	A	G
13	371533	G	A
13	371651	A	G
13	371667	C	A
13	371689	C	T
13	371760	A	T
13	371821	A	G
13	372297	A	G
13	372301	C	T
13	372322	C	T
13	372428	C	A
13	379425	A	C
13	379439	A	G
13	379602	G	C
13	379628	T	C
13	386662	A	G
13	386820	G	A
13	387027	A	T
13	387174	A	G
13	387573	T	C
13	387621	C	T
13	387870	A	G
13	387876	G	A
13	387879	A	C
13	388149	A	C
13	388450	A	G
13	388831	G	A
13	389020	A	G
13	389031	C	T
13	389517	C	T
13	390351	T	C
13	390358	C	A
13	390486	T	G
13	390609	C	G
13	390664	C	G
13	390879	A	G
13	391419	T	C
13	391443	T	C
13	391619	A	G
13	395714	T	C
13	395972	T	C
13	396438	C	T
13	396594	C	A
13	396704	C	T
13	396782	T	C
13	396913	C	T
13	397176	T	C
13	397273	A	G
13	397553	G	A
13	398046	T	C
13	398240	A	G
13	398295	A	G
13	403758	T	C
13	404584	A	G
13	404983	A	G
13	405305	A	G
13	405350	C	T
13	405438	T	C
13	405754	T	G
13	406116	C	T
13	406917	G	C
13	407275	A	G
13	407557	T	C
13	407891	C	T
13	407898	T	C
13	407930	T	C
13	408326	A	G
13	408412	G	A
13	408413	G	A
13	408552	C	T
13	408564	T	C
13	408620	C	A
13	412745	C	T
13	412783	C	T
13	412878	C	G
13	412883	A	G
13	413447	C	T
13	414251	G	A
13	414299	G	A
13	414344	G	A
13	414432	A	G
13	414447	C	T
13	414462	G	C
13	416274	A	G
13	416283	C	T
13	420568	C	T
13	420689	C	T
13	420702	G	C
13	421708	A	C
13	421766	G	A
13	422548	A	G
13	422714	T	C
13	423463	C	T
13	423541	G	A
13	424537	A	G
13	424591	G	A
13	424897	T	G
13	425123	A	T
13	425898	T	C
13	426590	T	C
13	426685	C	T
13	426779	G	A
13	427028	A	G
13	427123	G	A
13	427279	T	C
13	427327	A	G
13	427483	T	C
13	429080	G	C
13	429465	G	C
13	429559	G	A
13	430438	A	G
13	430487	G	A
13	430624	A	C
13	430685	G	A
13	430694	A	G
13	430776	G	A
13	430800	T	C
13	430847	T	C
13	430856	G	A
13	430895	A	T
13	431689	C	T
13	431692	A	C
13	431890	A	G
13	432019	T	A
13	432356	G	C
13	433201	C	T
13	433223	A	G
13	433274	T	C
13	433409	A	C
13	433461	G	A
13	433474	G	A
13	433519	A	G
13	433544	G	T
13	433720	A	G
13	433952	A	G
13	434151	G	A
13	434219	A	G
13	434234	G	A
13	434450	C	T
13	434776	G	A
13	434958	G	A
13	435924	T	C
13	436033	C	T
13	436081	A	G
13	436089	A	C
13	436140	C	T
13	438469	C	T
13	438637	G	A
13	438807	C	T
13	438983	G	A
13	439294	A	T
13	439409	T	A
13	439833	C	T
13	439839	T	C
13	439990	A	G
13	448333	G	A
13	448334	A	G
13	501921	C	T
13	672129	T	C
13	792993	G	A
13	859917	A	G
13	859986	C	A
13	863208	C	T
13	863229	T	C
13	863526	G	A
13	863539	T	C
14	137285	A	G
14	164061	C	T
14	172738	C	T
14	383709	A	T
14	471767	A	G
14	500290	G	A
14	544744	G	A
14	544998	T	C
14	545273	T	C
14	545433	G	C
14	546338	A	G
14	546371	A	G
14	546726	T	G
14	547958	T	C
14	548516	T	C
14	686681	T	C
14	686786	T	C
14	686798	T	C
14	744953	G	A
15	50010	A	T
15	50012	C	T
15	79297	C	G
15	79305	T	A
15	287386	A	G
15	288644	G	A
15	288781	G	A
15	288813	A	T
15	289536	G	A
15	289707	G	T
15	289728	T	C
15	289797	C	A
15	289980	C	T
15	290026	C	T
15	290144	C	T
15	290259	A	G
15	290268	G	A
15	290808	A	G
15	290822	T	G
15	290826	C	T
15	290902	A	T
15	290908	C	T
15	290923	T	C
15	291072	A	G
15	291394	A	G
15	291397	G	A
15	291472	T	G
15	291517	G	A
15	291532	A	G
15	291583	G	A
15	291594	G	A
15	291607	A	G
15	291799	C	T
15	293132	A	G
15	293200	T	C
15	294178	C	T
15	294330	G	A
15	294382	G	A
15	294636	A	G
15	294723	T	C
15	294840	A	G
15	294882	A	G
15	295275	A	G
15	295276	A	G
15	299739	C	T
15	299793	G	C
15	299796	C	A
15	299808	C	A
15	301024	A	G
15	301075	T	G
15	301083	T	C
15	301193	C	G
15	301568	C	T
15	301621	C	G
15	301631	T	C
15	301658	G	A
15	301737	T	G
15	302184	T	C
15	302514	T	C
15	303924	C	T
15	304268	T	C
15	304269	G	A
15	304525	C	G
15	304796	T	C
15	304893	C	T
15	304912	T	A
15	305296	G	A
15	305531	G	A
15	305540	G	A
15	305753	T	C
15	306087	C	T
15	306089	G	A
15	306275	C	T
15	307049	A	G
15	307994	A	G
15	308124	A	G
15	308212	G	A
15	308387	C	T
15	308420	A	C
15	308792	G	A
15	309615	T	C
15	311312	T	C
15	311429	A	C
15	311450	G	A
15	311489	G	A
15	312220	A	G
15	312454	A	G
15	312534	T	C
15	312575	C	A
15	312919	A	G
15	313924	T	G
15	313948	A	G
15	314073	G	T
15	314514	G	A
15	315048	G	T
15	315191	G	C
15	315837	A	G
15	315972	G	A
15	316038	A	G
15	316312	C	A
15	316327	A	C
15	316342	T	C
15	316353	T	C
15	316361	T	A
15	316591	A	T
15	316611	A	G
15	316882	G	A
15	317034	T	A
15	317483	T	C
15	317789	A	T
15	317798	C	T
15	317858	T	C
15	318077	T	A
15	318084	C	T
15	318136	C	T
15	318668	C	G
