Citrus CAPS Marker Database


Locus info		Cultivar Idenification							SNP info	Target on C. clementina (v1.0)				Target on C. unshiu (v1.0)					AGI map info (Shimada et al. 2014 Takehiko Shimada, Hiroshi Fujii, Tomoko Endo, Takanori Ueda, Aiko Sugiyama, Michiharu Nakano, Masayuki Kita, Terutaka Yoshioka, Tokuro Shimizu, Hirohisa Nesumi, Yoshinori Ikoma, Takaya Moriguchi, Mitsuo Omura (2014) Construction of a citrus framework genetic map anchored by 708 gene-based markers. Tree Genetics & Genomes. 10: 1001-1013. )		KmMg map info (Omura et al. 2003 Mitsuo Omura, Takanori Ueda, Masayuki Kita, Akira Komatsu, Yuko Takanokura, Takehiko Shimada, Tomoko Endo, Hirohisa Nesumi, ToshioYoshida (2003) EST mapping of Citrus. Proceedings of the International Society of Citriculture IX Congress 2000. 71-74. )		JtTr map info (Omura et al. 2003 Mitsuo Omura, Takanori Ueda, Masayuki Kita, Akira Komatsu, Yuko Takanokura, Takehiko Shimada, Tomoko Endo, Hirohisa Nesumi, ToshioYoshida (2003) EST mapping of Citrus. Proceedings of the International Society of Citriculture IX Congress 2000. 71-74. )		Km/O41 map info (Nakano et al. 2003 Mutsuko Nakano, Hirohisa Nesumi, Terutaka Yoshioka, Mitsuo Omura, Toshio Yoshida (2003) Linkage analysis between male sterility of citrus and STS markers. Proceedings of the International Society of Citriculture IX Congress 2000. 179-180 )		Rp/Sa map info (Ohta et al. 2011 Satoshi Ohta, Tomoko Endo, Takehiko Shimada, Hiroshi Fujii, Tokuro Shimizu, Takeshi Kuniga, Terutaka Yoshioka, Hiroshisa Nesumi, Toshio Yoshida, Mitsuo Omura (2011) PCR primers for marker assisted backcrossing to introduce a CTV resistance gene from Poncirus trifoliata (L.) Raf. into citrus. Journal of the Japanese Society for Horticultural Science. 80: 295-307. )
Locus name ▲▼	Locus name alias ▲▼	Rank hybrid cultivar ▲▼	Citrus collection O -	Cultivar identifi- cation manual O -	Ninomiya et al. 2015 Taizo Ninomiya, Takehiko Shimada, Tomoko Endo, Keisuke Nonaka, Mitsuo Omura, Hiroshi Fujii (2015) Development of Citrus Cultivar Identification by CAPS Markers and Parentage Analysis. Hort. Res. (Japan) 14: 127-133. O -	Nonaka et al. 2017 Keisuke Nonaka, Hiroshi Fujii, Masayuki Kita, Takehiko Shimada, Tomoko Endo, Terutaka Yoshioka, Mituso Omura (2017) Identification and parentage analysis of citrus cultivars developed in Japan by CAPS Markers. The Horticulture Journal. 86: 208-221. O -	Graphical map O -	Genotype O -	Fujii et al. 2013 Hiroshi Fujii, Takehiko Shimada, Keisuke Nonaka, Masayuki Kita, Takeshi Kuniga,Tomoko Endo, Yoshinori Ikoma, Mitsuo Omura (2013) High-throughput genotyping in citrus accessions using an SNP genotyping array. Tree Genetics & Genomes. 9: 145-153. ▲▼	Transcript ID ▲▼	Scaffold ▲▼	Start	End	Transcript ID ▲▼	Scaffold ▲▼	Start	End	Gene function ▲▼	AGI LG ▲▼	AGI cM	KmMg LG ▲▼	KmMg cM	JtTr LG ▲▼	JtTr cM	Km/O41 LG ▲▼	Km/O41 cM	Rp/Sa LG ▲▼	Rp/Sa cM
Af1432			-	-	-	-	-	-		Ciclev10032069m	scaffold_4	23666784	23669594	C_unshiu_00001:mRNA_103.1	C_unshiu_00001	659252	662036	UDP-galactose/UDP-glucose transporter 5B	AGI-07	72.828
Tf0198		AAvailable marker	O	-	-	-	-	O		Ciclev10032275m	scaffold_4	23695766	23697703	C_unshiu_00001:mRNA_105.2	C_unshiu_00001	685451	687250	Homeobox-leucine zipper protein HAT7
Gn0048		AAvailable marker	-	O	-	-	O	O	SI289	Ciclev10032275m	scaffold_4	23695766	23697703	C_unshiu_00001:mRNA_105.2	C_unshiu_00001	685451	687250	Homeobox-leucine zipper protein HAT7	AGI-07	74.225	KmG-07	7.964	JtR-07	4.200
Al0408			O	-	-	-	-	-		Ciclev10031487m	scaffold_4	23737757	23740513	C_unshiu_00001:mRNA_109.1	C_unshiu_00001	727392	729266	F-box/kelch-repeat protein SKIP11	AGI-07	75.917	KmG-07	13.235	JtR-07	1.788
Cp0089		Bno homozygous cultivar with minor allele	O	-	O	-	-	-		Ciclev10032543m	scaffold_4	23858830	23861090	C_unshiu_00001:mRNA_128.1	C_unshiu_00001	852968	856494	CAAX amino terminal protease family protein	AGI-07	77.194
Cp0059			O	-	-	-	-	-		Ciclev10031015m	scaffold_4	23075728	23081009	C_unshiu_00001:mRNA_13.1	C_unshiu_00001	89828	96147	Protein NLRC3	AGI-08	86.856
Tf0424			-	-	-	-	-	-		Ciclev10031190m	scaffold_4	23908189	23912723	C_unshiu_00001:mRNA_134.1	C_unshiu_00001	904872	908655	Apyrase	AGI-07	77.041
Af1690			-	-	-	-	-	-		Ciclev10032651m	scaffold_4	23923757	23925178	C_unshiu_00001:mRNA_137.1	C_unshiu_00001	920379	924128	Hypothetical protein	AGI-07	77.752
Tf0094			-	-	-	-	-	-	SI006	Ciclev10031937m	scaffold_4	23957038	23959134	C_unshiu_00001:mRNA_145.1	C_unshiu_00001	950657	954895	Myb family transcription factor APL	AGI-07	77.141
Gmom22			-	-	-	-	-	-		Ciclev10032304m	scaffold_4	24041593	24043549	C_unshiu_00001:mRNA_158.1	C_unshiu_00001	1037727	1039688	NAC transcription factor NAM-B1	AGI-07	78.469	KmG-07	2.659
Tf0323			-	-	-	-	-	-	SI030	Ciclev10032304m	scaffold_4	24041593	24043549	C_unshiu_00001:mRNA_158.1	C_unshiu_00001	1037727	1039688	NAC transcription factor NAM-B1
Tf0339			-	-	-	-	-	-	SI019	Ciclev10032304m	scaffold_4	24041593	24043549	C_unshiu_00001:mRNA_158.1	C_unshiu_00001	1037727	1039688	NAC transcription factor NAM-B1
Cp0057			-	-	-	-	-	-		Ciclev10031335m	scaffold_4	24227703	24230754	C_unshiu_00001:mRNA_187.1	C_unshiu_00001	1244353	1247404	DUF1336 family protein	AGI-07	79.269
Tf0321			-	-	-	-	-	-	SI003	Ciclev10032283m	scaffold_4	24341642	24346244	C_unshiu_00001:mRNA_213.1	C_unshiu_00001	1358115	1363266	Putative WRKY transcription factor 57
Wy0040		AAvailable marker	O	-	-	-	-	O		Ciclev10011622m	scaffold_6	25349417	25351949	C_unshiu_00001:mRNA_217.1	C_unshiu_00001	1378378	1380557	Hypothetical protein			KmG-04	12.855
Af3017			-	-	-	-	-	-		Ciclev10031492m	scaffold_4	24401841	24406470	C_unshiu_00001:mRNA_224.1	C_unshiu_00001	1415778	1420221	Serine/threonine-protein kinase PBS1	AGI-07	83.217
Wy0011		OOthers	O	-	-	-	-	-	SI091	Ciclev10032364m	scaffold_4	24417602	24419019	C_unshiu_00001:mRNA_226.1	C_unshiu_00001	1429943	1431279	Enoyl CoA hydratase/isomerase	AGI-07	86.288
Wy0025			-	-	-	-	-	-	SI004	Ciclev10032547m	scaffold_4	24434005	24435526	C_unshiu_00001:mRNA_229.1	C_unshiu_00001	1446446	1447952	NAC domain-containing protein 29
Af1405			-	-	-	-	-	-		Ciclev10032481m	scaffold_4	24503838	24505365	C_unshiu_00001:mRNA_238.1	C_unshiu_00001	1513811	1515209	FH interacting protein 1	AGI-07	83.026
Bf1243			-	-	-	-	-	-		Ciclev10032276m	scaffold_4	24657015	24660141	C_unshiu_00001:mRNA_262.1	C_unshiu_00001	1663630	1666687	U3 small nucleolar ribonucleoprotein IMP4	AGI-07	84.114
Tf0043			-	-	-	-	-	-		Ciclev10032519m	scaffold_4	24820269	24824732	C_unshiu_00001:mRNA_295.1	C_unshiu_00001	1871301	1874281	Agamous-like MADS-box protein AGL15	AGI-07	84.593
Af1187			-	-	-	-	-	-		Ciclev10031748m	scaffold_4	24996017	25000652	C_unshiu_00001:mRNA_314.1	C_unshiu_00001	1991693	1996431	Tocopherol O-methyltransferase	AGI-07	85.027
Cp0454			-	-	-	-	-	-		Ciclev10030551m	scaffold_4	23200936	23206254	C_unshiu_00001:mRNA_32.1	C_unshiu_00001	214996	218740	DEAD-box ATP-dependent RNA helicase ISE2, chloroplastic	AGI-07	73.034
Fb0343		AAvailable marker	O	-	-	-	-	O		Ciclev10033061m	scaffold_4	25059045	25061910	C_unshiu_00001:mRNA_322.1	C_unshiu_00001	2042062	2044301	U6 snRNA-associated Sm-like protein LSm7			KmG-07
Gn0061.2		MDisagree by Marco analysis	O	-	-	-	-	-		Ciclev10031014m	scaffold_4	25500601	25505812	C_unshiu_00001:mRNA_343.1	C_unshiu_00001	2191017	2199824	9-cis-epoxycarotenoid dioxygenase 4	AGI-06	20.248
Gn0071		Bno homozygous cultivar with minor allele	O	-	-	-	-	-	SI363	Ciclev10031039m	scaffold_4	25506446	25511133	C_unshiu_00001:mRNA_343.1	C_unshiu_00001	2191017	2199824	9-cis-epoxycarotenoid dioxygenase 4	AGI-07	86.113
Tf0045			-	-	-	-	-	-	SI303,SI321	Ciclev10032837m	scaffold_4	23496020	23497466	C_unshiu_00001:mRNA_74.1	C_unshiu_00001	490607	491890	Homeobox transcription factor	AGI-07	74.573
Ov0105		MDisagree by Marco analysis	O	-	-	-	-	-	SI126,SI278	Ciclev10031362m	scaffold_4	23552856	23556415	C_unshiu_00001:mRNA_81.1	C_unshiu_00001	545345	548897	Receptor-like kinase plant							NAT-07	36.023	RP-07
Ov0105.2	Ov0106.2		-	-	-	-	-	-		Ciclev10031362m	scaffold_4	23552856	23556415	C_unshiu_00001:mRNA_81.1	C_unshiu_00001	545345	548897	Receptor-like kinase plant	AGI-07	74.064	KmG-07	15.390	JtR-07	5.947
Af1509			-	-	-	-	-	-		Ciclev10032314m	scaffold_4	23564251	23568956	C_unshiu_00001:mRNA_83.3	C_unshiu_00001	555659	560336	Hypersensitive-induced response protein 1	AGI-07	73.796
Vs0015		OOthers	-	-	-	-	-	-						C_unshiu_00001:mRNA_84.1	C_unshiu_00001	561308	564986	Mitochondrial outer membrane protein porin of 34 kDa	AGI-09	115.452	KmG-09	34.185	JtR-09S	15.823
Cp0452		AAvailable marker	-	-	-	-	O	O		Ciclev10030661m	scaffold_4	23575399	23582495	C_unshiu_00001:mRNA_85.1	C_unshiu_00001	566935	573821	Alpha-amylase-like 3 isoform 1	AGI-07	75.350
Cp0093		Bno homozygous cultivar with minor allele	O	-	-	-	-	-		Ciclev10032427m	scaffold_4	23596434	23599906	C_unshiu_00001:mRNA_89.1	C_unshiu_00001	587949	598235	Putative WRKY transcription factor 72	AGI-07	74.537
Al0633		OOthers	O	-	-	-	-	O	SI123	Ciclev10015092m	scaffold_2	33837403	33842156	C_unshiu_00002:mRNA_126.1	C_unshiu_00002	901824	911260	Vascular plant one zinc finger protein isoform 1			KmG-06	55.857	JtR-06S	59.645	NAT-06S	51.106	RP-06.2	27.837
Tf0344		AAvailable marker	O	-	-	-	O	O		Ciclev10016433m	scaffold_2	34624236	34631123	C_unshiu_00002:mRNA_17.1	C_unshiu_00002	124392	131264	Floral homeotic protein AGAMOUS	AGI-06	24.216
Vs0005		OOthers	O	-	-	-	-	-	SI022,SI075	Ciclev10016009m	scaffold_2	33216839	33219042	C_unshiu_00002:mRNA_211.1	C_unshiu_00002	1511809	1513915	Epoxide hydrolase 2	AGI-06	31.521	KmG-02	59.329	JtR-06S	50.000	NAT-06S	50.000
Cp0537		AAvailable marker	O	-	-	-	O	O		Ciclev10016779m	scaffold_2	34189216	34193815	C_unshiu_00002:mRNA_71.2	C_unshiu_00002	543564	547918	Protein LIGHT-DEPENDENT SHORT HYPOCOTYLS 10	AGI-06	25.930
Fb0708			-	-	-	-	-	-		Ciclev10005455m	scaffold_9	31237089	31243737	C_unshiu_00003:mRNA_112.1	C_unshiu_00003	803488	808730	Zinc finger CCCH domain-containing protein 32	AGI-03	74.195			JtR-032	19.857
Tf0022		MDisagree by Marco analysis	O	-	-	-	-	-	SI116	Ciclev10005681m	scaffold_9	31237089	31243866	C_unshiu_00003:mRNA_112.1	C_unshiu_00003	803488	808730	Zinc finger CCCH domain-containing protein 32	AGI-03	78.631
Cp0336			-	-	-	-	-	-		Ciclev10004655m	scaffold_9	31244440	31250356	C_unshiu_00003:mRNA_113.1	C_unshiu_00003	809668	815079	ABC transporter D family member 2, chloroplastic	AGI-03	79.515
Ov0109		MDisagree by Marco analysis	O	-	-	-	-	-	SI172,SI202	Ciclev10004309m	scaffold_9	30513333	30517676	C_unshiu_00003:mRNA_13.1	C_unshiu_00003	122283	126575	Elongation factor 2	AGI-03	71.060			JtR-032	13.729			RP-03	71.532
Al0204			-	-	-	-	-	-		Ciclev10008298m	scaffold_1	275263	280936	C_unshiu_00003:mRNA_150.2	C_unshiu_00003	1127884	1133567	Myosin heavy chain-like protein					JtR-09S	5.527
Tf0176			-	-	-	-	-	-		Ciclev10008476m	scaffold_1	385469	388179	C_unshiu_00003:mRNA_163.1	C_unshiu_00003	1226924	1232429	Hypothetical protein									RP-01
Tf0177			-	-	-	-	-	-	SI133	Ciclev10008476m	scaffold_1	385469	388179	C_unshiu_00003:mRNA_163.1	C_unshiu_00003	1226924	1232429	Hypothetical protein
Tf0334			-	-	-	-	-	-	SI034	Ciclev10007003m	scaffold_9	30983347	30984159	C_unshiu_00003:mRNA_76.2	C_unshiu_00003	557862	561962	Nuclear transcription factor Y subunit C-9
Af1589			-	-	-	-	-	-		Ciclev10005524m	scaffold_9	30995129	30999295	C_unshiu_00003:mRNA_80.1	C_unshiu_00003	574672	576940	Peroxisomal 2,4-dienoyl-CoA reductase	AGI-03	77.744
Bf0150			-	-	-	-	-	-	SI316,SI370	Ciclev10004834m	scaffold_9	31018836	31027361	C_unshiu_00003:mRNA_85.1	C_unshiu_00003	596288	610960	Aldehyde dehydrogenase	AGI-03	77.920							RP-03	77.748
Tf0292		OOthers	O	-	-	-	-	-		Ciclev10006112m	scaffold_9	31139789	31143240	C_unshiu_00003:mRNA_98.2	C_unshiu_00003	698480	711976	Protein strawberry notch	AGI-03	77.793
Af1447			-	-	-	-	-	-		Ciclev10031155m	scaffold_4	22802995	22807340	C_unshiu_00004:mRNA_35.1	C_unshiu_00004	275820	279748	Aldehyde dehydrogenase	AGI-07	70.744
