##fileformat=VCFv4.2
##FILTER=<ID=PASS,Description="All filters passed">
##filedate=20191027
##source="beagle.28Sep18.793.jar"
##INFO=<ID=AF,Number=A,Type=Float,Description="Estimated ALT Allele Frequencies">
##INFO=<ID=DR2,Number=1,Type=Float,Description="Dosage R-Squared: estimated squared correlation between estimated REF dose [P(RA) + 2*P(RR)] and true REF dose">
##INFO=<ID=IMP,Number=0,Type=Flag,Description="Imputed marker">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=DS,Number=A,Type=Float,Description="estimated ALT dose [P(RA) + P(AA)]">
##FORMAT=<ID=GP,Number=G,Type=Float,Description="Estimated Genotype Probability">
##contig=<ID=9>
##bcftools_mergeVersion=1.9+htslib-1.9
##bcftools_mergeCommand=merge --output /local/workdir/mw489/EMBRAPA_2020GS/data/chr9_ImputationReferencePanel_C1progenyAdded_EMBRAPA.vcf.gz --merge snps --output-type z --threads 6 /local/workdir/mw489/EMBRAPA_2020GS/data/chr9_ImputationReferencePanel_EMBRAPA_Phased_102619.vcf.gz /local/workdir/mw489/EMBRAPA_2020GS/data/chr9_EMBRAPA_C1progeny_FromDCas19_4301_REFimputed_102619.vcf.gz; Date=Mon Aug 31 20:02:40 2020
#CHROM	POS	ID	REF	ALT
9	30615	S9_30615	A	T
9	30626	S9_30626	T	A
9	40368	S9_40368	C	T
9	40764	S9_40764	A	G
9	81113	S9_81113	A	T
9	82430	S9_82430	T	C
9	84192	S9_84192	T	C
9	84761	S9_84761	A	G
9	88258	S9_88258	T	G
9	88265	S9_88265	G	A
9	100658	S9_100658	C	T
9	100661	S9_100661	A	G
9	100693	S9_100693	T	C
9	100699	S9_100699	G	T
9	100794	S9_100794	C	T
9	100801	S9_100801	G	C
9	101044	S9_101044	C	T
9	102042	S9_102042	T	G
9	102818	S9_102818	T	C
9	102839	S9_102839	A	T
9	103029	S9_103029	T	C
9	118450	S9_118450	A	C
9	118473	S9_118473	C	T
9	120697	S9_120697	T	C
9	188537	S9_188537	A	T
9	188538	S9_188538	A	C
9	188539	S9_188539	G	T
9	210542	S9_210542	T	G
9	210549	S9_210549	A	G
9	213446	S9_213446	A	C
9	213452	S9_213452	C	A
9	220377	S9_220377	T	A
9	221752	S9_221752	T	A
9	221753	S9_221753	G	T
9	221754	S9_221754	A	G
9	224007	S9_224007	G	C
9	224020	S9_224020	T	C
9	232929	S9_232929	T	G
9	235846	S9_235846	T	C
9	235849	S9_235849	C	T
9	235853	S9_235853	T	A
9	235891	S9_235891	A	G
9	271303	S9_271303	C	T
9	374589	S9_374589	T	G
9	414065	S9_414065	T	C
9	414067	S9_414067	C	T
9	414088	S9_414088	G	T
9	414100	S9_414100	C	A
9	416008	S9_416008	G	A
9	416040	S9_416040	G	A
9	416138	S9_416138	A	C
9	416215	S9_416215	G	A
9	416226	S9_416226	A	C
9	416245	S9_416245	G	C