15	318818	T	C
15	319505	C	T
15	319628	G	A
15	320174	T	G
15	320590	A	G
15	321352	C	T
15	321766	C	T
15	321972	T	C
15	322108	C	T
15	322138	G	T
15	322263	G	A
15	322341	A	G
15	322819	C	T
15	323813	C	G
15	324302	T	G
15	325269	A	C
15	327020	T	C
15	327917	T	C
15	328185	A	G
15	328373	C	T
15	328457	C	T
15	328714	T	C
15	328719	C	G
15	328735	C	T
15	329561	C	G
15	330217	T	C
15	331119	A	T
15	331262	T	C
15	331265	C	T
15	331520	T	A
15	331655	T	A
15	331895	T	C
15	332034	G	T
15	332096	A	T
15	332111	G	A
15	332285	A	G
15	332378	G	A
15	333897	C	T
15	334869	C	G
15	335001	A	G
15	335413	A	G
15	336579	G	C
15	336629	C	T
15	336821	T	C
15	337296	A	G
15	337546	A	G
15	338127	T	C
15	338259	G	A
15	338406	A	G
15	338412	G	A
15	339097	A	G
15	339178	T	C
15	339568	A	G
15	339637	G	A
15	341821	C	A
15	343319	T	C
15	343550	A	G
15	343770	G	A
15	344523	T	C
15	345165	C	T
15	345183	C	T
15	345678	C	T
15	346267	A	G
15	346309	A	G
15	346376	G	A
15	346416	T	C
15	347064	A	G
15	347117	T	A
15	347325	A	G
15	347552	C	G
15	347788	T	C
15	347793	A	G
15	347863	G	T
15	347922	C	T
15	348030	A	G
15	348098	T	C
15	349164	T	C
15	349328	T	C
15	351607	C	T
15	351721	A	G
15	351787	C	T
15	351979	T	C
15	352012	C	T
15	352075	T	C
15	352138	G	A
15	352379	C	T
15	352665	A	G
15	352775	A	G
15	353226	C	G
15	353491	T	C
15	389237	T	G
15	429969	A	G
15	478679	A	G
15	479020	A	T
15	479060	C	T
15	479709	G	A
15	493377	T	G
15	493684	G	A
15	493975	T	C
15	494571	A	G
15	494590	C	T
15	494669	T	C
15	494728	G	A
15	557722	T	C
15	557758	A	G
15	559459	T	C
15	560186	A	G
15	560189	T	A
15	560585	A	G
15	560857	G	A
15	561115	A	T
15	561511	G	A
15	562357	G	A
15	562468	A	G
15	562672	G	C
15	562688	A	C
15	562828	G	A
15	563008	G	A
15	563917	G	A
15	566126	T	A
15	566165	T	C
15	566210	A	G
15	566820	A	T
15	567262	G	A
15	567267	C	T
15	567276	A	G
15	568141	T	C
15	569058	T	A
15	569259	A	G
15	569787	A	G
15	570373	A	T
15	571079	T	C
15	571108	C	T
15	571256	A	C
15	571445	G	C
15	571945	C	T
15	572041	G	A
15	572070	C	T
15	572098	G	A
15	572102	C	T
15	572407	T	C
15	572419	T	C
15	572941	A	G
15	573228	T	C
15	573248	A	G
15	573262	G	A
15	573312	T	C
15	573324	A	T
15	573358	A	G
15	573377	A	G
15	574266	A	T
15	574378	G	A
15	574716	C	T
15	574776	T	C
15	577639	A	G
15	577890	C	T
15	577985	G	T
15	578881	T	G
15	578986	T	C
15	579079	A	G
15	579277	G	A
15	580206	A	G
15	580924	G	A
15	988096	G	A
16	39105	A	G
16	39420	C	T
16	191944	C	T
16	339840	A	G
16	372490	G	T
16	373351	T	C
16	373946	G	A
16	374363	G	A
16	374826	A	G
16	376139	C	T
16	432091	C	T
16	433340	A	G
16	433445	C	T
16	433481	T	C
16	435620	T	C
16	444434	A	G
16	444685	A	G
16	444755	G	A
16	444899	A	G
16	444920	T	A
16	445300	T	C
16	445378	G	T
16	446457	T	C
16	446756	T	C
16	447294	G	T
16	447414	T	C
16	448089	T	C
16	448143	G	A
16	448407	A	G
16	448559	T	C
16	463543	G	A
16	463700	C	T
16	463818	T	C
16	464146	C	T
16	464194	A	G
16	464559	G	A
16	464709	C	T
16	465889	A	G
16	466824	G	C
16	467054	C	T
16	467077	T	C
16	467087	G	C
16	467237	C	T
16	467571	T	C
16	468262	T	C
16	468512	A	C
16	470616	A	G
16	470860	C	G
16	471189	G	T
16	471267	T	C
16	471834	A	G
16	472110	A	G
16	472894	G	T
16	473286	T	C
16	473391	T	C
16	473949	G	T
16	474003	T	C
16	474526	C	T
16	475484	G	C
16	475496	G	A
16	475831	T	C
16	476232	G	T
16	476836	T	C
16	477481	C	G
16	499388	G	A
16	499635	C	T
16	499678	A	G
16	499739	A	G
16	500000	G	A
16	500007	G	A
16	500244	C	T
16	500351	C	T
16	500426	C	G
16	500598	A	G
16	500824	T	C
16	500964	G	T
16	500975	G	C
16	502052	G	A
16	502118	T	C
16	503010	G	T
16	503041	A	T
16	503157	C	G
16	503305	A	C
16	503314	A	G
16	503888	T	C
16	504262	G	A
16	504666	G	A
16	505150	G	A
16	505698	C	G
16	505721	A	G
16	505749	T	C
16	505836	A	G
16	505893	G	A
16	506129	T	C
16	506265	C	A
16	506274	A	C
16	506349	G	T
16	506565	G	A
16	506806	C	T
16	506954	T	C
16	507169	A	G
16	507218	C	A
16	507220	A	G
16	507225	A	G
16	507326	C	T
16	507401	G	C
16	507608	A	G
16	507635	T	C
16	507854	A	G
16	508010	A	G
16	508199	C	T
16	508243	A	G
16	508709	G	A
16	511211	C	T
16	511425	T	A
16	511469	A	T
16	514990	G	A
16	515057	T	C
16	515138	A	G
16	515495	C	G
16	516787	A	G
16	517187	T	C
16	517281	T	C
16	517540	A	G
16	517615	G	T
16	517881	G	A
16	517980	C	T
16	518836	A	G
16	519322	A	G
16	520194	A	T
16	890346	T	A
16	900838	C	T
16	906158	C	T
16	908485	C	T
16	918824	C	T


