Lp0212			O	-	-	-	-	-		Ciclev10030930m	scaffold_4	22697056	22699336	C_unshiu_00004:mRNA_48.1	C_unshiu_00004	381547	383756	Polygalacturonase 1 beta-like protein 3	AGI-07	69.544
Bf0212			-	-	-	-	-	-	SI332	Ciclev10016442m	scaffold_2	9206686	9211152	C_unshiu_00004:mRNA_52.2	C_unshiu_00004	401860	406444	Carbonate dehydratase	AGI-06	117.593
Af1495			-	-	-	-	-	-		Ciclev10032113m	scaffold_4	22523092	22528307	C_unshiu_00004:mRNA_77.1	C_unshiu_00004	548746	553542	UDP-N-acetylglucosamine--N-acetylmuramyl-pyrophosphoryl-undecaprenol N-acetylglucosamine transferase isoform 3	AGI-07	69.544
Gn0017			-	-	-	-	-	-		Ciclev10007311m	scaffold_1	25880824	25887976	C_unshiu_00005:mRNA_103.1	C_unshiu_00005	841899	847089	Sucrose phosphate synthase	AGI-01	30.293	KmG-01	17.862
Cp0672			-	-	-	-	-	-		Ciclev10007769m	scaffold_1	28262202	28267878	C_unshiu_00005:mRNA_26.1	C_unshiu_00005	170218	174432	Putative eukaryotic translation initiation factor 4 gamma	AGI-01	101.472
Al0014			O	-	-	-	-	-	SI058,SI153,SI312	Ciclev10008225m	scaffold_1	1070373	1072218	C_unshiu_00005:mRNA_43.1	C_unshiu_00005	281165	283012	CBL-interacting serine/threonine-protein kinase 20	AGI-01	97.525							RP-01	3.295
Wy0055	Wy0055.em		-	-	-	-	-	-						C_unshiu_00005:mRNA_81.1	C_unshiu_00005	686926	696896	Neurochondrin	AGI-01	118.691
Tf0092			-	-	-	-	-	-	SI099	Ciclev10007435m	scaffold_1	3285601	3291534	C_unshiu_00006:mRNA_60.1	C_unshiu_00006	496127	502071	Class III HD-Zip family protein
Cp0996		Bno homozygous cultivar with minor allele	-	-	-	-	-	-	SI340	Ciclev10004474m	scaffold_9	543444	546746	C_unshiu_00007:mRNA_105.1	C_unshiu_00007	630727	633783	Neutral/alkaline invertase	AGI-03	9.366
Bf0005			-	-	-	-	-	-	SI194	Ciclev10005100m	scaffold_9	465444	468143	C_unshiu_00007:mRNA_115.1	C_unshiu_00007	710354	712926	Phosphatase 2C family protein	AGI-03	8.177
Tf0140			-	-	-	-	-	-		Ciclev10004457m	scaffold_9	225971	232459	C_unshiu_00007:mRNA_144.1	C_unshiu_00007	929895	935477	Squamosa promoter-binding-like protein 1	AGI-03	9.830
Fb0231			-	-	-	-	-	-		Ciclev10004999m	scaffold_9	1169260	1172055	C_unshiu_00007:mRNA_2.1	C_unshiu_00007	6589	14596	Two-component response regulator ARR12-like protein									RP-03	1.143
Tf0106			-	-	-	-	-	-		Ciclev10006161m	scaffold_9	1128046	1129318	C_unshiu_00007:mRNA_6.1	C_unshiu_00007	49599	50702	GATA transcription factor 15	AGI-03	7.674
Gmom26			-	-	-	-	-	-		Ciclev10005911m	scaffold_9	713868	716708	C_unshiu_00007:mRNA_76.1	C_unshiu_00007	473625	476336	Prefoldin subunit 3	AGI-03	10.918
Al0223			-	-	-	-	-	-		Ciclev10011771m	scaffold_6	17438270	17440122	C_unshiu_00008:mRNA_127.1	C_unshiu_00008	890026	891371	CBL-interacting serine/threonine-protein kinase 11									RP-04	17.965
Ov0419		AAvailable marker	-	-	-	-	-	O		Ciclev10011593m	scaffold_6	16709179	16712039	C_unshiu_00008:mRNA_31.2	C_unshiu_00008	178086	180944	Pyruvate decarboxylase									RP-04	11.143
Ov0305		MDisagree by Marco analysis	O	-	-	-	-	-	SI028,SI292	Ciclev10012499m	scaffold_6	16909492	16912088	C_unshiu_00008:mRNA_65.1	C_unshiu_00008	366943	369504	40S ribosomal protein S4	AGI-08	88.433	KmG-04	45.755					RP-04	15.410
Bf0189			-	-	-	-	-	-						C_unshiu_00008:mRNA_66.1	C_unshiu_00008	372226	374586	Ferritin									RP-04	15.774
Lp0118		MDisagree by Marco analysis	-	-	-	-	-	-						C_unshiu_00008:mRNA_8.1	C_unshiu_00008	46363	54318	Protein trichome birefringence-like 33	AGI-02	73.759	KmG-02	75.522	JtR-02	24.745
Al0402		AAvailable marker	O	-	-	-	O	O						C_unshiu_00008:mRNA_88.1	C_unshiu_00008	564906	567158	Peptide upstream ORF protein, putative	AGI-08	81.190	KmG-04	44.163			NAT-04	28.388
Vs0003		AAvailable marker	-	-	-	-	O	O	SI077					C_unshiu_00009:mRNA_117.1	C_unshiu_00009	675718	677501	Cysteine proteinase RD19a	AGI-09	35.312	KmG-09	72.447			NAT-09	93.467
Al0639		AAvailable marker	O	-	-	-	O	O		Ciclev10001091m	scaffold_5	41703787	41708779	C_unshiu_00009:mRNA_141.1	C_unshiu_00009	874868	888901	IQ calmodulin-binding motif protein	AGI-01	70.494	KmG-01	48.992	JtR-01S	110.675	NAT-01S	94.639	RP-01	28.746
Ov0313		OOthers	-	-	-	-	-	-		Ciclev10002372m	scaffold_5	41844984	41847835	C_unshiu_00009:mRNA_157.1	C_unshiu_00009	1013478	1016014	Diphthine synthase			KmG-09	79.072
Tf0019			-	-	-	-	-	-	SI056,SI347	Ciclev10001255m	scaffold_5	41881297	41883386	C_unshiu_00009:mRNA_161.1	C_unshiu_00009	1049324	1051358	C2H2-like zinc finger protein	AGI-09	34.799
Af1443			-	-	-	-	-	-		Ciclev10011413m	scaffold_6	25048398	25053494	C_unshiu_00009:mRNA_3.1	C_unshiu_00009	15765	28846	Pentatricopeptide repeat-containing family protein	AGI-04	33.808
Cp1887		MDisagree by Marco analysis	-	-	-	-	-	-		Ciclev10010991m	scaffold_6	25193617	25201413	C_unshiu_00009:mRNA_34.1	C_unshiu_00009	183041	190334	ATP-dependent chaperone ClpB
Af1011			O	-	-	-	-	-		Ciclev10013781m	scaffold_6	25306829	25315243	C_unshiu_00009:mRNA_53.1	C_unshiu_00009	289462	299397	Hypothetical protein									RP-04	60.491
Ov0513		OOthers	O	-	-	-	-	-		Ciclev10011622m	scaffold_6	25349417	25351949	C_unshiu_00009:mRNA_59.1	C_unshiu_00009	325807	333424	Hypothetical protein	AGI-04	38.903	KmG-04	5.110					RP-04	60.491
Al0022			-	-	-	-	-	-		Ciclev10011465m	scaffold_6	25364317	25368608	C_unshiu_00009:mRNA_62.1	C_unshiu_00009	346583	350755	Mitochondrial-processing peptidase subunit alpha									SA-09	42.503
Fb0219			-	-	-	-	-	-		Ciclev10031436m	scaffold_4	21153791	21158006	C_unshiu_00010:mRNA_101.1	C_unshiu_00010	718703	722812	F-box only protein 6	AGI-03	46.274
Lp0232			O	-	-	-	-	-		Ciclev10030590m	scaffold_4	21120135	21127140	C_unshiu_00010:mRNA_105.1	C_unshiu_00010	751317	757205	CHASE-domain containing histidine kinase 1									RP-07	19.079
Gn0037			-	-	-	-	-	-		Ciclev10032578m	scaffold_4	21042049	21048279	C_unshiu_00010:mRNA_111.3	C_unshiu_00010	823068	829158	Agamous-like MADS-box protein AGL9 homolog	AGI-08	55.656
Tf0005.2		AAvailable marker	O	-	-	-	-	O		Ciclev10032578m	scaffold_4	21042049	21048279	C_unshiu_00010:mRNA_111.3	C_unshiu_00010	823068	829158	Agamous-like MADS-box protein AGL9 homolog
Tf0148		AAvailable marker	O	-	-	-	O	O	SI119	Ciclev10032816m	scaffold_4	20998708	21001535	C_unshiu_00010:mRNA_116.1	C_unshiu_00010	869802	872410	Putative WRKY transcription factor 75	AGI-07	64.812
Tf0227		AAvailable marker	O	-	-	-	O	O		Ciclev10031750m	scaffold_4	21666061	21671693	C_unshiu_00010:mRNA_30.1	C_unshiu_00010	183508	188843	Trihelix transcription factor GT-1	AGI-08	35.927
Al0411		AAvailable marker	O	-	-	-	O	O		Ciclev10029439m	scaffold_8	19760077	19761961	C_unshiu_00011:mRNA_19.2	C_unshiu_00011	188649	189649	Zinc finger A20 and AN1 domain-containing stress-associated protein 8	AGI-08	40.857
Bf0202			-	-	-	-	-	-		Ciclev10000607m	scaffold_5	24103753	24107361	C_unshiu_00011:mRNA_55.1	C_unshiu_00011	511309	514460	Protein ETHYLENE INSENSITIVE 3									RP-09	27.641
Mf0034		OOthers	O	-	-	-	-	-		Ciclev10031304m	scaffold_4	1559490	1563887	C_unshiu_00012:mRNA_100.1	C_unshiu_00012	732963	736971	DEAD-box ATP-dependent RNA helicase 27									RP-07	73.631
Al0505			-	-	-	-	-	-		Ciclev10032306m	scaffold_4	947943	949892	C_unshiu_00012:mRNA_14.1	C_unshiu_00012	117194	125051	Plasma membrane intrinsic protein									RP-07	51.815
Al0617		AAvailable marker	O	-	-	-	O	O		Ciclev10033546m	scaffold_4	1021179	1023023	C_unshiu_00012:mRNA_24.1	C_unshiu_00012	188654	191971	Ubiquitin-binding WIYLD domain protein	AGI-07	8.553			JtR-07	74.121
Bf0021			O	-	-	-	-	-		Ciclev10031010m	scaffold_4	1058825	1062698	C_unshiu_00012:mRNA_26.1	C_unshiu_00012	227838	231495	Anthranilate synthase component I									RP-07	52.587
Af1505			-	-	-	-	-	-		Ciclev10031326m	scaffold_4	1531262	1535758	C_unshiu_00012:mRNA_96.1	C_unshiu_00012	704342	708725	Multiple inositol polyphosphate phosphatase 1	AGI-07	12.283
Cp0039			O	-	-	-	-	-		Ciclev10032929m	scaffold_4	1549679	1551396	C_unshiu_00012:mRNA_98.1	C_unshiu_00012	722822	724539	LOB domain-containing protein 12	AGI-07	11.882
Tf0076			-	-	-	-	-	-	SI266	Ciclev10031150m	scaffold_4	7200135	7204232	C_unshiu_00013:mRNA_63.3	C_unshiu_00013	459064	463137	NAC domain-containing protein 78	AGI-07	38.565
Cp0933		OOthers	-	-	-	-	-	-		Ciclev10019734m	scaffold_3	49821906	49825730	C_unshiu_00014:mRNA_26.1	C_unshiu_00014	159299	162719	Hypothetical protein	AGI-03	47.283
Tf0214			-	-	-	-	-	-	SI020	Ciclev10020053m	scaffold_3	50133837	50139049	C_unshiu_00014:mRNA_67.1	C_unshiu_00014	458017	462942	Transcription factor UNE10
Gn0050			-	-	-	-	-	-		Ciclev10024602m	scaffold_3	5382490	5385009	C_unshiu_00014:mRNA_87.1	C_unshiu_00014	637698	638678	CRT binding factor 3	AGI-05	29.035	KmG-05S	21.884	JtR-05	19.008
Cp0675		AAvailable marker	O	-	-	-	O	O		Ciclev10030633m	scaffold_4	20294240	20301426	C_unshiu_00015:mRNA_33.1	C_unshiu_00015	302440	309360	DNA-directed RNA polymerase	AGI-07	59.793
If0005		OOthers	-	-	-	-	-	-		Ciclev10032438m	scaffold_4	20629463	20633356	C_unshiu_00015:mRNA_81.1	C_unshiu_00015	667011	671011	Glucosamine/galactosamine-6-phosphate isomerase family protein					JtR-07	25.458	NAT-07	15.764
Cp0431		AAvailable marker	O	-	-	-	O	O		Ciclev10015731m	scaffold_2	27084177	27089027	C_unshiu_00017:mRNA_35.1	C_unshiu_00017	248152	252850	E3 ubiquitin protein ligase RIE1	AGI-06	60.660
Al0602		AAvailable marker	-	-	-	-	-	O		Ciclev10017248m	scaffold_2	27141148	27141869	C_unshiu_00017:mRNA_42.1	C_unshiu_00017	304994	305523	Hypothetical protein			KmG-06	18.450	JtR-06S	3.805
Cp0459			-	-	-	-	-	-		Ciclev10016822m	scaffold_2	27549660	27551146	C_unshiu_00017:mRNA_86.1	C_unshiu_00017	707192	708314	NADH dehydrogenase-like complex L	AGI-06	74.140
Al0039			-	-	-	-	-	-						C_unshiu_00018:mRNA_107.1	C_unshiu_00018	723553	725648	Bifunctional protein FolD	AGI-05	95.305
Tf0265			-	-	-	-	-	-	SI197	Ciclev10019232m	scaffold_3	49318106	49324231	C_unshiu_00018:mRNA_126.1	C_unshiu_00018	839780	845037	Homeobox-leucine zipper protein ANTHOCYANINLESS 2
Tf0363			-	-	-	-	-	-	SI002,SI096	Ciclev10019714m	scaffold_3	49318106	49324231	C_unshiu_00018:mRNA_126.1	C_unshiu_00018	839780	845037	Homeobox-leucine zipper protein ANTHOCYANINLESS 2
Tf0354			-	-	-	-	-	-	SI070	Ciclev10021202m	scaffold_3	48704416	48708817	C_unshiu_00018:mRNA_33.1	C_unshiu_00018	219801	223933	Transcription factor ASG4
Tf0279			-	-	-	-	-	-	SI073	Ciclev10019219m	scaffold_3	49031441	49035202	C_unshiu_00018:mRNA_78.1	C_unshiu_00018	562898	566588	Putative anthocyanin regulator	AGI-05	80.539
Tf0293		AAvailable marker	O	O	O	-	-	O		Ciclev10019219m	scaffold_3	49031441	49035202	C_unshiu_00018:mRNA_78.1	C_unshiu_00018	562898	566588	Putative anthocyanin regulator
Tf0087			-	-	-	-	-	-	SI166,SI271,SI287	Ciclev10031120m	scaffold_4	11412331	11417624	C_unshiu_00019:mRNA_18.1	C_unshiu_00019	190344	195992	Two-component response regulator-like APRR2	AGI-07	35.897
Tf0375			-	-	-	-	-	-		Ciclev10022365m	scaffold_3	13034654	13036082	C_unshiu_00020:mRNA_62.1	C_unshiu_00020	527751	528816	Homeobox leucine zipper protein	AGI-05	40.558
Edp005		HDisagree on Clementine haploid genotype	-	-	-	-	-	-		Ciclev10000211m	scaffold_5	21203994	21212595	C_unshiu_00020:mRNA_80.1	C_unshiu_00020	742433	758888	Retinoblastoma protein 2	AGI-09	105.195							RP-09	23.442
Cp2188		AAvailable marker	-	-	-	-	O	O		Ciclev10028997m	scaffold_8	24666729	24669708	C_unshiu_00021:mRNA_116.1	C_unshiu_00021	778469	782836	Phytol kinase	AGI-08	2.186
Gn0065		Bno homozygous cultivar with minor allele	O	-	-	-	-	-						C_unshiu_00021:mRNA_4.1	C_unshiu_00021	34178	38574	Phytoene desaturase	AGI-09	79.316
Lp0119		AAvailable marker	-	-	-	-	O	O	SI276	Ciclev10028631m	scaffold_8	24315720	24317671	C_unshiu_00021:mRNA_65.1	C_unshiu_00021	426040	431920	Hypothetical protein	AGI-08	8.544
Fb2130			-	-	-	-	-	-	SI069,SI117	Ciclev10030030m	scaffold_8	24341129	24344795	C_unshiu_00021:mRNA_68.1	C_unshiu_00021	452003	461315	Hypothetical protein	AGI-08	11.809	KmG-08	11.813
Cp2190		Bno homozygous cultivar with minor allele	-	-	-	-	-	-		Ciclev10028681m	scaffold_8	24416582	24418982	C_unshiu_00021:mRNA_82.1	C_unshiu_00021	526890	529253	Kinase PfkB	AGI-08	13.780