9	451607	S9_451607	A	G
9	451615	S9_451615	G	T
9	473650	S9_473650	G	A
9	473707	S9_473707	C	T
9	582757	S9_582757	C	G
9	582779	S9_582779	G	A
9	582825	S9_582825	C	T
9	582837	S9_582837	A	G
9	585110	S9_585110	A	G
9	585136	S9_585136	A	G
9	585274	S9_585274	C	G
9	596662	S9_596662	C	A
9	599632	S9_599632	C	T
9	605255	S9_605255	C	T
9	605377	S9_605377	T	C
9	651418	S9_651418	T	A
9	651435	S9_651435	T	G
9	658382	S9_658382	A	G
9	659632	S9_659632	G	A
9	659844	S9_659844	A	T
9	659880	S9_659880	A	G
9	659923	S9_659923	T	C
9	659942	S9_659942	A	T
9	659950	S9_659950	G	C
9	716745	S9_716745	A	G
9	772225	S9_772225	C	T
9	772246	S9_772246	A	G
9	772261	S9_772261	A	G
9	773711	S9_773711	T	G
9	773712	S9_773712	T	G
9	781918	S9_781918	A	G
9	845161	S9_845161	C	A
9	901738	S9_901738	G	A
9	901766	S9_901766	C	G
9	901784	S9_901784	T	G
9	901807	S9_901807	T	C
9	906873	S9_906873	T	A
9	906880	S9_906880	A	T
9	906925	S9_906925	A	T
9	911125	S9_911125	T	G
9	911175	S9_911175	G	A
9	911194	S9_911194	C	A
9	937988	S9_937988	C	G
9	938254	S9_938254	C	T
9	938284	S9_938284	G	A
9	938884	S9_938884	T	C
9	943818	S9_943818	T	G
9	944308	S9_944308	A	T
9	944325	S9_944325	A	T
9	970523	S9_970523	T	C
9	1036746	S9_1036746	C	T
9	1036751	S9_1036751	G	A
9	1036785	S9_1036785	C	T
9	1038620	S9_1038620	C	T
9	1106220	S9_1106220	G	T
9	1218563	S9_1218563	G	T
9	1295279	S9_1295279	C	T
9	1301148	S9_1301148	G	C
9	1354224	S9_1354224	T	C
9	1354227	S9_1354227	G	A
9	1354262	S9_1354262	A	C
9	1354263	S9_1354263	G	A
9	1354382	S9_1354382	A	G
9	1371759	S9_1371759	A	C
9	1371767	S9_1371767	A	G
9	1371772	S9_1371772	T	G
9	1371773	S9_1371773	A	G
9	1375564	S9_1375564	T	A
9	1419062	S9_1419062	G	C
9	1517749	S9_1517749	T	G
9	1517853	S9_1517853	C	A
9	1517890	S9_1517890	C	G
9	1521140	S9_1521140	G	A
9	1521141	S9_1521141	T	C
9	1534436	S9_1534436	T	C
9	1534842	S9_1534842	C	T
9	1534888	S9_1534888	A	G
9	1534889	S9_1534889	G	C
9	1569047	S9_1569047	A	T
9	1569056	S9_1569056	G	T
9	1579366	S9_1579366	C	T
9	1586496	S9_1586496	A	T
9	1586497	S9_1586497	A	T
9	1586498	S9_1586498	A	C
9	1586502	S9_1586502	T	A
9	1586503	S9_1586503	G	C
9	1586504	S9_1586504	T	A
9	1586505	S9_1586505	G	A
9	1598662	S9_1598662	A	T
9	1598717	S9_1598717	G	A
9	1598808	S9_1598808	A	C
9	1663576	S9_1663576	G	A
9	1663682	S9_1663682	G	A
9	1663703	S9_1663703	C	A
9	1667784	S9_1667784	C	T
9	1667800	S9_1667800	G	A
9	1667871	S9_1667871	T	C
9	1667896	S9_1667896	C	T
9	1668112	S9_1668112	A	T