Supplementary Materials 2 SNMs List

Line ID	Chromosome	Position	Ref	Alt	Notes
2	3	4433	C	T	
2	10	741951	A	G	
2	10	741984	A	G	
2	12	385774	A	G	
2	12	600874	T	G	
2	15	746492	T	G	
2	15	1028315	C	T	
3	2	552010	G	A	
3	5	501077	C	G	
3	7	703919	A	G	
3	8	43153	G	T	
3	8	200720	A	G	
3	8	431212	T	G	
3	12	807022	C	T	
3	13	160111	A	G	
3	13	504886	C	A	
3	14	751570	C	T	
3	15	507812	G	A	
3	15	917583	G	T	Double SNM
3	15	917584	A	T	Double SNM
5	3	224604	C	T	
5	4	980280	C	T	
5	4	1092901	C	T	
5	7	15266	G	C	
5	8	197613	C	A	
5	10	34211	C	A	
5	12	157802	C	T	
5	14	112938	A	G	
5	15	720676	A	T	
6	3	138367	G	T	
6	4	696003	T	G	
6	8	494577	G	C
6	9	129109	T	C
6	13	149001	A	G
6	13	727256	C	T
6	14	360606	A	G
6	15	30088	C	G
6	15	385972	A	G
6	16	803030	C	G
7	2	192332	T	C
7	3	259830	T	G
7	5	553581	T	G
7	7	338397	T	G
7	7	341594	T	C
7	8	258188	T	G
7	13	456040	G	T
7	14	561201	T	A
7	15	284445	C	A
7	15	659964	C	A
7	16	611987	G	A
9	4	398592	A	G
9	8	513849	T	C
9	10	525610	T	A
9	13	411751	C	A
9	16	95321	C	G
9	16	102161	A	C
10	2	509837	G	C
10	4	709488	A	T
10	4	1263884	G	T
10	4	1501332	C	A
10	7	287468	C	T
10	9	378296	C	A
10	11	106423	A	G
10	15	159908	G	C
11	4	1246901	C	T
11	7	482611	T	C
11	13	43178	C	A
11	13	445927	A	G
11	13	799928	A	C
11	16	13482	G	C
11	16	42294	G	A
12	1	27628	G	C
12	7	695231	C	T
12	8	504655	C	T
12	9	89529	G	A
12	12	258778	G	T
12	12	258859	G	A
12	12	673314	G	C
13	1	198194	C	A
13	7	101658	C	A
14	2	311846	C	G
14	4	886354	A	G
14	7	772837	A	G
14	11	169067	G	A
14	12	691179	G	A
14	12	771107	C	G
14	12	1012782	C	A
15	3	22431	A	T
15	10	48507	G	C
15	10	581234	G	T
15	10	672045	G	A
15	11	183943	G	A
15	16	474751	G	C
15	16	692856	T	C
16	9	339530	G	A
17	2	567559	T	C
17	6	16375	T	C
17	7	1068932	G	T
17	8	13967	G	T
17	11	598260	T	G
17	12	709837	T	C
17	12	875050	G	A
17	15	195740	C	G
18	2	87066	G	A
18	4	1202140	G	A
18	6	266436	A	C
18	7	2050	G	A
18	14	109167	G	A
18	14	754933	A	T
20	2	125386	T	C
20	4	17637	C	T
20	4	17640	A	G
20	4	17646	A	T
20	4	17649	G	A
20	4	17661	A	G
20	4	17667	A	T
20	4	17670	A	G
20	7	598468	A	G
20	8	5904	A	T
20	11	109612	G	A
20	11	441605	G	A
20	13	392871	C	T
20	14	57635	C	T
20	15	1030920	A	G
21	3	107500	A	G
21	4	667754	A	T
21	4	1169732	C	T
21	8	493730	A	G
21	11	419422	C	A
21	13	511087	C	A
21	14	196782	C	A
21	15	658974	T	G
21	15	835935	G	C
22	4	585080	A	C
22	7	610599	T	G
22	8	526067	G	T
22	13	403741	C	T
23	1	38100	C	A
23	2	158284	C	T
23	2	290420	T	C
23	8	171337	T	C
23	8	410046	A	T
23	10	386739	T	C
23	12	290556	T	A
23	15	264629	C	T
23	16	541455	A	G
24	7	854135	T	C
24	13	239818	A	C
24	13	868076	C	T
24	15	997357	G	T
24	16	386083	G	A
25	7	40158	A	T
25	12	265145	C	A
25	12	970196	A	T
27	1	31930	T	C
27	4	1042700	T	A
27	5	192081	C	A
27	6	70753	T	G
27	8	126524	G	A
27	9	322221	A	G
27	12	961864	C	T
27	13	16377	C	T
27	13	527567	C	T
27	15	781043	A	C
27	16	42327	G	C
27	16	357749	T	G
28	7	496811	C	T
28	8	420903	G	T
28	10	140997	A	C
28	12	186786	G	C
28	13	10419	T	C
28	14	146836	A	T
28	14	310295	G	C
28	14	602259	A	C
28	15	110757	T	A
28	15	605434	A	T
28	15	779575	G	A
28	16	296919	T	C
29	7	1037014	C	A
29	8	258791	C	T
29	9	243794	T	A
29	11	597342	G	T
29	12	34206	A	G
29	14	214768	A	C
29	14	540613	A	T
29	14	600071	A	T
29	15	237350	C	G
29	16	790415	G	C
30	3	61007	A	C
30	5	74255	G	T
30	6	30145	A	C
30	11	366037	A	C
30	12	275550	A	T
30	12	774931	A	C
30	13	652303	A	C
30	14	642241	G	T
31	2	256190	G	A
31	4	937556	T	C
31	7	671014	A	G
31	10	266172	G	C
31	12	730710	G	A
32	3	71986	G	A
32	4	373087	T	C
32	4	520995	A	G
32	8	268954	C	A
32	9	51276	C	T
32	11	65293	A	C
32	13	858263	G	C
33	2	195360	T	C
33	4	141749	T	C
33	4	233660	A	C
33	4	391517	T	C
33	5	535423	T	C
33	9	168073	C	T
33	13	546501	G	A
33	13	642183	T	G
33	15	582380	C	A
33	16	744925	G	A
34	2	681336	C	A
34	2	768506	A	G
34	4	1269271	G	A