Al0308			-	-	-	-	-	-	SI045	Ciclev10028262m	scaffold_8	24521116	24524868	C_unshiu_00021:mRNA_97.1	C_unshiu_00021	630527	634212	NAD(P)H dehydrogenase B2	AGI-05	56.788
Bf0200		OOthers	-	-	-	-	-	-	SI335	Ciclev10014367m	scaffold_2	29022433	29030724	C_unshiu_00022:mRNA_44.1	C_unshiu_00022	308324	316293	Glutamine-tRNA ligase / glutaminyl-tRNA synthetas, putative isoform 1
Af1312			-	-	-	-	-	-		Ciclev10014367m	scaffold_2	29022433	29030537	C_unshiu_00022:mRNA_44.1	C_unshiu_00022	308324	316293	Glutamine-tRNA ligase / glutaminyl-tRNA synthetas, putative isoform 1	AGI-06	37.883
Wy0058	Wy0058.em		-	-	-	-	-	-		Ciclev10016274m	scaffold_2	29140509	29143804	C_unshiu_00022:mRNA_58.1	C_unshiu_00022	424974	428249	Plastid ribosomal protein L15
Tf0343		AtAvailable marker	O	-	-	-	O	O		Ciclev10016587m	scaffold_2	29204680	29206501	C_unshiu_00022:mRNA_67.1	C_unshiu_00022	489282	490950	High mobility group B protein 7	AGI-06	44.393
Wy0060	Wy0060.em		-	-	-	-	-	-		Ciclev10020776m	scaffold_3	46998745	47002683	C_unshiu_00023:mRNA_2.1	C_unshiu_00023	7129	11067	Pto kinase interactor 1	AGI-02	14.597
Tf0370			-	-	-	-	-	-		Ciclev10019820m	scaffold_3	47121093	47124518	C_unshiu_00023:mRNA_20.1	C_unshiu_00023	123134	131389	Hypothetical protein	AGI-05	69.117
Gmom04			-	-	-	-	-	-		Ciclev10019228m	scaffold_3	47476188	47479361	C_unshiu_00023:mRNA_74.1	C_unshiu_00023	480170	486801	Protein LHY	AGI-05	73.504
Gmom16			-	-	-	-	-	-		Ciclev10019228m	scaffold_3	47476188	47479361	C_unshiu_00023:mRNA_74.1	C_unshiu_00023	480170	486801	Protein LHY	AGI-05	73.007
Tf0419		AAvailable marker	O	O	O	-	-	O		Ciclev10019228m	scaffold_3	47476188	47479361	C_unshiu_00023:mRNA_74.1	C_unshiu_00023	480170	486801	Protein LHY
Al0247		T3 or more alleleic model	O	-	-	-	-	-		Ciclev10029281m	scaffold_8	2227827	2230752	C_unshiu_00024:mRNA_15.1	C_unshiu_00024	104182	106823	Somatic embryogenesis receptor kinase 1	AGI-08	77.316	KmG-08	91.101			NAT-082	73.850
Cp0297			-	-	-	-	-	-		Ciclev10028989m	scaffold_8	2135445	2138606	C_unshiu_00024:mRNA_26.2	C_unshiu_00024	197656	201866	ATP-dependent Clp protease, proteolytic subunit ClpP	AGI-08	78.209
Edw002			-	-	-	-	-	-		Ciclev10029316m	scaffold_8	2012329	2014782	C_unshiu_00024:mRNA_48.2	C_unshiu_00024	335678	337129	LIM transcription factor	AGI-08	77.720
Gn0049			-	-	-	-	-	-		Ciclev10028366m	scaffold_8	1604460	1606311	C_unshiu_00024:mRNA_95.1	C_unshiu_00024	699386	701126	DUF1005 family protein	AGI-08	77.688			JtR-08	17.757
Tf0020			-	-	-	-	-	-	SI154	Ciclev10026414m	scaffold_7	2289455	2291216	C_unshiu_00025:mRNA_31.1	C_unshiu_00025	258446	260200	Homeobox leucine zipper protein	AGI-02	71.294
Wy0034			-	-	-	-	-	-	SI367	Ciclev10026310m	scaffold_7	2299638	2302863	C_unshiu_00025:mRNA_32.1	C_unshiu_00025	269762	270443	Flavoprotein wrbA
Cp1085			-	-	-	-	-	-		Ciclev10025935m	scaffold_7	2390010	2391658	C_unshiu_00025:mRNA_42.1	C_unshiu_00025	337060	338142	Putative geranylgeranyl pyrophosphate synthase 3-like	AGI-02	70.082
Vt0015			-	-	-	-	-	-		Ciclev10025952m	scaffold_7	2441452	2443391	C_unshiu_00025:mRNA_49.1	C_unshiu_00025	381829	383760	Hexosyltransferase	AGI-02	70.082	KmG-02	67.054	JtR-02	21.082
Cp2263		AAvailable marker	-	-	-	-	O	O		Ciclev10026034m	scaffold_7	2586384	2588513	C_unshiu_00025:mRNA_69.1	C_unshiu_00025	530588	532071	Hypothetical protein	AGI-02	70.082
Cp1716		AAvailable marker	-	-	-	-	O	O		Ciclev10026303m	scaffold_7	2607670	2609433	C_unshiu_00025:mRNA_77.1	C_unshiu_00025	553145	554831	Thiol disulfide interchange protein	AGI-02	70.068
Fb1916			-	-	-	-	-	-	SI336	Ciclev10016275m	scaffold_2	12043969	12046230	C_unshiu_00026:mRNA_12.1	C_unshiu_00026	110679	112686	Histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH4									RP-06.1	24.027
Bf0146			O	-	-	-	-	-		Ciclev10022345m	scaffold_3	48528820	48531316	C_unshiu_00026:mRNA_37.1	C_unshiu_00026	280361	282836	RRNA-processing protein FCF1	AGI-05	78.274
Ov0310			-	-	-	-	-	-		Ciclev10023404m	scaffold_3	48463395	48465325	C_unshiu_00026:mRNA_46.1	C_unshiu_00026	334715	336716	Lanatoside 15-O-acetylesterase			KmG-01	21.291	JtR-01S	61.287
Cp1216		AAvailable marker	-	-	-	-	O	O		Ciclev10017113m	scaffold_2	12112790	12113903	C_unshiu_00026:mRNA_6.1	C_unshiu_00026	46658	47677	CCR protein	AGI-06	76.905
Ov0501			-	-	-	-	-	-		Ciclev10019938m	scaffold_3	48089473	48091232	C_unshiu_00026:mRNA_86.1	C_unshiu_00026	712172	713868	Nepenthesin II									RP-05	61.026
Af1693			-	-	-	-	-	-		Ciclev10016657m	scaffold_2	32069149	32072079	C_unshiu_00027:mRNA_31.2	C_unshiu_00027	205885	208484	DERLIN-2.2 isoform 1	AGI-06	35.794
Em0001			-	-	-	-	-	-		Ciclev10016968m	scaffold_2	31927342	31929229	C_unshiu_00027:mRNA_54.1	C_unshiu_00027	345067	346727	50S ribosomal protein L14, chloroplastic	AGI-06	35.643
Wy0056	Wy0056.em	AAvailable marker	-	-	-	-	O	O		Ciclev10014198m	scaffold_2	31740431	31747095	C_unshiu_00027:mRNA_81.1	C_unshiu_00027	521555	527308	Auxin response factor	AGI-06	36.788
Af1086			-	-	-	-	-	-		Ciclev10031563m	scaffold_4	10510018	10517939	C_unshiu_00028:mRNA_1.2	C_unshiu_00028	4115	12036	AP-2 complex subunit mu	AGI-05	41.306
Al0422		T3 or more alleleic model	O	-	-	-	-	-		Ciclev10013176m	scaffold_6	14495473	14496662	C_unshiu_00032:mRNA_34.1	C_unshiu_00032	369423	370581	Subtilisin inhibitor 1, putative	AGI-08	93.695
Al0501		Bno homozygous cultivar with minor allele	-	-	-	-	-	-		Ciclev10012221m	scaffold_6	14625884	14628443	C_unshiu_00032:mRNA_48.1	C_unshiu_00032	462609	490932	Tropinone reductase I
Tf0304			-	-	-	-	-	-		Ciclev10000491m	scaffold_5	953167	960232	C_unshiu_00033:mRNA_32.1	C_unshiu_00033	311804	317751	Auxin response factor	AGI-09	113.306
Fb0110			O	-	-	-	-	-	SI246	Ciclev10000900m	scaffold_5	8512380	8517835	C_unshiu_00033:mRNA_4.1	C_unshiu_00033	37755	43368	Bifunctional protein thiED	AGI-09	85.810	KmG-09	23.401	JtR-09S	5.362
Ov0111		AAvailable marker	-	-	-	-	O	O		Ciclev10000069m	scaffold_5	8532280	8539677	C_unshiu_00033:mRNA_6.1	C_unshiu_00033	57678	65071	TSA: Wollemia nobilis transcribed RNA sequence	AGI-09	85.810	KmG-09	11.923	JtR-09S	6.157			RP-09	20.238
Fb0373			O	-	-	-	-	-		Ciclev10000030m	scaffold_5	6404463	6435349	C_unshiu_00034:mRNA_15.1	C_unshiu_00034	150102	178260	ATP-dependent RNA helicase DHX29	AGI-09	85.810	KmG-09	22.909	JtR-09S	7.995			RP-09	0.104
Wy0062	Wy0062.em		-	-	-	-	-	-		Ciclev10011305m	scaffold_6	15214969	15222324	C_unshiu_00034:mRNA_76.1	C_unshiu_00034	634791	641934	Peptidyl-prolyl cis-trans isomerase PASTICCINO1	AGI-02	78.531
If0206		DDominant marker	-	-	-	-	-	-	SI208	Ciclev10012955m	scaffold_6	15192652	15194091	C_unshiu_00034:mRNA_78.1	C_unshiu_00034	662958	664402	Universal stress protein A-like protein
Mf0047		DDominant marker	-	-	-	-	-	-		Ciclev10006308m	scaffold_9	1685407	1687081	C_unshiu_00036:mRNA_24.2	C_unshiu_00036	126753	128428	Late embryogenesis abundant protein Lea5-D	AGI-03	14.323	KmG-031	7.139			NAT-03	50.708
Gmom19			-	-	-	-	-	-		Ciclev10011554m	scaffold_6	21450811	21454133	C_unshiu_00037:mRNA_27.1	C_unshiu_00037	166873	170276	Protein CCA1	AGI-04	54.804
Tf0373			-	-	-	-	-	-	SI088	Ciclev10011502m	scaffold_6	21229813	21233537	C_unshiu_00037:mRNA_60.1	C_unshiu_00037	387538	391239	Uridylate kinase, putative	AGI-04	61.716
Ov0020		AAvailable marker	O	-	-	-	O	O	SI055,SI143,SI213	Ciclev10011842m	scaffold_6	21598429	21600967	C_unshiu_00037:mRNA_7.2	C_unshiu_00037	37719	40241	Magnesium-protoporphyrin IX monomethyl ester [oxidative] cyclase	AGI-04	55.145	KmG-04	22.465			NAT-04	3.806	RP-04	40.905
Fb2159			-	-	-	-	-	-	SI205,SI300	Ciclev10021136m	scaffold_3	39606431	39608387	C_unshiu_00037:mRNA_76.1	C_unshiu_00037	551437	553057	Pirin family protein	AGI-05	49.856	KmG-05S	68.781	JtR-05	41.770			SA-09
Lp0133		AtAvailable marker	O	-	-	-	O	O		Ciclev10021187m	scaffold_3	39657613	39660222	C_unshiu_00037:mRNA_84.1	C_unshiu_00037	603033	605555	Class I chitinase	AGI-05	48.590	KmG-05S	60.040			NAT-05	26.483	RP-05	65.128
Al0304		MDisagree by Marco analysis	-	-	-	-	-	-	SI259,SI293	Ciclev10013536m	scaffold_6	22616979	22619271	C_unshiu_00038:mRNA_27.1	C_unshiu_00038	174815	175255	Nutrient reservoir, putative	AGI-04	46.361	KmG-04	16.744			NAT-04		RP-04	54.617
Bf0008			-	-	-	-	-	-	SI309	Ciclev10012950m	scaffold_6	22467565	22470029	C_unshiu_00038:mRNA_5.1	C_unshiu_00038	40983	43503	Pollen-specific C2 domain containing protein	AGI-04	47.391							RP-04	50.862
Af1600			-	-	-	-	-	-		Ciclev10013134m	scaffold_6	22758027	22760875	C_unshiu_00038:mRNA_51.4	C_unshiu_00038	305110	307864	Negatively light-regulated protein	AGI-04	5.122
Af1059			-	-	-	-	-	-		Ciclev10011827m	scaffold_6	23066384	23072168	C_unshiu_00038:mRNA_98.1	C_unshiu_00038	554982	560549	Plastidic glucose transporter 4	AGI-04	44.840
Tf0213		OOthers	O	-	-	-	-	-		Ciclev10030571m	scaffold_4	18839546	18848948	C_unshiu_00039:mRNA_19.1	C_unshiu_00039	154778	176393	Enhancer OF AG-4-like protein, putative	AGI-07	48.581
Tf0251			-	-	-	-	-	-	SI005					C_unshiu_00039:mRNA_19.1	C_unshiu_00039	154778	176393	Enhancer OF AG-4-like protein, putative
Vt0028			-	-	-	-	-	-		Ciclev10032489m	scaffold_4	18947498	18950949	C_unshiu_00039:mRNA_34.1	C_unshiu_00039	255025	269908	Hypothetical protein	AGI-07	51.998	KmG-07	44.183	JtR-07	39.088
Ks9013			-	-	-	-	-	-		Ciclev10032489m	scaffold_4	18947498	18950949	C_unshiu_00039:mRNA_34.1	C_unshiu_00039	255025	269908	Hypothetical protein			KmG-07	45.284	JtR-07	39.119
Fb0225			-	-	-	-	-	-		Ciclev10008570m	scaffold_1	4873970	4878979	C_unshiu_00039:mRNA_6.1	C_unshiu_00039	54980	59746	Protein arginine N-methyltransferase 1									RP-05	33.168
Al0415		AAvailable marker	-	-	-	-	O	O	SI120,SI310	Ciclev10004660m	scaffold_9	2732900	2738896	C_unshiu_00040:mRNA_76.1	C_unshiu_00040	632823	638463	Mitogen-activated protein kinase 14	AGI-03	24.885	KmG-031				NAT-03	41.576
Cp1697		AAvailable marker	-	-	-	-	O	O		Ciclev10028645m	scaffold_8	966124	968846	C_unshiu_00041:mRNA_89.1	C_unshiu_00041	555334	558046	Urease accessory protein UreH	AGI-02	73.770
Tf0356			-	-	-	-	-	-	SI134,SI160	Ciclev10029063m	scaffold_8	998289	1001763	C_unshiu_00041:mRNA_95.3	C_unshiu_00041	588335	591780	Basic-leucine zipper (BZIP) transcription factor family	AGI-08	83.743
Fb0372			-	-	-	-	-	-	SI343,SI052	Ciclev10002666m	scaffold_5	35123213	35124730	C_unshiu_00042:mRNA_34.1	C_unshiu_00042	237022	238272	Ubiquitin-fold modifier-conjugating enzyme 1	AGI-09	59.896
Gn0066.2		HDisagree on Clementine haploid genotype	O	-	-	-	-	-		Ciclev10011230m	scaffold_6	19578179	19583475	C_unshiu_00043:mRNA_12.1	C_unshiu_00043	90212	94791	Carotenoid isomerase	AGI-04
Em0003			-	-	-	-	-	-		Ciclev10011201m	scaffold_6	19840881	19844299	C_unshiu_00043:mRNA_48.1	C_unshiu_00043	360776	363775	BEL1-like homeodomain protein 1	AGI-08	56.724
Wy0048	Wy0048.k		-	-	-	-	-	-		Ciclev10010999m	scaffold_6	19900235	19904192	C_unshiu_00043:mRNA_54.1	C_unshiu_00043	424252	427984	Putative receptor protein kinase TMK1	AGI-04	63.371					NAT-04	21.157
Mf0007		ULess informative for main cultivars	-	-	-	-	-	-		Ciclev10008907m	scaffold_1	17471330	17472833	C_unshiu_00044:mRNA_52.1	C_unshiu_00044	424343	425685	NADPH-dependent codeinone reductase-like protein
Tf0072			-	-	-	-	-	-		Ciclev10005403m	scaffold_9	28757274	28759075	C_unshiu_00045:mRNA_48.1	C_unshiu_00045	372168	373811	Heat stress transcription factor B-4	AGI-03	35.962
Tf0074			O	-	-	-	-	-		Ciclev10005366m	scaffold_9	28444512	28446074	C_unshiu_00045:mRNA_7.1	C_unshiu_00045	62608	63842	TCP family transcription factor	AGI-03	37.816
Al0628			-	-	-	-	-	-		Ciclev10004696m	scaffold_9	28974337	28977865	C_unshiu_00045:mRNA_76.1	C_unshiu_00045	547196	550605	O-glucosyltransferase rumi like			KmG-031	5.650
Af1638			-	-	-	-	-	-		Ciclev10004755m	scaffold_9	28984972	28989373	C_unshiu_00045:mRNA_79.1	C_unshiu_00045	556440	562091	Tubulin	AGI-03	34.554
Ks9011		AAvailable marker	-	-	-	-	-	O		Ciclev10004755m	scaffold_9	28984972	28989373	C_unshiu_00045:mRNA_79.1	C_unshiu_00045	556440	562091	Tubulin					JtR-032
Cp0813			-	-	-	-	-	-	SI047	Ciclev10011980m	scaffold_6	20638049	20641557	C_unshiu_00046:mRNA_46.1	C_unshiu_00046	406041	409549	Alpha/beta fold hydrolase	AGI-04	58.655