9	1668122	S9_1668122	A	T
9	1669702	S9_1669702	C	T
9	1669733	S9_1669733	C	G
9	1669945	S9_1669945	A	T
9	1669949	S9_1669949	G	T
9	1673969	S9_1673969	G	A
9	1673996	S9_1673996	T	G
9	1674449	S9_1674449	A	G
9	1770083	S9_1770083	C	T
9	1782213	S9_1782213	A	T
9	1782236	S9_1782236	A	C
9	1784066	S9_1784066	A	T
9	1785770	S9_1785770	A	G
9	1785839	S9_1785839	G	A
9	1790589	S9_1790589	C	T
9	1790595	S9_1790595	C	T
9	1818155	S9_1818155	T	C
9	1857054	S9_1857054	C	T
9	1857388	S9_1857388	C	T
9	1857390	S9_1857390	C	G
9	1868274	S9_1868274	C	A
9	1893971	S9_1893971	C	A
9	1894172	S9_1894172	C	T
9	1894176	S9_1894176	G	C
9	1894179	S9_1894179	T	G
9	1906571	S9_1906571	T	C
9	1906630	S9_1906630	A	G
9	1906673	S9_1906673	A	G
9	1906744	S9_1906744	C	A
9	1907277	S9_1907277	T	A
9	1917126	S9_1917126	G	T
9	1917336	S9_1917336	A	G
9	1917368	S9_1917368	A	G
9	1918175	S9_1918175	C	G
9	1918245	S9_1918245	A	G
9	1922619	S9_1922619	A	G
9	1942405	S9_1942405	G	T
9	1942440	S9_1942440	T	G
9	1942542	S9_1942542	C	G
9	1942559	S9_1942559	A	C
9	1942563	S9_1942563	T	C
9	1943386	S9_1943386	T	C
9	1943394	S9_1943394	A	G
9	1943868	S9_1943868	A	T
9	1943877	S9_1943877	G	C
9	1960050	S9_1960050	T	G
9	1964701	S9_1964701	A	C
9	1964738	S9_1964738	G	A
9	1981904	S9_1981904	T	A
9	1982712	S9_1982712	T	C
9	1992527	S9_1992527	G	A
9	1992589	S9_1992589	A	C
9	2012343	S9_2012343	C	T
9	2012349	S9_2012349	C	G
9	2015484	S9_2015484	C	T
9	2015509	S9_2015509	T	G
9	2015568	S9_2015568	C	G
9	2016235	S9_2016235	T	G
9	2162458	S9_2162458	T	C
9	2162461	S9_2162461	T	C
9	2481677	S9_2481677	A	C
9	2481697	S9_2481697	C	T
9	2481700	S9_2481700	G	C
9	2481703	S9_2481703	C	G
9	2481706	S9_2481706	G	A
9	2481708	S9_2481708	A	G
9	2481717	S9_2481717	G	T
9	2481718	S9_2481718	A	C
9	2481719	S9_2481719	C	A
9	2481721	S9_2481721	C	G
9	2481722	S9_2481722	C	A
9	2481724	S9_2481724	G	C
9	2481727	S9_2481727	C	T
9	2481730	S9_2481730	C	G
9	2481731	S9_2481731	A	C
9	2482027	S9_2482027	A	C
9	2482140	S9_2482140	G	A
9	2482302	S9_2482302	G	T
9	2487930	S9_2487930	T	A
9	2487942	S9_2487942	G	C
9	2490778	S9_2490778	A	T
9	2491562	S9_2491562	G	C
9	2491606	S9_2491606	T	G
9	2492205	S9_2492205	G	T
9	2492332	S9_2492332	A	G
9	2492410	S9_2492410	C	T
9	2501343	S9_2501343	C	G
9	2513749	S9_2513749	T	G
9	2515721	S9_2515721	A	T
9	2515727	S9_2515727	C	A
9	2515845	S9_2515845	G	A
9	2515855	S9_2515855	T	C
9	2515859	S9_2515859	T	C
9	2515874	S9_2515874	A	G