34	7	965234	G	A
34	8	205673	T	A
34	11	312748	C	T
34	13	210716	C	T
34	13	352335	A	T
34	15	627259	T	G
34	16	368633	A	C
34	16	399382	G	T
35	9	354242	T	C
36	3	114366	G	A
36	4	763525	G	A
36	4	1264547	C	T
36	5	204889	G	A
37	2	757725	C	T
38	2	340440	A	C
38	4	136508	G	T
38	4	961395	A	C
38	6	179442	C	A
38	7	159326	A	G
38	7	243287	T	C
38	10	564098	G	T
38	14	751634	A	G
39	2	373148	G	C
39	2	445011	C	T
39	2	621786	A	C
39	7	474126	G	A
39	7	691824	T	C
39	8	506987	C	T
39	9	35845	G	A
39	10	596434	C	G
39	12	993372	T	G
39	12	1039606	T	C
39	13	210070	C	A
39	14	39777	C	G
39	16	79038	G	A
39	16	772149	C	G
40	14	83085	G	C
41	7	359825	G	A
41	10	530858	T	G
41	12	286363	G	A
42	4	1119859	G	C
42	4	1321116	T	C
42	4	1412126	C	T
42	10	507718	T	G
42	11	65957	G	A
42	14	21796	C	T
42	14	375246	A	C
42	16	898707	G	T
42	16	909565	G	A
43	4	135845	T	A
43	7	4656	A	C
43	7	194153	C	T
43	9	185812	G	T
43	14	418617	T	C
43	16	524385	G	A
44	4	1507548	A	C
44	6	114080	A	C
44	10	163368	G	A
44	10	197398	T	C
44	12	214755	T	C
44	12	917784	C	T
44	12	966867	G	A
45	5	250946	C	G
45	11	67097	G	A
45	11	250143	T	G
45	11	250149	T	G
45	11	390881	T	C
45	13	74357	A	C
46	4	1385071	T	G
46	11	69660	G	A
46	12	369488	G	A
46	12	571816	T	A
46	13	532423	T	G
46	13	689739	T	G
46	14	765545	G	A
46	15	173679	C	G
48	2	590148	G	A
48	7	134544	T	G
48	7	412206	A	G
48	11	38582	T	G
48	12	645775	T	G
49	1	2070	C	T
49	3	66489	C	A
49	4	522250	A	T
49	5	100873	T	G
49	11	18884	A	G
49	11	406497	T	A
49	11	540269	G	A
49	15	365328	C	A
49	16	46418	T	G
49	16	449180	T	C
49	16	920407	G	T
49	16	934038	A	G
52	4	434272	A	C
52	4	1017707	G	A
52	4	1402346	A	C
52	7	856878	T	C
52	7	1052876	G	A
52	7	1067863	C	A
52	8	237887	T	C
52	11	328192	A	G
52	13	120379	C	T
52	13	466719	G	C
52	13	598083	A	C
53	2	116246	T	C
53	5	352785	G	T
53	7	438552	T	C
54	4	413270	G	A
54	7	1047089	G	T
54	13	24958	G	A
54	15	64203	T	C
55	3	248224	C	A
55	4	1163811	G	T
55	5	70992	C	T
55	6	203316	T	G
55	10	256757	G	A
55	11	246348	T	G
55	12	638978	C	T
55	13	904345	C	T
55	16	15973	C	G
56	1	131441	G	A
56	10	531866	G	T
56	11	129665	A	G
57	2	807692	C	G
57	4	1495482	G	A
57	14	387241	C	T
57	15	853779	C	A
58	1	37335	G	C
59	2	523154	G	A
59	4	1504914	A	G
59	6	99555	G	A
59	8	192452	A	G
59	12	443294	T	C
59	13	30576	C	T
59	15	383574	T	C
59	15	948836	C	A
62	4	488746	A	C
62	5	424574	C	G
62	7	61080	G	A
62	7	215809	A	G
62	10	112735	G	T
62	10	435181	G	A
62	10	502446	C	T
62	11	230053	G	A
62	13	152563	C	G
62	14	115533	G	A
62	14	373383	C	A
62	15	1019524	A	G
62	16	281278	T	C
63	1	93248	A	T
63	2	506477	A	C
63	4	256514	C	A
63	6	232158	T	C
63	7	620016	A	C
63	12	459767	A	G
64	5	27234	T	G
64	7	918147	G	C
64	8	146275	C	A
64	9	20107	G	A
64	9	20113	C	T
64	9	52027	C	T
64	9	351373	T	C
64	14	411470	A	C
64	16	718360	T	A
64	16	940410	A	G
65	5	97648	T	C
65	8	341136	G	A
65	14	280249	G	A
65	15	1016094	G	A
65	16	680456	C	A
66	7	779612	C	A
66	10	471633	C	T
66	12	13604	C	T
66	12	23801	C	T
66	14	403052	C	T
66	14	619872	G	A
66	14	734740	A	G
66	15	141787	A	G
67	4	217607	G	T
67	5	130284	C	T
67	5	322915	A	G
67	8	104105	G	A
67	12	106660	C	T
67	12	553928	C	T
67	14	258859	T	C
67	15	265574	C	T
67	16	263283	G	C
68	4	742865	G	A
68	4	941271	T	G
68	5	351199	C	T
68	7	672239	C	A
68	8	187705	T	A
68	11	507716	G	T
68	15	193343	C	T
68	15	332584	G	A
68	16	288085	C	T
69	2	689014	T	G
69	4	441026	G	A
69	4	602133	G	C
69	6	33503	C	T
69	7	599350	T	A
69	13	722658	G	A
69	15	101858	T	G
69	15	961903	C	T
69	16	131047	A	T
69	16	420562	G	T
70	12	832031	G	T
70	15	1012031	G	A
71	4	504443	C	T
72	7	917114	T	G
72	11	379781	G	T
73	2	241364	T	A
73	4	1378886	G	A
73	7	25855	C	A
73	7	365419	A	C
73	12	24021	T	C
73	13	861512	C	T
73	14	179491	C	T
73	15	687699	A	C
74	2	634506	A	C
74	3	113062	T	C
74	6	37669	T	C
74	6	241760	C	G
74	7	655128	G	C