If0205		Bno homozygous cultivar with minor allele	-	-	-	-	-	-	SI256					C_unshiu_00046:mRNA_66.1	C_unshiu_00046	551244	556744	Hypothetical protein	AGI-04	86.280	KmG-04	52.960
Af1467			-	-	-	-	-	-		Ciclev10008651m	scaffold_1	24171632	24175378	C_unshiu_00047:mRNA_19.1	C_unshiu_00047	116658	120038	Putative amino acid permease 7	AGI-01	29.784
Tf0049			-	-	-	-	-	-	SI328	Ciclev10008919m	scaffold_1	24273993	24277800	C_unshiu_00047:mRNA_33.1	C_unshiu_00047	212549	221653	WD domain protein-like	AGI-01	26.841
Ks9001			-	-	-	-	-	-		Ciclev10008207m	scaffold_1	24548109	24552107	C_unshiu_00047:mRNA_72.1	C_unshiu_00047	475125	488565	Inter-alpha-trypsin inhibitor heavy chain-related isoform 1	AGI-01	27.192			JtR-01S	61.287
If0003		Bno homozygous cultivar with minor allele	-	-	-	-	-	-	SI130	Ciclev10015433m	scaffold_2	35470078	35472862	C_unshiu_00048:mRNA_13.1	C_unshiu_00048	64652	67377	Aminomethyltransferase	AGI-06	18.136			JtR-06S	67.371
Cp0384		AAvailable marker	O	-	-	-	O	O		Ciclev10015162m	scaffold_2	35422598	35425980	C_unshiu_00048:mRNA_23.2	C_unshiu_00048	111764	114820	APS reductase	AGI-06	19.002
Bf0028		DDominant marker	O	-	-	O	-	-	SI001	Ciclev10014319m	scaffold_2	35354776	35363026	C_unshiu_00048:mRNA_32.1	C_unshiu_00048	179733	188796	Soluble starch synthase III-1	AGI-06	17.966
Bf0110			-	-	-	-	-	-	SI297	Ciclev10014639m	scaffold_2	35235517	35237892	C_unshiu_00048:mRNA_48.1	C_unshiu_00048	306412	308620	9-cis-epoxycarotenoid dioxygenase 1
Al0417		MDisagree by Marco analysis	O	-	-	-	-	-	SI244,SI255	Ciclev10015483m	scaffold_2	35212691	35214865	C_unshiu_00048:mRNA_50.1	C_unshiu_00048	328418	330513	Kelch repeat-containing F-box family protein	AGI-06	20.297	KmG-06	62.256			NAT-06S	56.647
Ov0325			-	-	-	-	-	-		Ciclev10016692m	scaffold_2	35180594	35182774	C_unshiu_00048:mRNA_54.1	C_unshiu_00048	359734	361893	SGS domain-containing protein							NAT-082	48.374
Af1580			-	-	-	-	-	-		Ciclev10016368m	scaffold_2	35013848	35015439	C_unshiu_00048:mRNA_76.1	C_unshiu_00048	512885	514767	NAD(P)-binding Rossmann-fold superfamily protein isoform 2	AGI-06	20.932
Cp0077			O	-	-	-	-	-		Ciclev10015497m	scaffold_2	9849133	9852098	C_unshiu_00049:mRNA_29.1	C_unshiu_00049	210181	212829	Altered inheritance of mitochondria protein 32	AGI-08	54.867
Tf0166			-	-	-	-	-	-	SI156	Ciclev10000524m	scaffold_5	19682579	19686163	C_unshiu_00050:mRNA_13.1	C_unshiu_00050	140837	153470	Hypothetical protein	AGI-09	101.351
Tf0130			-	-	-	-	-	-		Ciclev10001027m	scaffold_5	19740133	19745806	C_unshiu_00050:mRNA_15.1	C_unshiu_00050	195528	200204	Transcription factor GAMYB	AGI-09	103.217
Bf0128			O	-	-	-	-	-		Ciclev10025298m	scaffold_7	3323269	3331038	C_unshiu_00051:mRNA_2.2	C_unshiu_00051	25872	40163	Hypothetical protein	AGI-02	70.082					NAT-02S	77.157	RP-02.2	9.835
Cp1925		AAvailable marker	-	-	-	-	O	O		Ciclev10005182m	scaffold_9	3115971	3120271	C_unshiu_00051:mRNA_29.1	C_unshiu_00051	224928	229203	YjeF family domain-containing protein	AGI-03	24.457
Lp0202			O	-	-	-	-	-		Ciclev10006509m	scaffold_9	3131006	3134438	C_unshiu_00051:mRNA_31.2	C_unshiu_00051	239802	243699	NEDD8-activating enzyme E1 catalytic subunit	AGI-03	23.085
Fb1227			-	-	-	-	-	-		Ciclev10004375m	scaffold_9	3367718	3376062	C_unshiu_00051:mRNA_60.1	C_unshiu_00051	463042	471084	Chloride channel protein	AGI-03	19.631
Wy0029			-	-	-	-	-	-		Ciclev10012640m	scaffold_6	21145703	21148279	C_unshiu_00052:mRNA_26.1	C_unshiu_00052	161014	162179	Type II peroxiredoxin	AGI-04
Mf0092		AAvailable marker	-	-	-	-	O	O	SI138	Ciclev10012056m	scaffold_6	21137783	21142157	C_unshiu_00052:mRNA_27.2	C_unshiu_00052	168316	172622	Phosphopyruvate hydratase	AGI-04	59.190	KmG-04	30.795			NAT-04	11.576
Al0514		ULess informative for main cultivars	-	-	-	-	-	-		Ciclev10012145m	scaffold_6	21035910	21038368	C_unshiu_00052:mRNA_38.1	C_unshiu_00052	265461	267883	Fructose-bisphosphate aldolase, cytoplasmic isozyme			KmG-04	32.217
If0210			-	-	-	-	-	-	SI042	Ciclev10012145m	scaffold_6	21035910	21038368	C_unshiu_00052:mRNA_38.1	C_unshiu_00052	265461	267883	Fructose-bisphosphate aldolase, cytoplasmic isozyme	AGI-02	73.759
Lp0206			O	-	-	-	-	-		Ciclev10011764m	scaffold_6	20836509	20840107	C_unshiu_00052:mRNA_56.1	C_unshiu_00052	452105	455631	Monodehydroascorbate reductase	AGI-04	58.655
Af1332			-	-	-	-	-	-		Ciclev10013051m	scaffold_6	20834427	20836151	C_unshiu_00052:mRNA_57.1	C_unshiu_00052	455959	457684	60S acidic ribosomal protein	AGI-04
Ov0127	Ov0126.2		-	-	-	-	-	-	SI124,SI284	Ciclev10022482m	scaffold_3	46814909	46817474	C_unshiu_00053:mRNA_57.3	C_unshiu_00053	477728	479995	ADP-ribosylation factor A1F	AGI-05	65.510	KmG-05S	81.631	JtR-05	45.715			RP-05	64.195
Mf0058		T3 or more alleleic model	-	-	-	-	-	-		Ciclev10022378m	scaffold_3	46818817	46822856	C_unshiu_00053:mRNA_58.1	C_unshiu_00053	481338	485184	Nitrogen regulatory protein P-II	AGI-08	57.196			JtR-05	39.516
Al0008			-	-	-	-	-	-		Ciclev10001908m	scaffold_5	40317721	40321609	C_unshiu_00054:mRNA_1.1	C_unshiu_00054	5765	8674	26S proteasome non-ATPase regulatory subunit 14									SA-09	50.699
Cp0741		AAvailable marker	O	-	-	-	O	O		Ciclev10008230m	scaffold_1	3746864	3749903	C_unshiu_00055:mRNA_22.1	C_unshiu_00055	168281	172005	Ferrochelatase	AGI-01	75.964
Ks9010		AAvailable marker	-	-	-	-	O	O		Ciclev10007188m	scaffold_9	29460866	29463385	C_unshiu_00056:mRNA_15.1	C_unshiu_00056	116304	118823	Receptor-like protein kinase HERK 1	AGI-04	62.499	KmG-04	39.019
Gn0014.2		Bno homozygous cultivar with minor allele	O	-	-	-	-	-		Ciclev10005481m	scaffold_9	29488658	29491181	C_unshiu_00056:mRNA_20.1	C_unshiu_00056	144107	146527	Beta-carotene hydroxylase 1
Af1513			-	-	-	-	-	-		Ciclev10006024m	scaffold_9	29523786	29526379	C_unshiu_00056:mRNA_24.1	C_unshiu_00056	181282	183151	40S ribosomal protein S10	AGI-03	63.545
Bf0004			-	-	-	-	-	-	SI273	Ciclev10005212m	scaffold_9	29563003	29568705	C_unshiu_00056:mRNA_33.1	C_unshiu_00056	220997	225323	Pentatricopeptide repeat superfamily protein, putative isoform 1	AGI-03	58.312
Cp0018			-	-	-	-	-	-		Ciclev10005068m	scaffold_9	5605470	5610840	C_unshiu_00057:mRNA_49.1	C_unshiu_00057	415460	428173	Putative E3 ubiquitin-protein ligase HERC1	AGI-03	44.848
Bf0402			-	-	-	-	-	-		Ciclev10020232m	scaffold_3	9137249	9144663	C_unshiu_00058:mRNA_19.1	C_unshiu_00058	104866	110977	TRNA-specific adenosine deaminase-like protein 3	AGI-05	43.970
Af1037			-	-	-	-	-	-		Ciclev10032461m	scaffold_4	1969590	1972842	C_unshiu_00058:mRNA_65.1	C_unshiu_00058	521901	525000	Uroporphyrinogen decarboxylase	AGI-04	50.972
Bf0109			-	-	-	-	-	-	SI233	Ciclev10032461m	scaffold_4	1970129	1972842	C_unshiu_00058:mRNA_65.1	C_unshiu_00058	521901	525000	Uroporphyrinogen decarboxylase									RP-07	51.394
Af1437			-	-	-	-	-	-		Ciclev10002114m	scaffold_5	1474396	1479079	C_unshiu_00060:mRNA_37.1	C_unshiu_00060	309328	313345	Short-chain alcohol dehydrogenase	AGI-09	92.804
Af1629			-	-	-	-	-	-		Ciclev10012332m	scaffold_6	2969527	2973147	C_unshiu_00060:mRNA_62.1	C_unshiu_00060	539807	543307	Mitochondrial carnitine/acylcarnitine carrier protein CACL	AGI-07	39.420
Cp0233			-	-	-	-	-	-		Ciclev10031694m	scaffold_4	11210879	11216325	C_unshiu_00061:mRNA_64.1	C_unshiu_00061	550725	556167	Ribose-phosphate pyrophosphokinase 4	AGI-07	37.826
Cp1044		Bno homozygous cultivar with minor allele	-	-	-	-	-	-		Ciclev10015927m	scaffold_2	4354278	4358516	C_unshiu_00062:mRNA_38.1	C_unshiu_00062	326045	332995	Iron-sulfur cluster formation ABC transporter ATP-binding subunit	AGI-07	39.420
Al0413		AAvailable marker	-	-	-	O	O	O	SI275,SI299	Ciclev10004620m	scaffold_9	7579900	7583093	C_unshiu_00063:mRNA_61.1	C_unshiu_00063	483279	486427	Chloroplast beta-amylase 3	AGI-03	46.197	KmG-032	19.570	JtR-031	10.395			RP-03	33.559
Al0601			-	-	-	-	-	-						C_unshiu_00065:mRNA_8.1	C_unshiu_00065	39268	43421	Probable GTP diphosphokinase RSH2, chloroplastic	AGI-08	93.624
Lp0237	Lp0237.k		-	-	-	-	-	-		Ciclev10007524m	scaffold_1	25987803	25992258	C_unshiu_00066:mRNA_23.1	C_unshiu_00066	112710	117006	Pyrophosphate-energized vacuolar membrane proton pump	AGI-01	29.815	KmG-01	13.444	JtR-01S	57.629	NAT-01S	8.967
Lp0211			O	-	-	-	-	-		Ciclev10009567m	scaffold_1	25816949	25818472	C_unshiu_00066:mRNA_48.1	C_unshiu_00066	279404	280861	Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin superfamily protein isoform 1	AGI-01	30.175							RP-01	24.533
Ov0319			-	-	-	-	-	-		Ciclev10009395m	scaffold_1	25761570	25764926	C_unshiu_00066:mRNA_53.1	C_unshiu_00066	333477	336681	Ubiquitin system component Cue protein			KmG-032	19.158
Af1094			-	-	-	-	-	-		Ciclev10009395m	scaffold_1	25761570	25764926	C_unshiu_00066:mRNA_53.1	C_unshiu_00066	333477	336681	Ubiquitin system component Cue protein	AGI-01	30.175
Cp1998		AAvailable marker	-	-	-	-	-	O		Ciclev10009395m	scaffold_1	25761570	25764926	C_unshiu_00066:mRNA_53.1	C_unshiu_00066	333477	336681	Ubiquitin system component Cue protein
Af1084			-	-	-	-	-	-		Ciclev10008467m	scaffold_1	25716862	25720071	C_unshiu_00066:mRNA_57.1	C_unshiu_00066	369928	382143	Hypothetical protein	AGI-01	24.643
Mf0086		AAvailable marker	O	-	-	-	O	O	SI220,SI315	Ciclev10009756m	scaffold_1	25592494	25593617	C_unshiu_00066:mRNA_75.1	C_unshiu_00066	500992	501833	17.9 kDa class II heat shock protein	AGI-01	26.428	KmG-01	19.692	JtR-01S	57.666			RP-01	69.936
Tf0455		OOthers	O	-	-	-	-	-		Ciclev10017004m	scaffold_2	9338651	9341271	C_unshiu_00067:mRNA_10.1	C_unshiu_00067	74696	88429	Hypothetical protein	AGI-06	114.172
Tf0042.2		AAvailable marker	O	-	-	-	-	O		Ciclev10016820m	scaffold_2	9338651	9341271	C_unshiu_00067:mRNA_10.1	C_unshiu_00067	74696	88429	Hypothetical protein
Cp1880		AAvailable marker	-	-	-	-	-	O		Ciclev10016235m	scaffold_2	9351630	9354621	C_unshiu_00067:mRNA_9.1	C_unshiu_00067	71252	74672	Peptide deformylase
Mf0041		AAvailable marker	-	-	-	-	O	O		Ciclev10022012m	scaffold_3	45076821	45080633	C_unshiu_00069:mRNA_16.1	C_unshiu_00069	123654	127483	Histidine-containing phosphotransfer protein 1	AGI-05	56.534	KmG-05S	73.977	JtR-05	38.393
Al0614			-	-	-	-	-	-		Ciclev10022348m	scaffold_3	44987719	44991534	C_unshiu_00069:mRNA_32.1	C_unshiu_00069	220620	224375	Methyl-CpG-binding domain 4	AGI-05	56.788	KmG-06	35.565
Al0309		AAvailable marker	O	-	-	-	-	O		Ciclev10022019m	scaffold_3	44900059	44900865	C_unshiu_00069:mRNA_47.1	C_unshiu_00069	301188	317479	Hypothetical protein			KmG-05S	73.967	JtR-05	38.749			RP-05	86.332
Mf0073		HDisagree on Clementine haploid genotype	-	-	-	-	-	-						C_unshiu_00069:mRNA_5.1	C_unshiu_00069	25589	28375	Hypothetical protein					JtR-05	38.749	NAT-05	44.567
Lp0140		MDisagree by Marco analysis	O	-	-	-	-	-		Ciclev10016399m	scaffold_2	32629908	32634194	C_unshiu_00070:mRNA_52.1	C_unshiu_00070	393864	397918	Universal stress protein A-like protein			KmG-02	12.229	JtR-02	2.765			RP-02	8.172
Al0647		MDisagree by Marco analysis	O	-	-	-	-	-		Ciclev10016069m	scaffold_2	32640743	32643349	C_unshiu_00070:mRNA_53.1	C_unshiu_00070	403765	406305	Nitric oxide synthase-interacting protein homolog	AGI-06		KmG-06	46.877
Fb0478			-	-	-	-	-	-		Ciclev10008010m	scaffold_1	14592248	14596429	C_unshiu_00071:mRNA_18.1	C_unshiu_00071	196512	200666	Beta-glucosidase 44	AGI-01	61.025
Bf0161			-	-	-	-	-	-	SI089,SI348	Ciclev10015189m	scaffold_2	6658003	6660691	C_unshiu_00072:mRNA_47.1	C_unshiu_00072	364436	365812	Sequence-specific DNA binding transcription factors	AGI-06	144.849
Af1636			-	-	-	-	-	-		Ciclev10016216m	scaffold_2	6611813	6619116	C_unshiu_00072:mRNA_53.1	C_unshiu_00072	416072	423443	Zinc transporter ZTP29	AGI-06	150.228
Cp0214		OOthers	-	-	-	-	-	-		Ciclev10016075m	scaffold_2	29732249	29735969	C_unshiu_00073:mRNA_25.1	C_unshiu_00073	178507	182191	MOSC domain-containing protein 2, mitochondrial	AGI-06	46.660
Cp0415			-	-	-	-	-	-		Ciclev10011681m	scaffold_6	22213544	22219300	C_unshiu_00074:mRNA_13.1	C_unshiu_00074	81301	86950	ATA15 protein	AGI-04	50.134