9	2515910	S9_2515910	C	T
9	2516023	S9_2516023	C	T
9	2516075	S9_2516075	G	A
9	2516082	S9_2516082	G	A
9	2519519	S9_2519519	G	A
9	2618422	S9_2618422	T	C
9	2625035	S9_2625035	T	A
9	2625045	S9_2625045	T	A
9	2625138	S9_2625138	A	T
9	2631214	S9_2631214	G	A
9	2631218	S9_2631218	T	C
9	2631300	S9_2631300	A	G
9	2631308	S9_2631308	G	C
9	2631339	S9_2631339	A	G
9	2633604	S9_2633604	C	T
9	2633657	S9_2633657	T	A
9	2661138	S9_2661138	A	T
9	2661150	S9_2661150	T	C
9	2661166	S9_2661166	G	A
9	2661167	S9_2661167	G	A
9	2661201	S9_2661201	T	G
9	2668173	S9_2668173	A	G
9	2668389	S9_2668389	A	T
9	2682688	S9_2682688	C	T
9	2684373	S9_2684373	C	T
9	2684553	S9_2684553	G	A
9	2690384	S9_2690384	G	T
9	2690392	S9_2690392	T	C
9	2690405	S9_2690405	T	C
9	2690414	S9_2690414	G	A
9	2690442	S9_2690442	A	T
9	2690494	S9_2690494	T	C
9	2691608	S9_2691608	C	T
9	2749271	S9_2749271	A	C
9	2779668	S9_2779668	C	T
9	2786292	S9_2786292	C	T
9	2829876	S9_2829876	T	A
9	2878993	S9_2878993	C	A
9	2879013	S9_2879013	A	G
9	2883736	S9_2883736	A	G
9	2883762	S9_2883762	C	T
9	2883769	S9_2883769	C	A
9	2883814	S9_2883814	G	A
9	2884178	S9_2884178	T	A
9	2891447	S9_2891447	G	A
9	2891629	S9_2891629	T	C
9	2891632	S9_2891632	C	T
9	2891647	S9_2891647	C	A
9	2891650	S9_2891650	T	C
9	2891995	S9_2891995	A	G
9	2892035	S9_2892035	A	G
9	2958468	S9_2958468	T	G
9	2985141	S9_2985141	A	G
9	2985160	S9_2985160	A	C
9	2985161	S9_2985161	G	T
9	2985312	S9_2985312	T	A
9	2998051	S9_2998051	A	C
9	3054916	S9_3054916	A	G
9	3055060	S9_3055060	G	A
9	3064374	S9_3064374	A	T
9	3064391	S9_3064391	T	C
9	3064393	S9_3064393	T	C
9	3065929	S9_3065929	A	G
9	3065947	S9_3065947	G	A
9	3065959	S9_3065959	T	C
9	3065961	S9_3065961	A	C
9	3066000	S9_3066000	G	T
9	3066570	S9_3066570	A	G
9	3066640	S9_3066640	G	A
9	3066645	S9_3066645	T	A
9	3075300	S9_3075300	T	C
9	3077336	S9_3077336	A	G
9	3077421	S9_3077421	G	C
9	3077460	S9_3077460	T	G
9	3077550	S9_3077550	C	A
9	3077572	S9_3077572	A	G
9	3101872	S9_3101872	A	G
9	3102207	S9_3102207	G	C
9	3102292	S9_3102292	C	T
9	3103390	S9_3103390	C	T
9	3109592	S9_3109592	G	T
9	3131709	S9_3131709	G	A
9	3131730	S9_3131730	C	A
9	3168818	S9_3168818	T	C
9	3170398	S9_3170398	T	C
9	3171172	S9_3171172	C	T
9	3171187	S9_3171187	G	C
9	3171212	S9_3171212	G	T
9	3171325	S9_3171325	A	T
9	3184663	S9_3184663	C	T
9	3184694	S9_3184694	T	C
9	3184696	S9_3184696	T	A
9	3184718	S9_3184718	G	A
9	3260091	S9_3260091	A	T
9	3260144	S9_3260144	T	C