74	7	860637	C	T
74	8	358486	C	A
74	8	386844	C	T
74	11	235518	G	T
74	12	1016497	C	G
74	13	636011	T	C
74	15	226470	C	A
74	15	821670	T	C
74	15	878397	A	C
75	2	205678	A	C
75	4	457157	T	C
75	7	399536	C	T
75	7	932882	G	A
75	8	180746	C	T
75	8	493884	C	T
75	9	356593	C	T
75	10	589504	G	C
75	13	179238	G	T
75	14	202740	G	A
75	15	260436	C	T
76	1	131830	A	T
76	2	242375	C	G
76	2	469059	T	G
76	2	547151	A	G
76	4	291027	G	T
76	4	1461745	T	A
76	8	382222	G	C
76	10	123011	A	G
76	11	644942	T	A
76	15	432869	C	A
77	2	296603	G	T
77	2	653858	A	G
77	4	1018054	A	G
77	7	26654	C	T
77	7	136674	C	G	
77	8	233261	G	T	
77	8	475318	A	T	
77	11	495535	C	T	
77	12	72052	T	G	
77	14	384458	G	T	Double SNM
77	14	384459	C	G	Double SNM
77	15	190525	G	T	
77	15	890705	C	A	
77	16	742490	T	G	
78	4	731218	T	G	
78	8	317886	C	G	
78	10	461694	G	A	
78	10	617927	G	T	
78	15	174181	A	G	
78	16	247349	A	C	
79	4	1372065	C	G
79	12	522843	G	A
79	14	384458	G	T
79	15	142418	G	C
80	4	742668	T	G
80	7	924589	A	G
80	8	238609	G	T
80	10	394421	T	C
80	11	563030	G	A
80	12	19144	A	G
80	13	828866	T	C
80	14	273714	G	T
80	16	626928	C	T
80	16	817806	G	A
81	2	80271	T	G
81	4	777631	A	G
81	4	1129783	A	C
81	6	23963	G	T
81	8	444430	T	C
81	10	140202	C	G
81	14	674417	G	C
81	15	337143	A	T
81	16	919383	G	A
82	2	490566	A	G
82	3	50158	C	A
82	7	155313	C	T
82	7	842724	T	G
82	7	976231	A	G
82	12	37975	G	C
82	13	131036	C	T
82	15	285046	C	T
82	15	370913	C	T
82	15	1000322	T	C
82	16	408122	G	A
83	4	294670	C	G
83	4	575638	C	G
83	4	1002650	C	G
83	4	1081284	G	A
83	7	210950	G	A
83	12	27212	G	A
83	15	273704	T	A
84	4	367313	T	C
84	4	1458255	G	T
84	10	317058	T	C
84	13	837892	G	A
84	15	182680	A	G
84	15	288227	G	T
84	15	623067	A	G
85	7	720811	G	A
85	13	207834	T	C
85	13	371558	C	A
85	16	56232	G	A
85	16	248703	G	A
85	16	422703	A	G
86	1	93369	C	T
86	4	71918	G	A
86	4	424580	C	T
86	5	141559	T	C
86	6	254966	A	C
86	10	280605	C	A
86	11	607029	G	C
86	13	423441	C	A
86	14	780878	A	C
86	15	737856	G	A
87	4	1452447	T	A
87	7	177963	G	C
87	9	20611	C	T
87	10	522472	G	C
87	11	7880	G	C
87	13	474952	G	A
87	14	376051	T	A
87	16	76209	T	C
88	7	542945	G	C
88	8	10670	T	C
88	12	205774	G	A
88	14	426394	C	A
88	15	407629	G	T
88	16	137442	T	G
91	2	530065	C	G
91	7	256176	C	T
91	7	1018818	C	A
91	15	1044787	G	T
92	4	809583	C	A
92	4	1010009	A	C
92	11	465929	T	C
92	14	308065	T	G
94	5	534175	G	A
94	8	500448	C	T
94	11	34710	G	A
94	14	122455	G	T
94	16	899743	C	A
95	2	520875	G	A
95	4	164196	T	A
95	7	136546	T	G
95	7	1018665	T	C
95	10	121636	T	A
95	11	89040	A	G
95	11	326464	T	C
95	15	593299	C	G
96	5	347684	G	C
96	7	124417	G	A
96	7	949964	T	C
96	10	347562	T	A
96	11	512639	G	A
97	1	187562	G	T
97	2	640810	G	A
97	2	792861	A	G
97	4	438662	G	T
97	7	202975	A	C
97	8	10189	G	C
97	9	123338	C	G
97	14	752469	T	C
97	16	691960	G	C
98	2	318022	A	G
98	5	374870	A	G
98	7	112274	G	A
98	7	290252	A	T
98	9	378001	T	A
98	15	139861	G	A
102	4	855605	T	C
102	7	101616	T	G
102	7	943245	T	A
102	7	951925	T	A
102	8	382051	C	A
102	10	29478	A	T
102	12	801106	C	A
102	15	760090	C	T
102	16	252044	A	T
103	4	330437	T	G
103	15	481629	C	T
104	2	310941	C	T
104	2	500513	C	G
104	9	241863	C	G
104	10	159193	T	A
104	10	308246	G	C
104	16	492155	G	C
105	2	658047	C	T
105	3	8775	G	A
105	4	1505147	G	A
105	8	343925	A	G
106	2	715541	C	G
106	3	121899	C	G
106	4	37093	G	A
106	4	327834	A	T
106	8	258805	G	C
106	9	43051	C	G
106	9	382909	T	C
106	11	173391	G	T
106	14	652115	G	C
106	16	352080	C	A
107	2	276799	C	T
108	2	779818	G	T
108	5	277172	G	T
108	10	97436	C	G
108	12	1028636	T	C
108	14	657822	C	T
108	15	327451	C	G
108	16	857886	G	A
109	3	286562	T	C
109	7	576638	A	T
110	2	57667	T	A
110	4	453305	C	G
110	7	739146	G	C
110	16	727444	A	C
112	2	115439	A	G
112	2	139757	A	T
112	2	572649	T	C
112	4	884454	A	G
112	9	325864	T	C