Mf0033		AAvailable marker	-	-	-	-	O	O		Ciclev10010044m	scaffold_1	6227617	6228389	C_unshiu_00075:mRNA_11.1	C_unshiu_00075	123779	124531	Hypothetical protein	AGI-01	62.570	KmG-01	46.353	JtR-01S	106.811	NAT-01S	77.905
Tf0263			-	-	-	-	-	-	SI013	Ciclev10008768m	scaffold_1	6358030	6359568	C_unshiu_00075:mRNA_22.1	C_unshiu_00075	227733	229211	Heat shock transcription factor A7a1
Bf0193			O	-	-	-	-	-	SI100,SI109	Ciclev10014811m	scaffold_2	35970577	35973973	C_unshiu_00077:mRNA_15.2	C_unshiu_00077	102078	105358	Scarecrow-like transcription factor PAT1									RP-06.2	14.065
Tf0330			-	-	-	-	-	-	SI064,SI139	Ciclev10014811m	scaffold_2	35970577	35973973	C_unshiu_00077:mRNA_15.2	C_unshiu_00077	102078	105358	Scarecrow-like transcription factor PAT1	AGI-06	13.470
Gn0073		AAvailable marker	O	O	-	-	O	O		Ciclev10014770m	scaffold_2	35895662	35898841	C_unshiu_00077:mRNA_4.1	C_unshiu_00077	30410	32987	Tonoplast dicarboxylate transporter	AGI-06	12.402
Tf0402			-	-	-	-	-	-		Ciclev10015893m	scaffold_2	36211961	36216858	C_unshiu_00077:mRNA_57.1	C_unshiu_00077	335424	340163	MYB-CC type transfactor	AGI-06	9.560
Tf0021		AAvailable marker	-	-	-	-	-	O		Ciclev10011169m	scaffold_6	21905557	21908832	C_unshiu_00079:mRNA_39.1	C_unshiu_00079	273228	275864	BZIP transcription factor family protein
Af1499			-	-	-	-	-	-		Ciclev10011169m	scaffold_6	21905557	21908832	C_unshiu_00079:mRNA_39.1	C_unshiu_00079	273228	275864	BZIP transcription factor family protein	AGI-04
Bf1186			-	-	-	-	-	-	SI245	Ciclev10012047m	scaffold_6	21912438	21917736	C_unshiu_00079:mRNA_40.1	C_unshiu_00079	278696	283911	R3H domain-containing protein 2
Af1508			-	-	-	-	-	-		Ciclev10011580m	scaffold_6	21983044	21991500	C_unshiu_00079:mRNA_48.1	C_unshiu_00079	328854	336213	Stomatal closure-related actin-binding protein 3	AGI-04	1.342
Al0636		AAvailable marker	O	-	-	O	O	O	SI313	Ciclev10007493m	scaffold_1	23776796	23782088	C_unshiu_00080:mRNA_56.1	C_unshiu_00080	464290	469444	WW domain-containing protein	AGI-01	27.489	KmG-01	25.751	JtR-01S	63.210	NAT-01S	12.652	RP-01	48.896
Af1554			-	-	-	-	-	-		Ciclev10009386m	scaffold_1	23753759	23756754	C_unshiu_00080:mRNA_59.1	C_unshiu_00080	491826	492778	Protein CWC15	AGI-01	28.775
Ov0403		AAvailable marker	O	-	-	-	O	O	SI136,SI298,SI325	Ciclev10016280m	scaffold_2	23891814	23893095	C_unshiu_00081:mRNA_50.1	C_unshiu_00081	296655	297936	Chlorophyll a/b binding protein	AGI-06	61.779	KmG-06	12.610	JtR-06S
Ov0018		ULess informative for main cultivars	-	-	-	-	-	-		Ciclev10028443m	scaffold_8	22316999	22319482	C_unshiu_00082:mRNA_34.1	C_unshiu_00082	267163	269630	Elongation factor 1-alpha
Bf0204			-	-	-	-	-	-	SI326	Ciclev10025089m	scaffold_7	3222483	3228894	C_unshiu_00084:mRNA_14.1	C_unshiu_00084	139704	145312	Zeaxanthin epoxidase, chloroplastic									RP-02.2	9.835
Gn0068			-	-	-	-	-	-		Ciclev10025089m	scaffold_7	3222483	3228894	C_unshiu_00084:mRNA_14.1	C_unshiu_00084	139704	145312	Zeaxanthin epoxidase, chloroplastic	AGI-02	68.446							RP-02.2	9.814
Gn0068.2		HDisagree on Clementine haploid genotype	O	-	-	-	-	-		Ciclev10025089m	scaffold_7	3222483	3228894	C_unshiu_00084:mRNA_14.1	C_unshiu_00084	139704	145312	Zeaxanthin epoxidase, chloroplastic
Fb0227			-	-	-	-	-	-		Ciclev10026002m	scaffold_7	2938059	2940407	C_unshiu_00084:mRNA_42.1	C_unshiu_00084	428180	435326	Phospholipase, patatin family	AGI-02	70.082							RP-02.2	12.696
Af1177			-	-	-	-	-	-		Ciclev10005989m	scaffold_9	2168387	2170546	C_unshiu_00085:mRNA_13.1	C_unshiu_00085	78341	80308	CASP-like protein 1E1	AGI-03	18.579
Al0231			-	-	-	-	-	-		Ciclev10033829m	scaffold_4	16223771	16226683	C_unshiu_00086:mRNA_13.1	C_unshiu_00086	99963	109609	Shatterproof									RP-06.1	7.272
Edw001		AAvailable marker	-	-	-	-	-	O		Ciclev10033829m	scaffold_4	16223771	16226683	C_unshiu_00086:mRNA_13.1	C_unshiu_00086	99963	109609	Shatterproof
Gn0040		AAvailable marker	-	-	-	-	O	O	SI015,SI337	Ciclev10033176m	scaffold_4	16232756	16233365	C_unshiu_00086:mRNA_13.2	C_unshiu_00086	99963	109609	AG MADS-box protein	AGI-07	43.542	KmG-07	56.094	JtR-07	48.672
Tf0320			-	-	-	-	-	-	SI203	Ciclev10033829m	scaffold_4	16223771	16226683	C_unshiu_00086:mRNA_13.2	C_unshiu_00086	99963	109609	AG MADS-box protein	AGI-07	45.716
Tf0090		AAvailable marker	O	-	-	-	-	O		Ciclev10031135m	scaffold_4	16519046	16521918	C_unshiu_00086:mRNA_45.1	C_unshiu_00086	374812	377677	Transcription factor bHLH62
Fb0234			-	-	-	-	-	-	SI250,SI265	Ciclev10032271m	scaffold_4	16176836	16178421	C_unshiu_00086:mRNA_8.1	C_unshiu_00086	52764	54349	Protodermal factor 1.3, putative	AGI-07	45.424							RP-07	30.993
Fb0389			-	-	-	-	-	-		Ciclev10014121m	scaffold_2	25179668	25188103	C_unshiu_00087:mRNA_31.1	C_unshiu_00087	209767	218135	Putative pesticidal crystal cry8Ba-like	AGI-08	56.850
Lp0034		ULess informative for main cultivars	O	-	-	-	-	-						C_unshiu_00087:mRNA_54.1	C_unshiu_00087	395005	398280	Peroxisomal membrane protein 13
Cp1011			-	-	-	-	-	-		Ciclev10016354m	scaffold_2	25346439	25350875	C_unshiu_00087:mRNA_55.1	C_unshiu_00087	398683	402763	ZZ-type zinc finger-containing 3	AGI-09	115.692
Tf0075			-	-	-	-	-	-	SI059,SI248	Ciclev10010972m	scaffold_6	19142307	19156510	C_unshiu_00089:mRNA_11.1	C_unshiu_00089	108874	122025	Homoserine kinase	AGI-04	66.455
Ov0117		AAvailable marker	O	-	-	-	O	O	SI040	Ciclev10010926m	scaffold_6	19105139	19113780	C_unshiu_00089:mRNA_17.1	C_unshiu_00089	153791	161685	Hypothetical protein	AGI-04	66.455							RP-04	28.160
Cp0895		AAvailable marker	-	-	-	-	O	O		Ciclev10011406m	scaffold_6	19241700	19246874	C_unshiu_00089:mRNA_3.1	C_unshiu_00089	9945	14749	ATP-dependent RNA helicase	AGI-04	67.375
Cp0849			-	-	-	-	-	-	SI355	Ciclev10012425m	scaffold_6	17651466	17653457	C_unshiu_00090:mRNA_56.2	C_unshiu_00090	364770	367591	Non-green plastid inner envelope membrane protein
Tf0432		AAvailable marker	O	-	-	-	O	O		Ciclev10016685m	scaffold_2	31420457	31425299	C_unshiu_00091:mRNA_39.1	C_unshiu_00091	370141	375026	Nuclear transcription factor Y subunit A-7	AGI-06	38.958
Ov0012			-	-	-	-	-	-		Ciclev10019638m	scaffold_3	2933121	2937460	C_unshiu_00092:mRNA_50.1	C_unshiu_00092	356984	361021	Aldehyde dehydrogenase			KmG-05S	100.000
Al0637		AAvailable marker	O	-	-	-	-	O	SI353	Ciclev10019147m	scaffold_3	2939620	2941934	C_unshiu_00092:mRNA_51.1	C_unshiu_00092	363486	365791	Spotted leaf protein, putative
Al0317			-	-	-	-	-	-		Ciclev10021392m	scaffold_3	3006218	3008357	C_unshiu_00092:mRNA_60.1	C_unshiu_00092	425854	427887	CASP-like protein 4A2			KmG-05S	16.871	JtR-05	9.525
Tf0205		OOthers	O	-	-	-	-	-	SI274	Ciclev10005062m	scaffold_9	16383851	16393557	C_unshiu_00094:mRNA_29.1	C_unshiu_00094	262934	272307	UBX domain-containing protein 1	AGI-03	46.274
Bf0130			-	-	-	-	-	-	SI063,SI188	Ciclev10004858m	scaffold_9	26981498	26984277	C_unshiu_00095:mRNA_24.1	C_unshiu_00095	228406	230902	F-box family protein isoform 1	AGI-03	40.452
Fb2156	Fb2156.lg		O	-	-	-	-	-		Ciclev10000537m	scaffold_5	39992234	39996269	C_unshiu_00096:mRNA_31.1	C_unshiu_00096	198494	202358	Poly(A) binding protein 6, putative isoform 1	AGI-09	41.254
Cp1143		MDisagree by Marco analysis	O	-	-	-	-	-		Ciclev10000651m	scaffold_5	39858531	39862402	C_unshiu_00096:mRNA_9.1	C_unshiu_00096	70713	73505	Phosphoglycerate dehydrogenase	AGI-09	42.158
Cp1923		OOthers	-	-	-	-	-	-		Ciclev10005293m	scaffold_9	2946301	2950297	C_unshiu_00097:mRNA_22.1	C_unshiu_00097	195825	199499	UPF0613 protein PB24D3.06c	AGI-03	22.454
Gn0008		OOthers	-	-	-	-	-	-	SI176	Ciclev10005632m	scaffold_9	17789634	17793258	C_unshiu_00098:mRNA_1.1	C_unshiu_00098	5120	17442	Phytoene desaturase	AGI-03	46.274
Cp0085			O	-	-	-	-	-		Ciclev10012552m	scaffold_6	23364303	23366061	C_unshiu_00098:mRNA_21.1	C_unshiu_00098	143026	144827	Allene oxide cyclase	AGI-04	42.183
Al0020		OOthers	-	-	-	-	-	-		Ciclev10012552m	scaffold_6	23364303	23366061	C_unshiu_00098:mRNA_21.1	C_unshiu_00098	143026	144827	Allene oxide cyclase			KmG-04
Ov0315		ULess informative for main cultivars	-	-	-	-	-	-		Ciclev10013467m	scaffold_6	23430375	23436161	C_unshiu_00098:mRNA_32.2	C_unshiu_00098	207615	213748	Putative nuclear matrix constituent protein 1-like protein			KmG-04	7.092
Af1639			-	-	-	-	-	-		Ciclev10012116m	scaffold_6	23462487	23466580	C_unshiu_00098:mRNA_36.1	C_unshiu_00098	239683	243712	Bifunctional dihydroflavonol 4-reductase/flavanone 4-reductase isoform 1	AGI-04	6.635
Fb0365			O	-	-	-	-	-	SI036,SI320	Ciclev10026391m	scaffold_7	20872462	20874659	C_unshiu_00098:mRNA_41.1	C_unshiu_00098	264947	272086	Hypothetical protein	AGI-02	31.596	KmG-02		JtR-02	-4.953
Cp2026		AAvailable marker	-	-	-	-	O	O		Ciclev10011534m	scaffold_6	23506491	23509585	C_unshiu_00098:mRNA_44.1	C_unshiu_00098	286004	289150	Tryptophan synthase, beta subunit	AGI-04	43.239
Tf0208			-	-	-	-	-	-	SI181	Ciclev10012022m	scaffold_6	23593516	23595492	C_unshiu_00098:mRNA_56.1	C_unshiu_00098	370300	372260	COL1 protein
Tf0386		AAvailable marker	O	O	O	-	O	O	SI044,SI095	Ciclev10012022m	scaffold_6	23593516	23595492	C_unshiu_00098:mRNA_56.1	C_unshiu_00098	370300	372260	COL1 protein	AGI-04	41.367
Tf0397			-	-	-	-	-	-	SI008	Ciclev10013334m	scaffold_6	23657256	23657810	C_unshiu_00098:mRNA_65.1	C_unshiu_00098	441975	442704	Ocs element-binding factor 1	AGI-04	40.646
Tf0165		AAvailable marker	O	-	-	-	O	O		Ciclev10031793m	scaffold_4	19605473	19608059	C_unshiu_00099:mRNA_19.1	C_unshiu_00099	154500	156794	Two-component response regulator ARR18	AGI-07	55.503
Tf0337		AAvailable marker	O	-	-	-	O	O		Ciclev10031846m	scaffold_4	19635415	19637061	C_unshiu_00099:mRNA_23.1	C_unshiu_00099	186480	188051	Ap2 erf and b3 domain-containing transcription factor rav2	AGI-07	54.869
Tf0310			-	-	-	-	-	-		Ciclev10031598m	scaffold_4	19681884	19685929	C_unshiu_00099:mRNA_27.1	C_unshiu_00099	233334	237357	NAC domain-containing protein 8	AGI-07	54.869
Mf0010		Bno homozygous cultivar with minor allele	-	-	-	-	-	-	SI048,SI149	Ciclev10032902m	scaffold_4	19467669	19468803	C_unshiu_00099:mRNA_4.1	C_unshiu_00099	12446	13357	30S ribosomal protein 3, chloroplastic	AGI-07	55.503	KmG-07	42.271	JtR-07	35.215	NAT-07
Af1116			-	-	-	-	-	-		Ciclev10001154m	scaffold_5	6749024	6753178	C_unshiu_00100:mRNA_44.1	C_unshiu_00100	361556	365479	Magnesium transporter MRS2-like protein	AGI-09	85.810
Bf0171			-	-	-	-	-	-	SI381	Ciclev10006006m	scaffold_9	4116356	4117315	C_unshiu_00101:mRNA_25.1	C_unshiu_00101	280469	282533	Early light-induced protein, chloroplastic	AGI-03	52.548
Fb1430	Fb1430.lg		O	-	-	-	-	-		Ciclev10005994m	scaffold_9	1879675	1880523	C_unshiu_00102:mRNA_3.1	C_unshiu_00102	16507	17334	60S ribosome subunit biogenesis protein NIP7 homolog	AGI-03
Af1062			-	-	-	-	-	-		Ciclev10012766m	scaffold_6	14892939	14897320	C_unshiu_00102:mRNA_47.1	C_unshiu_00102	331172	333886	PRA1 family protein A1	AGI-08	93.624
Cp1852			-	-	-	-	-	-		Ciclev10010530m	scaffold_1	22711668	22715696	C_unshiu_00103:mRNA_19.2	C_unshiu_00103	116559	121057	Cell differentiation protein rcd1	AGI-02	9.592
Fb0103		OOthers	O	-	-	-	-	-	SI155	Ciclev10008255m	scaffold_1	22758712	22761740	C_unshiu_00103:mRNA_27.1	C_unshiu_00103	160138	163082	GDP-L-galactose phosphorylase	AGI-01	30.703			JtR-01S	6.418
Bf0036		AAvailable marker	O	O	-	O	O	O		Ciclev10008751m	scaffold_1	22840947	22844111	C_unshiu_00103:mRNA_45.1	C_unshiu_00103	244231	250643	GrpE protein homolog	AGI-01	29.144							RP-01	46.445
Cp2158		MDisagree by Marco analysis	-	-	-	-	-	-		Ciclev10007944m	scaffold_1	22847397	22852110	C_unshiu_00103:mRNA_47.1	C_unshiu_00103	254015	258614	Trigger factor type chaperone family protein	AGI-01	24.422
Bf1207			-	-	-	-	-	-		Ciclev10010835m	scaffold_1	22912695	22913798	C_unshiu_00103:mRNA_59.1	C_unshiu_00103	319187	320041	Hypothetical protein	AGI-01
Tf0224		OOthers	O	-	-	-	-	-		Ciclev10011741m	scaffold_6	7785328	7796808	C_unshiu_00104:mRNA_54.1	C_unshiu_00104	400959	412354	Zinc finger CCCH domain-containing protein 32	AGI-04	99.859
Tf0163		AAvailable marker	O	-	-	-	O	O		Ciclev10010423m	scaffold_1	26740822	26744016	C_unshiu_00105:mRNA_35.1	C_unshiu_00105	316978	320206	RING/FYVE/PHD zinc finger superfamily protein, putative isoform 1	AGI-01	31.240