9	3260911	S9_3260911	G	T
9	3261187	S9_3261187	A	T
9	3275993	S9_3275993	T	G
9	3282471	S9_3282471	C	T
9	3303244	S9_3303244	T	A
9	3303503	S9_3303503	T	C
9	3303535	S9_3303535	G	C
9	3305780	S9_3305780	C	T
9	3305785	S9_3305785	T	C
9	3464802	S9_3464802	C	A
9	3464811	S9_3464811	C	A
9	3465359	S9_3465359	A	G
9	3465398	S9_3465398	T	A
9	3465402	S9_3465402	T	G
9	3465403	S9_3465403	G	T
9	3465503	S9_3465503	G	A
9	3465969	S9_3465969	G	C
9	3466018	S9_3466018	A	C
9	3466033	S9_3466033	T	A
9	3466309	S9_3466309	A	C
9	3466342	S9_3466342	G	C
9	3482516	S9_3482516	A	T
9	3482556	S9_3482556	G	C
9	3489408	S9_3489408	T	A
9	3489414	S9_3489414	A	T
9	3492859	S9_3492859	A	G
9	3492906	S9_3492906	T	C
9	3493592	S9_3493592	T	A
9	3493851	S9_3493851	C	T
9	3493857	S9_3493857	T	A
9	3493938	S9_3493938	G	A
9	3500496	S9_3500496	G	A
9	3500533	S9_3500533	G	A
9	3500539	S9_3500539	C	G
9	3500582	S9_3500582	A	G
9	3500601	S9_3500601	A	T
9	3500626	S9_3500626	A	C
9	3500828	S9_3500828	A	G
9	3503639	S9_3503639	A	G
9	3530909	S9_3530909	C	T
9	3593026	S9_3593026	T	C
9	3593155	S9_3593155	T	C
9	3593156	S9_3593156	A	G
9	3593165	S9_3593165	G	A
9	3593987	S9_3593987	A	G
9	3593996	S9_3593996	T	C
9	3594004	S9_3594004	G	C
9	3594027	S9_3594027	C	T
9	3665461	S9_3665461	G	A
9	3666537	S9_3666537	G	A
9	3690307	S9_3690307	C	A
9	3742742	S9_3742742	G	A
9	3743947	S9_3743947	G	C
9	3743988	S9_3743988	G	A
9	3744088	S9_3744088	A	G
9	3744133	S9_3744133	T	C
9	3744137	S9_3744137	C	A
9	3744138	S9_3744138	A	G
9	3744141	S9_3744141	A	G
9	3744146	S9_3744146	C	A
9	3744573	S9_3744573	A	G
9	3771616	S9_3771616	G	A
9	3771986	S9_3771986	A	G
9	3772032	S9_3772032	C	T
9	3813311	S9_3813311	T	C
9	3813317	S9_3813317	A	G
9	3813338	S9_3813338	T	C
9	3815426	S9_3815426	C	T
9	3815659	S9_3815659	G	T
9	3975358	S9_3975358	A	G
9	3978001	S9_3978001	C	T
9	3992158	S9_3992158	G	A
9	3992184	S9_3992184	A	G
9	3992215	S9_3992215	T	C
9	4001209	S9_4001209	A	G
9	4009271	S9_4009271	C	T
9	4025759	S9_4025759	C	T
9	4282089	S9_4282089	A	C
9	4282109	S9_4282109	T	A
9	4282111	S9_4282111	G	A
9	4282131	S9_4282131	T	C
9	4282240	S9_4282240	G	A
9	4284979	S9_4284979	G	A
9	4293972	S9_4293972	C	T
9	4293995	S9_4293995	T	G
9	4294845	S9_4294845	A	T
9	4295212	S9_4295212	A	G
9	4300259	S9_4300259	T	C
9	4300307	S9_4300307	T	G
9	4300386	S9_4300386	G	T
9	4300413	S9_4300413	T	C
9	4300476	S9_4300476	A	T
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