112	11	312909	C	T
112	14	505136	A	T
115	1	23032	T	A
115	2	411010	T	G
115	3	78399	A	G
115	4	1651	C	T
115	7	866478	T	C
115	9	41545	C	A
115	9	118342	A	G
115	10	506590	A	G
115	11	377044	G	A
115	12	129499	A	G
115	13	553621	G	A
115	13	724559	G	A
115	14	410424	G	A
115	16	416982	C	G
116	7	922442	G	A
116	11	442356	C	T
116	12	743432	T	G
116	13	272269	C	T
116	13	381398	A	G
116	13	630032	C	T
116	14	121878	A	T
116	16	860066	C	G
117	2	413381	T	C
117	2	776556	C	T
117	10	151727	G	C
117	11	42432	T	G
117	16	799637	T	C
119	7	786911	G	C
119	10	352823	T	A
119	14	489101	A	C
119	15	286252	A	C
119	16	146118	G	C
120	2	469209	G	A
120	3	173713	C	G
120	9	309439	G	A
120	10	263377	G	C
120	10	340598	G	T
120	12	122686	G	A	
120	14	129576	G	A	
120	15	174414	A	G	
120	16	22900	C	G	
120	16	585707	A	G	
121	15	834079	A	G	Double SNM
121	15	834080	A	G	Double SNM
121	15	877557	G	A	
123	14	55057	C	T	
123	15	750556	T	G	
124	2	720025	C	T	
124	7	1026154	C	G	
124	9	333757	G	T	
124	10	23718	G	A	
124	10	721413	C	G	
124	11	57785	C	G	
124	12	704671	G	A
124	13	902535	T	C
125	2	506887	C	G
125	9	375922	G	T
125	10	31706	G	A
125	10	517864	C	A
126	3	201703	A	C
126	4	1496658	C	T
126	5	86077	G	C
126	7	266888	G	A
126	7	345858	A	G
126	12	323967	A	C
126	12	401222	G	T
126	15	252721	G	C
126	16	375142	G	A
126	16	572486	G	A
127	2	172489	C	A
127	4	923446	G	A
127	6	113309	C	A
127	12	750537	A	C
128	2	343362	T	C
128	4	635565	C	T
128	10	613273	C	A
128	11	365738	G	A
128	13	687075	C	T
128	14	86848	G	A
128	15	388316	G	T
128	16	288559	G	T
129	2	564427	A	C
129	5	402385	C	T
129	9	217294	A	G
129	10	65507	T	A
129	12	50214	C	A
129	14	738827	A	G
129	16	899607	A	C
130	6	85433	T	C
131	4	100294	G	C
131	4	406284	A	C
132	10	588187	T	C
132	12	377783	C	T
132	13	586656	C	A
133	3	249220	C	T
133	4	1461862	T	G
133	8	279231	C	T
134	4	1480721	G	A
134	7	1009063	C	A
134	9	423249	A	C
134	10	615591	C	T
134	11	351368	T	G
134	12	992568	G	A
134	13	318337	G	A
134	13	363515	G	T
134	15	38622	T	G
134	15	136311	C	T
135	3	297396	A	C
135	4	76824	A	C
135	4	227049	G	T
135	5	505743	C	A
135	10	490011	C	A
135	16	401916	G	C
136	2	326877	A	G
136	2	478469	A	G
136	4	147836	G	A
136	4	677905	T	G
136	7	81290	T	G
136	7	901091	A	C
136	13	342672	G	A
136	15	513918	C	A
136	16	770948	G	T
137	2	460236	A	G
137	4	797161	C	G
137	10	618461	G	A
137	12	217420	G	C
137	12	377506	A	G
137	12	753055	C	A
137	12	918234	G	A
137	14	729690	C	T
138	2	188833	G	T
138	4	191874	C	T
138	5	557640	G	A
138	6	25329	G	A
138	10	397171	G	A
138	12	603263	G	C
138	13	655011	C	T
139	9	433883	C	A
139	13	255482	G	C
139	16	560067	G	T
139	16	842620	T	C
139	16	881919	G	C
140	2	358043	C	T
140	2	618357	G	C
140	4	468917	A	T
140	5	139567	T	G
140	6	125138	G	C
140	6	243003	T	G
140	7	129959	A	T
140	7	847931	G	A
140	7	963960	G	A
140	12	127284	A	G
140	12	914109	C	A
140	16	92838	G	T
141	2	283626	G	C
141	4	1310323	C	T
141	7	1025064	C	A
141	8	306070	A	C
141	8	378817	C	G
141	8	398072	C	A
141	14	13452	C	T
141	15	1021366	A	G
141	16	493366	C	G
141	16	690316	A	T
141	16	717884	A	C
142	2	672872	C	G
142	4	806263	T	C
142	4	1329891	G	A
142	4	1476752	A	T
142	7	223373	C	A
142	7	751468	T	A
142	7	856233	C	G
142	8	60497	A	C
142	9	132583	C	G
142	12	866264	A	G
142	14	169508	T	A
142	15	755028	T	G
142	16	72397	C	A
144	5	119154	G	T
144	5	549379	T	G
144	7	1083624	A	T
144	8	5567	C	T
144	8	5572	C	A
144	13	313013	T	C
145	4	701933	G	A
145	6	181070	T	A
145	8	51281	A	C
145	10	573438	A	G
145	12	437442	G	C
145	14	17163	A	C
145	14	711933	C	T
149	4	29873	G	A
149	7	713477	C	G
149	10	438764	G	A
149	12	721392	G	A
149	15	218750	G	T
149	16	307342	A	G
150	2	755577	A	C
150	5	336062	G	A
150	10	184244	G	T
150	12	110728	C	T
150	12	323333	A	T
150	13	230788	G	T
150	14	303604	T	G
151	15	405929	C	T
151	16	193795	G	A
151	16	359201	T	G