Mf0088		OOthers	O	-	-	-	-	-		Ciclev10001453m	scaffold_5	5104067	5106917	C_unshiu_00108:mRNA_11.1	C_unshiu_00108	101283	105493	60S ribosomal protein L3									RP-09
Af1321			-	-	-	-	-	-		Ciclev10009751m	scaffold_1	16371168	16375666	C_unshiu_00108:mRNA_25.1	C_unshiu_00108	320409	344557	Hypothetical protein	AGI-06	34.500
Tf0264		AAvailable marker	O	-	-	-	O	O		Ciclev10015873m	scaffold_2	248256	250675	C_unshiu_00109:mRNA_29.1	C_unshiu_00109	175776	179005	GAN	AGI-06	103.728
Ks9005		AAvailable marker	O	-	-	-	O	O	SI342	Ciclev10015338m	scaffold_2	290799	294122	C_unshiu_00109:mRNA_36.1	C_unshiu_00109	219070	222359	TRNA-splicing ligase RtcB	AGI-02	13.646	KmG-02	23.647					RP-02	16.986
Tf0093.2		AAvailable marker	O	-	-	-	O	O		Ciclev10002569m	scaffold_5	29413143	29414562	C_unshiu_00110:mRNA_25.1	C_unshiu_00110	149681	150624	Auxin-responsive protein IAA4	AGI-09	86.512
Tf0393		AAvailable marker	O	-	-	-	-	O		Ciclev10002569m	scaffold_5	29413143	29414562	C_unshiu_00110:mRNA_25.1	C_unshiu_00110	149681	150624	Auxin-responsive protein IAA4									RP-09	29.347
Tf0149		HDisagree on Clementine haploid genotype	O	-	-	-	-	-	SI128,SI269	Ciclev10002290m	scaffold_5	29400846	29403554	C_unshiu_00110:mRNA_26.1	C_unshiu_00110	160409	163111	Auxin-responsive protein IAA16	AGI-09	85.976							RP-09	32.826
Al0331		AAvailable marker	-	-	-	-	-	O		Ciclev10033190m	scaffold_4	8406632	8407188	C_unshiu_00111:mRNA_9.1	C_unshiu_00111	83531	84087	Hypothetical protein			KmG-09	9.593	JtR-07	52.611			RP-07	19.079
Cp2118			-	-	-	-	-	-		Ciclev10032406m	scaffold_4	14565456	14568265	C_unshiu_00113:mRNA_23.1	C_unshiu_00113	169695	172465	Superoxide dismutase	AGI-07	37.152
Bf0027			-	-	-	-	-	-	SI372	Ciclev10032632m	scaffold_4	14565456	14567860	C_unshiu_00113:mRNA_23.1	C_unshiu_00113	169695	172465	Superoxide dismutase	AGI-07	40.515
Tf0219		Bno homozygous cultivar with minor allele	O	-	-	-	-	-	SI076,SI267	Ciclev10005087m	scaffold_9	25662049	25666791	C_unshiu_00115:mRNA_31.1	C_unshiu_00115	248109	252610	Transcription factor bHLH60	AGI-03	49.250
Tf0396		Bno homozygous cultivar with minor allele	O	-	-	-	-	-	SI035	Ciclev10005087m	scaffold_9	25662049	25666791	C_unshiu_00115:mRNA_31.1	C_unshiu_00115	248109	252610	Transcription factor bHLH60
Tf0423			-	-	-	-	-	-		Ciclev10005087m	scaffold_9	25662049	25666791	C_unshiu_00115:mRNA_31.1	C_unshiu_00115	248109	252610	Transcription factor bHLH60	AGI-03	50.361
Af0016			-	-	-	-	-	-		Ciclev10022861m	scaffold_3	25074163	25075916	C_unshiu_00117:mRNA_7.1	C_unshiu_00117	38949	40765	Hypothetical protein	AGI-05	41.306
Bf0020			-	-	-	-	-	-		Ciclev10005107m	scaffold_9	25185200	25188839	C_unshiu_00119:mRNA_25.1	C_unshiu_00119	238437	248656	Guanylate kinase	AGI-03	47.887							RP-03	37.189
Al0302		AAvailable marker	-	O	-	-	O	O	SI090,SI311	Ciclev10004372m	scaffold_9	25073693	25080376	C_unshiu_00119:mRNA_33.1	C_unshiu_00119	346131	352710	Putative seed imbibition protein	AGI-03	48.375	KmG-032	18.339	JtR-033		NAT-03	3.773	RP-03	36.113
Bf0174			O	-	-	-	-	-	SI282	Ciclev10019861m	scaffold_3	3551542	3555978	C_unshiu_00120:mRNA_17.1	C_unshiu_00120	130029	134158	Atp-dependent RNA helicase	AGI-05	25.049
Fb1751			-	-	-	-	-	-	SI264	Ciclev10025011m	scaffold_7	7977527	7984425	C_unshiu_00121:mRNA_40.1	C_unshiu_00121	250743	257054	Protein STRUBBELIG-RECEPTOR FAMILY 8
Bf0229			-	-	-	-	-	-	SI253	Ciclev10004848m	scaffold_9	17242218	17245901	C_unshiu_00122:mRNA_16.1	C_unshiu_00122	118693	122329	Selenium binding protein	AGI-03	46.274							RP-03	37.885
Lp0013			-	-	-	-	-	-		Ciclev10004852m	scaffold_9	16971264	16973312	C_unshiu_00122:mRNA_43.1	C_unshiu_00122	389000	391027	Adenosylhomocysteinase			KmG-09	15.606
Gn0041		AAvailable marker	-	-	-	-	-	O						C_unshiu_00123:mRNA_16.1	C_unshiu_00123	116817	119061	Homeobox-leucine zipper protein HAT5			KmG-05S	9.772	JtR-05	28.396
Al0618		AAvailable marker	-	-	-	-	O	O		Ciclev10000916m	scaffold_5	40872793	40877775	C_unshiu_00123:mRNA_34.1	C_unshiu_00123	204269	222067	Phosphatase 2c, putative isoform 6	AGI-09	38.004	KmG-09	73.330
Cp0221		ULess informative for main cultivars	-	-	-	-	-	-		Ciclev10016539m	scaffold_2	30648531	30649856	C_unshiu_00125:mRNA_61.1	C_unshiu_00125	360098	361069	Photosystem I reaction center subunit III
Wy0044.3			-	-	-	-	-	-		Ciclev10020328m	scaffold_3	49621665	49623875	C_unshiu_00126:mRNA_45.1	C_unshiu_00126	300225	314275	Hypothetical protein									RP-05	49.102
Af1645			-	-	-	-	-	-		Ciclev10000427m	scaffold_5	2472805	2477375	C_unshiu_00127:mRNA_11.1	C_unshiu_00127	52207	62775	Class I (E and Q) tRNA synthetase	AGI-09	90.878
Tf0258			-	-	-	-	-	-	SI234	Ciclev10000508m	scaffold_5	41372513	41377106	C_unshiu_00127:mRNA_21.1	C_unshiu_00127	163658	166645	BEL1-like homeodomain protein 6
Tf0088		MDisagree by Marco analysis	O	-	-	-	-	-	SI066	Ciclev10001291m	scaffold_5	41275201	41278829	C_unshiu_00127:mRNA_34.1	C_unshiu_00127	251592	254627	Basic helix-loop-helix DNA-binding superfamily protein, putative isoform 1	AGI-09	35.763
Vs0002		MDisagree by Marco analysis	-	-	-	-	-	-	SI103,SI115	Ciclev10000046m	scaffold_5	41184180	41190033	C_unshiu_00127:mRNA_46.1	C_unshiu_00127	341430	344325	Hypothetical protein	AGI-09	36.685	KmG-09	73.930	JtR-07	68.221
Tf0226		AAvailable marker	O	-	-	-	-	O		Ciclev10008836m	scaffold_1	526813	529150	C_unshiu_00129:mRNA_32.1	C_unshiu_00129	303106	311407	Exocyst subunit EXO70 family protein									RP-01	1.100
Al0630		AAvailable marker	O	-	-	-	-	O		Ciclev10008681m	scaffold_1	487184	489198	C_unshiu_00129:mRNA_38.1	C_unshiu_00129	342865	344872	Kelch repeat-containing F-box family protein									RP-01	1.092
Al0407		AAvailable marker	O	-	-	-	O	O		Ciclev10009315m	scaffold_1	26576059	26578193	C_unshiu_00131:mRNA_17.1	C_unshiu_00131	121152	123183	60S ribosomal protein L7	AGI-01	31.240	KmG-01	15.673	JtR-01S	57.666			RP-01	79.425
Bf0221			-	-	-	-	-	-		Ciclev10005970m	scaffold_9	24195180	24198282	C_unshiu_00132:mRNA_22.1	C_unshiu_00132	211597	223530	Hypothetical protein	AGI-03	47.887							RP-03	37.193
Gn0051		AAvailable marker	-	-	-	-	O	O	SI306,SI366	Ciclev10011780m	scaffold_6	24082263	24084635	C_unshiu_00133:mRNA_13.1	C_unshiu_00133	63870	65165	Protein UNUSUAL FLORAL ORGANS	AGI-04	39.510	KmG-04	0.447
Al0313		AAvailable marker	O	-	-	-	O	O		Ciclev10011272m	scaffold_6	23966039	23969583	C_unshiu_00133:mRNA_4.2	C_unshiu_00133	22485	26003	Putative phosphatidylinositol 4-kinase type 2-beta	AGI-04	38.152	KmG-04	9.748
Af1462			-	-	-	-	-	-		Ciclev10012884m	scaffold_6	24274031	24276658	C_unshiu_00133:mRNA_50.1	C_unshiu_00133	274230	284897	Hypothetical protein	AGI-04	37.527
Tf0143			-	-	-	-	-	-	SI127	Ciclev10004758m	scaffold_9	30040457	30044615	C_unshiu_00134:mRNA_22.1	C_unshiu_00134	203848	206784	Sigma factor	AGI-03	68.846
Lp0009		DDominant marker	-	-	-	-	-	-		Ciclev10005585m	scaffold_9	30171791	30177202	C_unshiu_00134:mRNA_8.1	C_unshiu_00134	71410	76705	Phosphatase 2C 76 isoform 1			KmG-05S	36.573	JtR-05	12.427
Tf0050			-	-	-	-	-	-	SI104,SI346	Ciclev10012152m	scaffold_6	24874840	24876388	C_unshiu_00135:mRNA_12.1	C_unshiu_00135	84260	85810	Myb-related protein 306	AGI-04	36.106
Tf0364		AAvailable marker	O	-	-	-	O	O		Ciclev10011266m	scaffold_6	24606501	24612654	C_unshiu_00135:mRNA_49.1	C_unshiu_00135	338118	344273	FACT complex subunit SSRP1	AGI-04	37.102
Tf0294		AAvailable marker	O	-	-	-	O	O		Ciclev10021365m	scaffold_3	4794701	4799518	C_unshiu_00135:mRNA_58.2	C_unshiu_00135	398519	403121	Ureidoglycine aminohydrolase isoform 1	AGI-05	27.135
Vt0009			-	-	-	-	-	-		Ciclev10012382m	scaffold_6	24932481	24935909	C_unshiu_00135:mRNA_6.1	C_unshiu_00135	25891	28913	Major intrinsic protein (MIP) family transporter	AGI-04	38.770	KmG-04	14.707
Lp0229			O	-	-	-	-	-		Ciclev10015636m	scaffold_2	24637053	24639946	C_unshiu_00136:mRNA_24.1	C_unshiu_00136	221432	223640	ARM repeat superfamily protein									RP-06.1	25.198
Af1026			O	-	-	-	-	-		Ciclev10016450m	scaffold_2	24690261	24692734	C_unshiu_00136:mRNA_33.1	C_unshiu_00136	278221	280719	Period circadian protein, putative isoform 1									RP-06.1	24.027
Af1424			-	-	-	-	-	-		Ciclev10008953m	scaffold_1	18688873	18690138	C_unshiu_00137:mRNA_44.1	C_unshiu_00137	354434	355481	CFE protein	AGI-01	43.613
Af1700			-	-	-	-	-	-		Ciclev10004322m	scaffold_9	18502293	18505531	C_unshiu_00138:mRNA_34.1	C_unshiu_00138	182719	186200	Putative receptor protein kinase TMK1	AGI-03	54.060
Gn0012			-	-	-	-	-	-		Ciclev10018889m	scaffold_3	46011238	46017249	C_unshiu_00139:mRNA_16.1	C_unshiu_00139	135708	141900	Sucrose synthase			KmG-05S	78.527
Gn0047			-	-	-	-	-	-		Ciclev10011938m	scaffold_6	18741181	18744166	C_unshiu_00139:mRNA_23.1	C_unshiu_00139	204645	207518	Squamosa promoter-binding-like protein 9			KmG-04	48.092
Al0625		AAvailable marker	O	-	-	-	O	O	SI329					C_unshiu_00139:mRNA_45.1	C_unshiu_00139	346138	349862	Regulator of chromosome condensation family protein	AGI-04	66.455							RP-04	23.717
Fb1134.2			-	-	-	-	-	-		Ciclev10030474m	scaffold_4	9547707	9559498	C_unshiu_00140:mRNA_14.1	C_unshiu_00140	164689	176715	DNA N-glycosylase/DNA-(Apurinic or apyrimidinic site) lyase, putative isoform 5	AGI-07	38.546
Ov0412		OOthers	-	-	-	-	O	O	SI050,SI222	Ciclev10015053m	scaffold_2	31036088	31038222	C_unshiu_00143:mRNA_11.1	C_unshiu_00143	67475	69537	SEC14 cytosolic factor family protein	AGI-06	42.110	KmG-06	39.373	JtR-06S	15.372
Wy0003		AAvailable marker	O	-	-	-	O	O		Ciclev10001202m	scaffold_5	37189653	37192231	C_unshiu_00144:mRNA_30.1	C_unshiu_00144	215223	217733	Aminotransferase	AGI-09	46.823	KmG-09	52.581			NAT-09	69.467
Lp0041		AAvailable marker	-	-	-	-	-	O		Ciclev10006136m	scaffold_9	6354796	6356630	C_unshiu_00146:mRNA_22.1	C_unshiu_00146	205279	207014	50S ribosomal protein L28			KmG-032	17.549	JtR-031	14.643			RP-03	29.608
Af1456			-	-	-	-	-	-		Ciclev10006136m	scaffold_9	6354796	6356630	C_unshiu_00146:mRNA_22.1	C_unshiu_00146	205279	207014	50S ribosomal protein L28	AGI-03	46.298
Cp1308		AAvailable marker	-	O	-	-	O	O		Ciclev10011420m	scaffold_6	6329421	6335005	C_unshiu_00147:mRNA_29.1	C_unshiu_00147	247701	253232	Unspecific monooxygenase	AGI-04	101.201
Af1586			-	-	-	-	-	-		Ciclev10005733m	scaffold_9	23119502	23122347	C_unshiu_00148:mRNA_17.1	C_unshiu_00148	145165	147922	Glycoprotein family protein	AGI-03	63.545
Tf0268		AAvailable marker	O	-	-	-	O	O		Ciclev10021157m	scaffold_3	10140904	10142752	C_unshiu_00149:mRNA_29.1	C_unshiu_00149	326478	328059	Transcription factor MYB21	AGI-05	43.800
Wy0028		AAvailable marker	-	-	-	-	O	O		Ciclev10007806m	scaffold_1	25001341	25004726	C_unshiu_00150:mRNA_3.1	C_unshiu_00150	18652	22079	Probable pectinesterase/pectinesterase inhibitor 61	AGI-01	26.171	KmG-01
Fb0143			-	-	-	-	-	-	SI361	Ciclev10007397m	scaffold_1	25283807	25291472	C_unshiu_00150:mRNA_43.1	C_unshiu_00150	325164	333089	LRR receptor-like serine/threonine-protein kinase ERL1	AGI-01	26.176							RP-01	64.368
Lp0226			O	-	-	-	-	-	SI210	Ciclev10027999m	scaffold_8	2831832	2837109	C_unshiu_00152:mRNA_19.1	C_unshiu_00152	138714	144356	Embryonic polyadenylate-binding protein	AGI-08	73.527
Ov0423		T3 or more alleleic model	O	-	-	-	-	-		Ciclev10023016m	scaffold_3	42954362	42955051	C_unshiu_00152:mRNA_28.1	C_unshiu_00152	189707	190632	Hypothetical protein	AGI-05	55.522
Tf0250		AAvailable marker	O	-	-	-	O	O		Ciclev10028849m	scaffold_8	2697793	2701440	C_unshiu_00152:mRNA_36.1	C_unshiu_00152	252884	256413	DNA-directed RNA polymerase II subunit RPB3-A	AGI-08	73.105
Tf0431		AAvailable marker	O	-	-	-	-	O		Ciclev10028849m	scaffold_8	2697793	2701440	C_unshiu_00152:mRNA_36.1	C_unshiu_00152	252884	256413	DNA-directed RNA polymerase II subunit RPB3-A
Fb0293			-	-	-	-	-	-	SI198,SI374					C_unshiu_00152:mRNA_37.1	C_unshiu_00152	259580	269499	Hypothetical protein	AGI-08	73.663
Al0515		Bno homozygous cultivar with minor allele	O	-	-	-	-	-	SI178	Ciclev10030023m	scaffold_8	2673135	2674232	C_unshiu_00152:mRNA_38.1	C_unshiu_00152	273851	275034	DNA-damage-repair/toleration protein DRT100	AGI-08	73.663			JtR-08	14.154	NAT-081	10.596