Supplementary Materials 3 Sanger Primers Used

MA ID	Chromosome	Position	Ref	SNM	Forward Primer	Reverse Primer
18	2	87066	G	A	TCTTTTCTGTGTTGTGTAGGGAGT	TGAAGATGATCCTGCACATTCTTTAA
18	2	104975	T	G	TGGGTATGGACATTTTCACTGCTCA	CCCTTCAATATTGGCTCGGTGGTA
18	4	1202140	G	A	AGCTTCTTAGTTCTGTCGGATCCA	CGTCGTCAACTTCAACATCATCCC
18	6	266436	A	C	TCGGTGGTTTTGTCGTGTAAAA	ACCATTCGATCCTGCGGTAATA
18	7	2050	G	A	CAGCCCGAGCCTGTACTAAATG	GTTAAATCCGAGGCAGTCCTCA
18	8	131681	T	G	CCCTTTTCACTTGGCAATTACTCGT	ACTAGCTAAACGGATACTAAAGAATTC
18	9	102536	CT	C	AGTCACTTGACACAGCCACAGG	TACATGGTTGCTGACCATCACA
18	14	754933	A	T	TCGAAACAAAAGCCCTGTCC	GGCAAGCAGGTCTGTCGAGT
27	1	31930	T	C	TTTCAGCAGGCTTACGATGAGA	AACGACTTGAAACGGATCTTGG
27	4	747085	G	GCAA	TAACCGAATCTTTGCCAGTGTG	TGTACCCTTTGTTGCTGCACTC
27	5	192081	C	A	CCAGACCAGATAACGTCTGCAA	CGCTCTGCAGCAACAAATACAT
27	5	407127	G	GA	TGTTTCCTTATGCCGCTCTTTC	TAACGACCATCCTCCTTGATGA
27	6	70753	T	G	TTACTTGATCTGCGATCCCTCA	CCGATTATCTCGCTCCAGAAAC
27	8	126524	G	A	AAGGCAGGTTTCCTGAAATTCTTT	GATAACAACCTTCTTACCGGCGTA
27	9	322221	A	G	AGAAGACCCAATGGCAGCAA	ATCGGCAGATCCGGTATCAA
27	12	961864	C	T	GCATTCTGTTTGGCTGTACGGA	CACCCGTGAGAATGGCCCTTAG
27	13	16377	C	T	TGACCAGCTATCAAAGTAAGAGCT	AGACCTGGCCGATTATTTACGTGA
27	13	527567	C	T	TGTTTTGGCCACGAGAACAC	CAATGGTTCCCTCGTGGAGT
27	15	781043	A	C	AGGGCTCTATGGGTGGGTACA	CATTGCAGGAGTTGCGTTTTT
27	16	42327	G	C	CGTTCGTTGCTGTTTTCGTTTA	TCAATTTGTAACCAGCCCAAGA
27	16	357749	T	G	TGTGAAACTGAGAGTATAAGGGACGT	ACAGTAAACGTAGACTTTGGGAGA
36	1	192901	T	C	ATCAGTAAGCCGCTGCTGAAGT	TTGTTGTTTGTGACGTCGATGA
36	3	114366	G	A	TTGCTACATATTGCTACCACTTCT	AGCAAAACTTCCACCAGTAAACGT
36	4	1264547	C	T	ATTACAAAGGCCATCACCAAGG	ACCTGGAACATGAGCAGAGACC
36	5	204889	G	A	CCGCAAAACATCTTCTTCATCA	ATCTGGTTCACCAACTGGTTCC
36	6	231134	C	T	GGCCACGTTTCTAATCGGTCCATA	GCGAACGAATTTAAATCACACCA
36	6	594218	T	C	TCAGATGGAGAATGCTAACGATACCA	CCTCGCTGGTTAATTTTAAATCATGCT
36	10	360541	G	T	TATGGCGATGACCCTACACCAGAT	GGTGACGACGTCCAAAGTAGCT
70	5	524449	G	C	GGTATTCGATACCGCAAGAGGA	ATGGTTGGGCATTTGAGAGTTC
70	8	160266	C	A	CACAAGAGGTGGAAAGACGTGA	GGCCTTGGCTATGAGTCTTTTG
70	8	186624	C	G	CTGCACGCTACTCTCGCAATAA	TCGCTTTATCCATTCAGCCTTT
70	14	495378	G	A	GCACGGTATTGCAAATTCATGT	CATGCGTTTGATCATCTGACCT
70	14	641608	G	A	AGGCCCTCTTTACGGTAATGGT	AAATCGATCTGGCTGGTGTTTC
75	4	457157	T	C	TCGAAAGAAACTAAGAGCTTTGCAG	GATAAACGAAAGGCCAAGCAATTTA
75	7	399536	C	T	ACCGATATGACTGATGATTGGACCA	TTCAAGTCGTATGCTAGACCAACT
75	7	932882	G	A	AGATAATCCAGACGCTTGGCAAAA	TAGCTTGTGTCATTTGTTCCGCAG
75	8	180746	C	T	AGCTGATGAGGAAGAAGATGACCG	TGGTTGCCAAGTGATGATTTGATCT
75	8	493884	C	T	TGAGAAGCACTGATTGATGCAGCT	TGCCTGATCTGATAAGTTTTAGGA
75	10	589504	G	C	TTGGGTGATATCGACAGAGATAAGG	TATGAAGAGGTTCCAGACACCAAAT
75	13	179238	G	T	CGGAGTGGAAGCTATCCAAGAA	AACTAGCGAGGCCAGTTTTTCA
75	14	202740	G	A	CGCTTGGAGGAAATGCATC	CGACCCCTGCGCCTGTAATATTAT
75	15	260436	C	T	TGACTTGTCTTCCTTCCAACCA	CTTAAGTTCGCTTTCGCTCGTT
75	22	205678	A	C	TGACAACCACGATGCCTATGAACA	TAGAACGGCGAAAGATTTAGTTTC
97	1	187562	G	T	CCGGCGGTAAAGGGGAAAGAA	TGCCTGGTAAAGTTGTGTGCTAGT
97	2	640810	G	A	CGAACGGCAATTTCACCTCTAT	GTGTGTGCCCACATGTCCTTTA
97	2	792861	A	G	CAGTTTTGCAAGGCAGATAACG	CTACACGGGATTCATTGGTGTG
97	4	23355	A	G	CGGTTACAGATACGACGAAGAGCA	GCTGCCTCTTCCTCAAAACGATATAAA
97	4	438662	G	T	CGGTGGCAAATGTCTCTTTTCT	TACCGGGTGCACCATAAAGAAT
97	7	202975	A	C	TCTTCTCAGCTTGCACGAGTCATT	TTGGAGACCGGTACCAAAACATGT
97	9	123338	C	G	TCCTCCGGAATTGACTCTAGACTACT	TCCAAACCTTCTAAACCGAACCTCT
97	10	502730	C	T	CCAACTCATAAGACACCGCCCTTA	TGATTTTCCAACCGGTAATAACGT
97	11	159169	G	C	TCGTCTACAACAGGTTTTAGTTCA	AGTACAGTTTGTTGCAGCGTTTCT
97	14	752469	T	C	CACCAGTGGACAAGTAGCCGATAA	GGTAACATATTCTCAACACACGAT
						