Cp1144		OOthers	-	-	-	-	-	-		Ciclev10028086m	scaffold_8	2649991	2655756	C_unshiu_00152:mRNA_43.1	C_unshiu_00152	288550	294174	Sodium:hydrogen antiporter 1 isoform 1	AGI-08	70.995
Lg2002			-	-	-	-	-	-		Ciclev10028055m	scaffold_8	2646458	2649562	C_unshiu_00152:mRNA_44.1	C_unshiu_00152	294607	297615	Phosphoglycerate dehydrogenase	AGI-08	69.974
Lg2004			-	-	-	-	-	-		Ciclev10028785m	scaffold_8	2599717	2602090	C_unshiu_00152:mRNA_53.1	C_unshiu_00152	347645	349890	Cinnamyl alcohol dehydrogenase	AGI-08	76.045
Af1362			-	-	-	-	-	-		Ciclev10027931m	scaffold_8	2888992	2895645	C_unshiu_00152:mRNA_9.1	C_unshiu_00152	72564	86513	Hypothetical protein	AGI-08	80.366
Al0201		ULess informative for main cultivars	-	-	-	-	-	-		Ciclev10014752m	scaffold_2	32780830	32782885	C_unshiu_00153:mRNA_49.1	C_unshiu_00153	346248	348256	Armadillo/beta-catenin-like repeat family protein, expressed
Tf0004			-	-	-	-	-	-	SI219,SI330	Ciclev10014045m	scaffold_2	33074821	33084014	C_unshiu_00153:mRNA_7.1	C_unshiu_00153	66406	75053	Putative SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 3-like 2	AGI-06	32.312
Tf0376		AAvailable marker	O	-	-	-	O	O	SI072	Ciclev10022680m	scaffold_3	8528292	8529236	C_unshiu_00154:mRNA_1.1	C_unshiu_00154	9832	10761	CRT binding factor 3	AGI-05	41.853
Cp1815		OOthers	-	-	-	-	-	-		Ciclev10022373m	scaffold_3	8256398	8257886	C_unshiu_00154:mRNA_28.1	C_unshiu_00154	274299	275412	Wiskott-Aldrich syndrome protein family member 2	AGI-05	51.501
Bf0177			-	-	-	-	-	-	SI060	Ciclev10022075m	scaffold_3	8186689	8189902	C_unshiu_00154:mRNA_43.2	C_unshiu_00154	341574	344576	Phosphoserine phosphatase	AGI-05	44.047
Tf0145			-	-	-	-	-	-	SI092	Ciclev10022479m	scaffold_3	8486491	8488997	C_unshiu_00154:mRNA_7.1	C_unshiu_00154	49131	60112	Floral homeotic protein APETALA 1
Bf1204			-	-	-	-	-	-	SI364	Ciclev10013297m	scaffold_6	13750671	13752605	C_unshiu_00155:mRNA_3.1	C_unshiu_00155	17608	19347	Hypothetical protein
Mf0072		AAvailable marker	-	-	-	-	O	O		Ciclev10013297m	scaffold_6	13750671	13752605	C_unshiu_00155:mRNA_3.1	C_unshiu_00155	17608	19347	Hypothetical protein	AGI-04	91.104	KmG-04	58.483					RP-04	8.126
Bf0145			O	-	-	O	-	-	SI272,SI327,SI368	Ciclev10027909m	scaffold_8	22730839	22737522	C_unshiu_00158:mRNA_13.1	C_unshiu_00158	102548	109253	Pseudo-response regulator 37	AGI-08	20.703							RP-08	5.775
Lp0143		Bno homozygous cultivar with minor allele	-	-	-	-	-	-		Ciclev10019139m	scaffold_3	6076949	6080875	C_unshiu_00159:mRNA_40.1	C_unshiu_00159	339926	343475	Translation elongation factor G	AGI-05	45.297			JtR-05	18.056
Cp1034		AtAvailable marker	-	-	-	-	O	O		Ciclev10005575m	scaffold_9	21107894	21109983	C_unshiu_00160:mRNA_22.1	C_unshiu_00160	182942	184946	Putative calcium-binding protein CML48	AGI-03	46.760
Mf0095		OOthers	O	-	-	-	-	-	SI290	Ciclev10005778m	scaffold_9	21216748	21221111	C_unshiu_00160:mRNA_34.1	C_unshiu_00160	290257	294371	Transmembrane proteins 14C, putative isoform 1			KmG-032		JtR-031	11.958			RP-03	43.323
Cp1500			-	-	-	-	-	-		Ciclev10004776m	scaffold_9	7080249	7086989	C_unshiu_00161:mRNA_19.1	C_unshiu_00161	150519	157206	3-isopropylmalate dehydratase large subunit	AGI-03	46.274
Af1253			-	-	-	-	-	-		Ciclev10020405m	scaffold_3	3201206	3204377	C_unshiu_00163:mRNA_29.1	C_unshiu_00163	211551	214568	Phosphate/phosphoenolpyruvate translocator	AGI-05	24.709
Af3822			-	-	-	-	-	-		Ciclev10004695m	scaffold_9	5494254	5497030	C_unshiu_00164:mRNA_13.1	C_unshiu_00164	74059	75936	Phosphate transporter	AGI-03	44.864
Wy0020			-	-	-	-	-	-	SI007	Ciclev10005394m	scaffold_9	5549195	5553148	C_unshiu_00164:mRNA_5.1	C_unshiu_00164	17046	20923	Malate dehydrogenase	AGI-03	43.563
Tf0319			-	-	-	-	-	-	SI152	Ciclev10026319m	scaffold_7	6872666	6877291	C_unshiu_00166:mRNA_10.1	C_unshiu_00166	78780	83374	Putative PHD finger protein ALFIN-LIKE 4-like	AGI-02	44.258
Al0210		MDisagree by Marco analysis	-	-	-	-	-	-		Ciclev10025724m	scaffold_7	6747139	6750382	C_unshiu_00166:mRNA_28.1	C_unshiu_00166	205256	208771	Eukaryotic initiation factor 4A-10			KmG-02	34.998	JtR-02	15.126
Tf0071			-	-	-	-	-	-	SI084,SI146	Ciclev10022102m	scaffold_3	26610747	26612959	C_unshiu_00167:mRNA_6.1	C_unshiu_00167	57300	62494	HAUS augmin-like complex subunit	AGI-03	46.274
Tf0410		AAvailable marker	O	-	-	-	O	O		Ciclev10032838m	scaffold_4	213798	215848	C_unshiu_00168:mRNA_34.1	C_unshiu_00168	273522	275858	Pollen-specific protein SF3	AGI-07	6.146
Cp1584		AAvailable marker	-	-	-	-	-	O		Ciclev10031523m	scaffold_4	201556	204527	C_unshiu_00168:mRNA_36.1	C_unshiu_00168	285304	287905	Cell division cycle 20.1, cofactor of APC complex
Em0005	Fb1892.em		-	-	-	-	-	-						C_unshiu_00168:mRNA_8.1	C_unshiu_00168	76386	80254	BEL1-like homeodomain protein 9	AGI-07
Mf0094		AAvailable marker	-	-	-	-	O	O		Ciclev10026594m	scaffold_7	3721375	3722616	C_unshiu_00169:mRNA_29.1	C_unshiu_00169	217948	219072	Maternal effect embryo arrest protein	AGI-02	67.666	KmG-02	52.124	JtR-02	25.334
Lp0040		Bno homozygous cultivar with minor allele	-	-	-	-	-	-		Ciclev10026107m	scaffold_7	3674156	3676384	C_unshiu_00169:mRNA_34.1	C_unshiu_00169	261779	263315	Transcription factor			KmG-02	52.181	JtR-02	25.334
Tf0259		AAvailable marker	O	-	-	-	O	O		Ciclev10026107m	scaffold_7	3674156	3676384	C_unshiu_00169:mRNA_34.1	C_unshiu_00169	261779	263315	Transcription factor	AGI-02	67.666
Tf0016			-	-	-	-	-	-	SI345	Ciclev10001979m	scaffold_5	39839984	39841860	C_unshiu_00169:mRNA_34.1	C_unshiu_00169	261779	263315	Transcription factor	AGI-09	42.158
Tf0117			-	-	-	-	-	-		Ciclev10005596m	scaffold_9	15107375	15113804	C_unshiu_00170:mRNA_11.1	C_unshiu_00170	91205	97326	Myb family transcription factor APL	AGI-03	46.274
Af1111			-	-	-	-	-	-		Ciclev10015086m	scaffold_2	23021193	23023457	C_unshiu_00172:mRNA_31.1	C_unshiu_00172	270783	273047	Glucan endo-1,3-beta-glucosidase 13	AGI-06	83.445
Bf0226		MDisagree by Marco analysis	O	-	-	-	-	-		Ciclev10008869m	scaffold_1	23654785	23658857	C_unshiu_00175:mRNA_30.1	C_unshiu_00175	321759	325671	SEC14 cytosolic factor	AGI-08	63.341
Cp1556		Bno homozygous cultivar with minor allele	-	-	-	-	-	-		Ciclev10018756m	scaffold_3	21432494	21440948	C_unshiu_00175:mRNA_9.1	C_unshiu_00175	91338	99600	Bifunctional aspartokinase/homoserine dehydrogenase 2, chloroplastic	AGI-05	40.337
Tf0085			-	-	-	-	-	-	SI094,SI211	Ciclev10012088m	scaffold_6	2067586	2073007	C_unshiu_00176:mRNA_13.1	C_unshiu_00176	89975	97731	Transcription factor-like protein DPB	AGI-08	96.807
Tf0069			-	-	-	-	-	-	SI199	Ciclev10001715m	scaffold_5	38566192	38571337	C_unshiu_00183:mRNA_2.1	C_unshiu_00183	20134	26910	Transcription factor RF2b	AGI-09	42.789							RP-09	77.126
Tf0084			-	-	-	-	-	-		Ciclev10000121m	scaffold_5	38288047	38296128	C_unshiu_00183:mRNA_40.1	C_unshiu_00183	305878	313881	Transcription elongation factor SPT5	AGI-09	44.096
Fb0138			-	-	-	-	-	-		Ciclev10000092m	scaffold_5	38499024	38504883	C_unshiu_00183:mRNA_7.1	C_unshiu_00183	86540	94072	Regulator of chromosome condensation (RCC1) family with FYVEzinc finger domain	AGI-09	43.862	KmG-09	54.172					SA-09	50.659
Fb0124			-	-	-	-	-	-	SI167,SI212	Ciclev10014164m	scaffold_2	11088808	11095416	C_unshiu_00184:mRNA_31.1	C_unshiu_00184	275231	281575	Phosphoenolpyruvate carboxylase
Cp0747			-	-	-	-	-	-		Ciclev10015418m	scaffold_2	11084960	11088767	C_unshiu_00184:mRNA_32.1	C_unshiu_00184	282295	285277	ATP synthase protein I	AGI-09	85.816
Ov0422		AAvailable marker	-	-	-	-	-	O		Ciclev10016314m	scaffold_2	11071587	11074479	C_unshiu_00184:mRNA_33.1	C_unshiu_00184	295953	298736	14-3-3-like protein GF14 mu									RP-06.1	28.576
Al0207		OOthers	-	-	-	-	-	-		Ciclev10020027m	scaffold_3	4366802	4370111	C_unshiu_00186:mRNA_18.1	C_unshiu_00186	178635	181547	SNF1-related protein kinase regulatory subunit gamma-1	AGI-09	84.537			JtR-09S	9.929
Af1679			-	-	-	-	-	-		Ciclev10021896m	scaffold_3	4260126	4262819	C_unshiu_00186:mRNA_34.1	C_unshiu_00186	288266	290432	Adenylate kinase	AGI-05	29.035
Cp1624		AAvailable marker	-	O	-	O	O	O	SI307	Ciclev10008537m	scaffold_1	18068297	18070262	C_unshiu_00187:mRNA_17.1	C_unshiu_00187	99220	100762	CBS domain-containing protein CBSX5	AGI-01	58.420	KmG-01	53.054
Af1622			-	-	-	-	-	-		Ciclev10008520m	scaffold_1	18117264	18119451	C_unshiu_00187:mRNA_23.3	C_unshiu_00187	141733	143877	Protochlorophyllide reductase, chloroplastic	AGI-01	54.754
Tf0066			-	-	-	-	-	-	SI221	Ciclev10008812m	scaffold_1	18270818	18273015	C_unshiu_00187:mRNA_34.1	C_unshiu_00187	287391	289585	NAC domain-containing protein 72	AGI-01	58.420
Cp0185			-	-	-	-	-	-		Ciclev10002024m	scaffold_5	34558362	34564638	C_unshiu_00190:mRNA_33.1	C_unshiu_00190	230947	237587	Adenine phosphoribosyltransferase	AGI-03	51.129
Al0513		OOthers	-	-	-	-	-	-		Ciclev10009222m	scaffold_1	8046181	8049306	C_unshiu_00191:mRNA_21.1	C_unshiu_00191	243988	246458	Stem 28 kDa glycoprotein	AGI-01	60.031	KmG-01	41.591
Lg2005			-	-	-	-	-	-		Ciclev10002751m	scaffold_5	42187714	42189727	C_unshiu_00192:mRNA_45.1	C_unshiu_00192	319592	321612	SCF ubiquitin ligase, SKP1 component	AGI-09	34.172
Af1109			-	-	-	-	-	-						C_unshiu_00194:mRNA_16.1	C_unshiu_00194	96415	98120	Putative H/ACA ribonucleoprotein complex subunit 1-like protein 1	AGI-05	48.590
Al0605		OOthers	-	-	-	-	-	-		Ciclev10022151m	scaffold_3	41434064	41437122	C_unshiu_00194:mRNA_5.1	C_unshiu_00194	38569	41571	Eukaryotic translation initiation factor 4E	AGI-05	48.750	KmG-05S	65.384
Fb0133			-	-	-	-	-	-						C_unshiu_00195:mRNA_19.1	C_unshiu_00195	140861	146843	Hypothetical protein	AGI-02	39.589	KmG-02	1.175	JtR-02	1.082
Af1205			-	-	-	-	-	-		Ciclev10002396m	scaffold_5	34161721	34162652	C_unshiu_00196:mRNA_4.1	C_unshiu_00196	15219	16117	Basic helix-loop-helix DNA-binding superfamily protein, putative	AGI-09	64.754
Al0635		AAvailable marker	-	-	-	-	O	O		Ciclev10015354m	scaffold_2	26435540	26438838	C_unshiu_00197:mRNA_27.1	C_unshiu_00197	251131	253300	GAGA-binding transcriptional activator	AGI-06	69.195	KmG-06	15.268	JtR-06S	1.903	NAT-06S	7.869
Al0306		Bno homozygous cultivar with minor allele	-	-	-	-	-	-	SI029	Ciclev10021897m	scaffold_3	7337405	7339222	C_unshiu_00199:mRNA_11.1	C_unshiu_00199	77240	79028	Expansin					JtR-05	23.944
Mf0017		Bno homozygous cultivar with minor allele	-	-	-	-	-	-		Ciclev10021897m	scaffold_3	7337405	7339222	C_unshiu_00199:mRNA_11.1	C_unshiu_00199	77240	79028	Expansin	AGI-05	44.674
Cp1268			-	-	-	-	-	-		Ciclev10021861m	scaffold_3	7327436	7329167	C_unshiu_00199:mRNA_13.1	C_unshiu_00199	87134	88461	Light-harvesting complex I protein subunit a4	AGI-05	44.864
Ov0526		OOthers	-	-	-	-	-	-		Ciclev10001212m	scaffold_5	21522433	21525218	C_unshiu_00201:mRNA_11.2	C_unshiu_00201	136005	138785	Aspartic proteinase nepenthesin-1			KmG-09		JtR-09S	0.758	NAT-09
Gn0046			-	-	-	-	-	-		Ciclev10001212m	scaffold_5	21522433	21525218	C_unshiu_00201:mRNA_11.2	C_unshiu_00201	136005	138785	Aspartic proteinase nepenthesin-1	AGI-07	64.812			JtR-08	23.181
Gn0069		ULess informative for main cultivars	O	-	-	-	-	-	SI086,SI375	Ciclev10008410m	scaffold_1	10946316	10949617	C_unshiu_00201:mRNA_19.1	C_unshiu_00201	212151	227232	Lycopene epsilon cyclase	AGI-01	57.863
Ov0508	Ov0507.2		-	-	-	-	-	-	SI322	Ciclev10031860m	scaffold_4	642157	644823	C_unshiu_00202:mRNA_16.4	C_unshiu_00202	127322	129988	Ribulose bisphosphate carboxylase/oxygenase activase, chloroplastic	AGI-07	8.291			JtR-07	76.060
Cp0870		Bno homozygous cultivar with minor allele	-	-	-	-	-	-	SI338	Ciclev10031974m	scaffold_4	642157	644823	C_unshiu_00202:mRNA_16.4	C_unshiu_00202	127322	129988	Ribulose bisphosphate carboxylase/oxygenase activase, chloroplastic	AGI-07	5.180
Ov0114			-	-	-	-	-	-						C_unshiu_00206:mRNA_12.3	C_unshiu_00206	75980	77488	Nucleoside diphosphate kinase			KmG-032	18.485	JtR-031	11.761
Fb0144		AAvailable marker	-	-	-	-	O	O	SI191	Ciclev10019665m	scaffold_3	50861813	50866146	C_unshiu_00206:mRNA_42.1	C_unshiu_00206	283219	294491	Hypothetical protein	AGI-05	107.806