Mapping and variant calling pipeline

Raw reads in fastq format were first mapped to S288C reference genome and variants called (steps 1-14 via bash script). Simple perl scripts were written to filter out variants called in all strains. These variants were incorporated into the reference genome to create the MA ancestral reference genome. All files were re-mapped to the MA reference following the same pipeline to minimize mapping errors.

Bwa alignment

1. bwa aln $ref_file $FASTQ1 > $FASTQ1.sai

2. bwa aln $ref_file $FASTQ2 > $FASTQ2.sai

3. bwa sampe $ref_file $FASTQ1.sai $FASTQ2.sai $FASTQ1 $FASTQ2 > $READNAME.sam

Formatted for GATK using samtools and picard tools

4. samtools import $ref_fai $READNAME.sam $READNAME.bam 

5. samtools sort $READNAME.bam $READNAME.sorted

6. samtools index $READNAME.sorted.bam

7. java AddOrReplaceReadGroups.jar I= $READNAME.sorted.bam O= $READNAME.sorted.fixed.bam SORT_ORDER=coordinate RGID=foo RGLB=
bar RGPL=illumina RGSM=$GROUPNAME RGPU=6 CREATE_INDEX=True VALIDATION_STRINGENCY=LENIENT

8. java MarkDuplicates.jar I=$READNAME.sorted.fixed.bam O=$READNAME.sorted.fixed.marked.bam M=$READNAME.metrics CREA
TE_INDEX=True VALIDATION_STRINGENCY=LENIENT

GATK local realignment

9. java GenomeAnalysisTK.jar -R $ref_file -I $READNAME.sorted.fixed.marked.bam -T RealignerTargetCreator -o $READNAME.intervals

10. java GenomeAnalysisTK.jar -R $ref_file -I $READNAME.sorted.fixed.marked.bam -T IndelRealigner -targetIntervals $READNAME.intervals -o $READNAME.sorted.fixed.marked.realigned.bam

11. java GenomeAnalysisTK.jar -R $ref_file -I $READNAME.sorted.fixed.marked.realigned.bam -T UnifiedGenotyper -o $READNAME.sorted.fixed.marked.realigned.vcf

12. java GenomeAnalysisTK.jar -T BaseRecalibrator -I $READNAME.sorted.fixed.marked.realigned.bam -R $ref_file -knownSites 
$READNAME.sorted.fixed.marked.realigned.vcf -o recal_data.grp

13. java GenomeAnalysisTK.jar -R $ref_file -I $READNAME.sorted.fixed.marked.realigned.bam -T PrintReads -o $READNAME.mapped.bam -BQSR recal_data.grp

GATK variant calling
(This step was carried out on all bam files simultaneously.  A few different values for Ðheterozygosity option was tested, including 1E-3, 1E-4, 1E-6, but no differences post heuristic filtering were observed.)

14. java GenomeAnalysisTK.jar -R $ref_file -I 1.bam -I 2.bam (É) -T UnifiedGenotyper Ñglm BOTH -o variants.vcf