Mf0076		AAvailable marker	-	-	-	-	O	O		Ciclev10012554m	scaffold_6	11704199	11706676	C_unshiu_00207:mRNA_15.1	C_unshiu_00207	132539	134984	Cytosolic ascorbate peroxidase	AGI-08	93.624
Tf0062		Bno homozygous cultivar with minor allele	O	-	-	O	-	-	SI223	Ciclev10012377m	scaffold_6	11826472	11830875	C_unshiu_00207:mRNA_24.2	C_unshiu_00207	252955	255240	Transcription factor ASG4	AGI-08	93.624
Af1619			-	-	-	-	-	-		Ciclev10026784m	scaffold_7	1608634	1610659	C_unshiu_00209:mRNA_18.2	C_unshiu_00209	147009	148975	Thioredoxin h	AGI-02	73.759
Tf0303			-	-	-	-	-	-	SI082	Ciclev10030491m	scaffold_4	6325180	6334300	C_unshiu_00210:mRNA_10.1	C_unshiu_00210	52148	60690	Putative lysine-specific demethylase ELF6
Cp1798		AAvailable marker	-	-	-	-	O	O		Ciclev10012134m	scaffold_6	20319677	20323198	C_unshiu_00215:mRNA_34.1	C_unshiu_00215	205164	208490	Orange 2	AGI-04	60.291
Af0015			-	-	-	-	-	-		Ciclev10019449m	scaffold_3	44021779	44027536	C_unshiu_00217:mRNA_10.1	C_unshiu_00217	86393	91294	Hypothetical protein	AGI-05	54.268
Tf0068			-	-	-	-	-	-	SI106	Ciclev10020724m	scaffold_3	44141305	44144453	C_unshiu_00217:mRNA_25.1	C_unshiu_00217	201916	205032	Heat shock transcription factor A7a1	AGI-05	54.268
Mf0080		MDisagree by Marco analysis	-	-	-	-	-	-		Ciclev10021936m	scaffold_3	44202968	44205663	C_unshiu_00217:mRNA_35.1	C_unshiu_00217	286418	288656	Transmembrane BAX inhibitor motif-containing protein 4	AGI-05	55.049	KmG-05S	64.740	JtR-05	38.503			RP-04	37.046
If0010		AAvailable marker	O	-	-	-	O	-		Ciclev10026308m	scaffold_7	1264965	1266960	C_unshiu_00218:mRNA_11.1	C_unshiu_00218	63403	65018	60S ribosomal protein L8	AGI-02	73.759	KmG-02	76.687	JtR-02	10.849	NAT-02S	71.041
Wy0041			-	-	-	-	-	-		Ciclev10025903m	scaffold_7	1295839	1297378	C_unshiu_00218:mRNA_18.1	C_unshiu_00218	93074	94183	GDP-mannose 4,6 dehydratase 2	AGI-02	75.406
Lp0024		HDisagree on Clementine haploid genotype	O	-	-	-	-	-	SI010,SI302	Ciclev10026549m	scaffold_7	1309884	1311067	C_unshiu_00218:mRNA_20.1	C_unshiu_00218	98317	107740	Heterogeneous nuclear ribonucleoprotein Q	AGI-02	74.555							RP-02.2	17.330
Lp0122		MDisagree by Marco analysis	O	-	-	-	-	-	SI170	Ciclev10026549m	scaffold_7	1309884	1311067	C_unshiu_00218:mRNA_20.1	C_unshiu_00218	98317	107740	Heterogeneous nuclear ribonucleoprotein Q							NAT-02S	69.942	RP-02.2	17.330
Tf0405			-	-	-	-	-	-		Ciclev10027952m	scaffold_8	6025802	6031497	C_unshiu_00220:mRNA_2.1	C_unshiu_00220	48148	53214	BEL1-like homeodomain protein 6	AGI-08	61.643
Al0638		OOthers	O	-	-	-	-	-		Ciclev10027380m	scaffold_7	8662041	8665543	C_unshiu_00221:mRNA_2.1	C_unshiu_00221	6658	10157	VHS domain-containing protein			KmG-07	23.435	JtR-07	17.224	NAT-07	24.049
Cp0321		AAvailable marker	-	-	-	-	-	O		Ciclev10026722m	scaffold_7	8898626	8899984	C_unshiu_00221:mRNA_33.1	C_unshiu_00221	211111	214358	Hypothetical protein
Af1377			-	-	-	-	-	-		Ciclev10001143m	scaffold_5	32780339	32783349	C_unshiu_00224:mRNA_50.1	C_unshiu_00224	297837	300694	Seryl-tRNA synthetase (Serin-tRNA ligase)	AGI-09	70.624
Tf0235		MDisagree by Marco analysis	O	-	-	O	-	-		Ciclev10030472m	scaffold_4	17057658	17074755	C_unshiu_00225:mRNA_13.1	C_unshiu_00225	75706	96678	TATA-binding protein-associated factor 172	AGI-07	43.879
Ov0413			-	-	-	-	-	-		Ciclev10028322m	scaffold_8	17809428	17813065	C_unshiu_00225:mRNA_26.1	C_unshiu_00225	238952	242235	Cellular nucleic acid-binding protein like			KmG-07	34.263
Al0632		HDisagree on Clementine haploid genotype	O	-	-	-	-	-		Ciclev10028775m	scaffold_8	17809428	17813065	C_unshiu_00225:mRNA_26.1	C_unshiu_00225	238952	242235	Cellular nucleic acid-binding protein like	AGI-08	56.724			JtR-08	18.952
Tf0112			O	-	-	-	-	-		Ciclev10031118m	scaffold_4	17014582	17026325	C_unshiu_00225:mRNA_9.1	C_unshiu_00225	37090	44898	Regulation of nuclear pre-mRNA domain-containing protein 1B	AGI-07	43.014
Lp0235			O	-	-	-	-	-		Ciclev10019848m	scaffold_3	9466071	9468445	C_unshiu_00227:mRNA_19.1	C_unshiu_00227	186549	194369	Nepenthesin II	AGI-05	43.412							RP-05	44.731
Bf0101			-	-	-	-	-	-		Ciclev10003680m	scaffold_5	32917826	32924241	C_unshiu_00229:mRNA_13.1	C_unshiu_00229	57438	62744	Hypothetical protein							NAT-09	50.353
Wy0059	Wy0059.em		-	-	-	-	-	-		Ciclev10012904m	scaffold_6	8562431	8564865	C_unshiu_00232:mRNA_33.1	C_unshiu_00232	292640	294683	DUF538 family protein	AGI-08	91.502
If0208		AAvailable marker	-	O	-	O	O	O	SI083,SI317	Ciclev10001680m	scaffold_5	40628244	40630241	C_unshiu_00234:mRNA_9.1	C_unshiu_00234	94988	99176	TRNA-processing ribonuclease BN	AGI-09	39.296	KmG-09	72.036	JtR-09S	115.150	NAT-09	89.867
Lp0112		AAvailable marker	O	-	-	-	-	-		Ciclev10032923m	scaffold_4	3749809	3751724	C_unshiu_00236:mRNA_28.1	C_unshiu_00236	161422	163318	ATP synthase subunit d, mitochondrial	AGI-07	19.603							RP-07	50.962
Tf0243			-	-	-	-	-	-	SI231	Ciclev10032893m	scaffold_4	3636667	3641089	C_unshiu_00236:mRNA_46.1	C_unshiu_00236	271647	281392	Nuclear transcription factor Y subunit B-8
Tf0348			-	-	-	-	-	-	SI118	Ciclev10012920m	scaffold_6	11611994	11614367	C_unshiu_00236:mRNA_46.1	C_unshiu_00236	271647	281392	Nuclear transcription factor Y subunit B-8	AGI-08	96.565
Tf0124			-	-	-	-	-	-		Ciclev10007717m	scaffold_1	27457358	27462893	C_unshiu_00237:mRNA_37.1	C_unshiu_00237	259818	273281	Dethiobiotin synthase	AGI-01	34.062
Cp0632		AAvailable marker	O	-	-	-	O	O		Ciclev10007941m	scaffold_1	27698934	27703620	C_unshiu_00237:mRNA_7.1	C_unshiu_00237	40930	45531	Protein translocase subunit SecY	AGI-08	56.724
Tf0003.2		OOthers	O	-	-	-	-	-		Ciclev10002471m	scaffold_5	37808878	37811097	C_unshiu_00238:mRNA_14.1	C_unshiu_00238	116142	129209	Hypothetical protein	AGI-09	44.054
Bf0213			-	-	-	-	-	-	SI097	Ciclev10000820m	scaffold_5	37693882	37699178	C_unshiu_00238:mRNA_2.1	C_unshiu_00238	14475	19398	DnaJ domain protein									RP-09	77.126
Tf0318		AAvailable marker	O	O	O	-	O	O		Ciclev10031873m	scaffold_4	13751433	13754767	C_unshiu_00240:mRNA_28.2	C_unshiu_00240	282002	285335	Transcription factor bHLH137	AGI-07	37.467
Ov0322		ULess informative for main cultivars	-	-	-	-	-	-		Ciclev10003485m	scaffold_5	36398988	36399239	C_unshiu_00241:mRNA_9.1	C_unshiu_00241	39546	40639	Microsomal signal peptidase 12 kDa protein	AGI-09	50.810	KmG-09	42.179	JtR-09S	62.873			RP-09	70.369
Bf1192			-	-	-	-	-	-		Ciclev10008160m	scaffold_1	10678653	10684627	C_unshiu_00242:mRNA_11.1	C_unshiu_00242	100038	105603	Casein kinase I-like protein	AGI-01	57.863
Mf0070		MDisagree by Marco analysis	O	-	-	-	-	-	SI017	Ciclev10017346m	scaffold_2	3067337	3069249	C_unshiu_00246:mRNA_8.1	C_unshiu_00246	68251	69988	Hypothetical protein	AGI-07	36.616			JtR-07	52.611			RP-07	19.079
Ov0408		AAvailable marker	-	-	-	-	-	O		Ciclev10011522m	scaffold_6	18491789	18493623	C_unshiu_00248:mRNA_30.1	C_unshiu_00248	247183	248778	UDP-glycosyltransferase 71C4			KmG-04	50.902					RP-04	23.745
Tf0275		AAvailable marker	O	-	-	-	O	O		Ciclev10006256m	scaffold_9	955176	957425	C_unshiu_00249:mRNA_31.1	C_unshiu_00249	191274	194861	Transposon protein, putative, Mutator sub-class	AGI-03	11.501
Ov0505		AAvailable marker	-	-	-	-	-	O		Ciclev10031252m	scaffold_4	16626338	16629094	C_unshiu_00250:mRNA_14.1	C_unshiu_00250	82573	84397	Tyrosine decarboxylase			KmG-07	53.887	JtR-07	48.672	NAT-07	3.814
Wy0019			-	-	-	-	-	-	SI031	Ciclev10029354m	scaffold_8	18064761	18071003	C_unshiu_00251:mRNA_10.1	C_unshiu_00251	118858	124101	Putative axial regulator YABBY 2
Tf0290		AAvailable marker	O	-	-	-	O	O		Ciclev10029354m	scaffold_8	18064761	18071003	C_unshiu_00251:mRNA_10.1	C_unshiu_00251	118858	124101	Putative axial regulator YABBY 2	AGI-08	57.802
Af1487			-	-	-	-	-	-		Ciclev10028531m	scaffold_8	18155481	18157658	C_unshiu_00251:mRNA_22.1	C_unshiu_00251	205180	207288	DnaJ	AGI-08	47.330
Fb0180			-	-	-	-	-	-	SI209	Ciclev10005370m	scaffold_9	27734482	27736035	C_unshiu_00252:mRNA_1.1	C_unshiu_00252	12109	13626	Hypothetical protein									RP-03	56.919
Ov0320			-	-	-	-	-	-		Ciclev10005968m	scaffold_9	27640074	27641178	C_unshiu_00252:mRNA_13.1	C_unshiu_00252	89281	90198	21 kDa protein									RP-03	56.919
Tf0056		AAvailable marker	O	-	-	-	O	O	SI061,SI137	Ciclev10012265m	scaffold_6	22305922	22308021	C_unshiu_00252:mRNA_6.1	C_unshiu_00252	48632	49537	Myb domain protein 42	AGI-04	49.225
Tf0254		Bno homozygous cultivar with minor allele	O	-	-	-	-	-		Ciclev10010885m	scaffold_6	23916876	23939827	C_unshiu_00253:mRNA_3.1	C_unshiu_00253	14647	20586	Hypothetical protein	AGI-04	38.226
Fb0207			-	-	-	-	-	-		Ciclev10006449m	scaffold_9	3771162	3771725	C_unshiu_00254:mRNA_35.1	C_unshiu_00254	237120	239518	Heat shock 22 kDa protein									RP-03	21.444
Bf0016			O	-	-	-	-	-		Ciclev10002605m	scaffold_5	35782419	35784765	C_unshiu_00255:mRNA_23.1	C_unshiu_00255	146364	148653	Protein CutA 1, chloroplastic									RP-09	67.943
Cp1162		AAvailable marker	-	-	-	-	O	O		Ciclev10001345m	scaffold_5	35908181	35912917	C_unshiu_00255:mRNA_35.1	C_unshiu_00255	260170	264872	Phosphoribosylaminoimidazolesuccinocarboxamide synthase	AGI-09	53.232							RP-09	69.673
Tf0173			O	-	-	-	-	-		Ciclev10015413m	scaffold_2	26097343	26099320	C_unshiu_00259:mRNA_35.1	C_unshiu_00259	219790	227265	Hypothetical protein									RP-06.1	28.110
Bf0147			-	-	-	-	-	-	SI165	Ciclev10014858m	scaffold_2	5975367	5977280	C_unshiu_00260:mRNA_18.1	C_unshiu_00260	124629	126502	Flavonoid 3'-monooxygenase									RP-06.1	47.841
Af1056			-	-	-	-	-	-		Ciclev10015905m	scaffold_2	26595972	26598955	C_unshiu_00262:mRNA_14.1	C_unshiu_00262	84573	87520	Purple acid phosphatase 3	AGI-06	66.320
Al0224		AAvailable marker	-	O	-	-	O	O		Ciclev10015872m	scaffold_2	26630154	26632900	C_unshiu_00262:mRNA_19.1	C_unshiu_00262	115955	118351	Probable xyloglucan endotransglucosylase/hydrolase protein 27	AGI-06	67.116	KmG-06	17.100	JtR-06S	3.805	NAT-06S	8.025	RP-06.1	28.576
Tf0014.2			-	-	-	-	-	-		Ciclev10030185m	scaffold_8	24976315	24979483	C_unshiu_00271:mRNA_9.1	C_unshiu_00271	56325	61820	Transcription factor	AGI-08
Cp0160			-	-	-	-	-	-		Ciclev10019883m	scaffold_3	21940551	21944032	C_unshiu_00272:mRNA_20.1	C_unshiu_00272	187755	191248	Endoglucanase	AGI-05	41.267
Ov0318		ULess informative for main cultivars	-	-	-	-	-	-		Ciclev10012779m	scaffold_6	19405285	19407278	C_unshiu_00273:mRNA_20.1	C_unshiu_00273	103250	105183	40S ribosomal protein S5
Ov0510		MDisagree by Marco analysis	-	-	-	-	-	-		Ciclev10011175m	scaffold_6	10016564	10019369	C_unshiu_00279:mRNA_11.1	C_unshiu_00279	116848	119657	Phenylalanine ammonia-lyase 1			KmG-04	62.284	JtR-04	3.789
Bf0123			-	-	-	-	-	-	SI141	Ciclev10011473m	scaffold_6	15803864	15809998	C_unshiu_00284:mRNA_13.1	C_unshiu_00284	114758	120828	Sulfoquinovosyldiacylglycerol 2	AGI-08	92.221							RP-04	10.226
Af1087			O	-	-	-	-	-		Ciclev10019689m	scaffold_3	24796351	24800588	C_unshiu_00286:mRNA_17.1	C_unshiu_00286	132648	135466	Glycine hydroxymethyltransferase	AGI-05	41.306
Ov0420		MDisagree by Marco analysis	-	-	-	-	-	-		Ciclev10019489m	scaffold_3	24840386	24845254	C_unshiu_00286:mRNA_25.1	C_unshiu_00286	176709	181573	Methylenetetrahydrofolate reductase (NAD(P)H)	AGI-05	41.306			JtR-05	41.208
Bf0184			O	-	-	-	-	-		Ciclev10021248m	scaffold_3	24893551	24898675	C_unshiu_00286:mRNA_27.1	C_unshiu_00286	216376	220366	Cysteine protease ATG4B	AGI-05	41.306
Cp0278			-	-	-	-	-	-		Ciclev10022561m	scaffold_3	24750794	24752907	C_unshiu_00286:mRNA_8.1	C_unshiu_00286	73068	81236	Hypothetical protein	AGI-04	122.142
Tf0315		AAvailable marker	O	-	-	-	O	O		Ciclev10012089m	scaffold_6	14087181	14090115	C_unshiu_00287:mRNA_20.1	C_unshiu_00287	221944	222997	Phantastica	AGI-08	93.657
Al0212			O	-	-	-	-	-		Ciclev10026128m	scaffold_7	5258045	5259521	C_unshiu_00288:mRNA_19.1	C_unshiu_00288	142758	144183	Mitochondrial uncoupling protein 3			KmG-02	43.821	JtR-02	30.507			RP-08
Fb0275			O	-	-	-	-	-		Ciclev10008562m	scaffold_1	15883118	15887517	C_unshiu_00288:mRNA_9.1	C_unshiu_00288	55910	60461	Malate dehydrogenase	AGI-01	55.687
Cp2262		AAvailable marker	-	-	-	-	-	O		Ciclev10026121m	scaffold_7	1870933	1874304	C_unshiu_00289:mRNA_20.1	C_unshiu_00289	113542	116894	Galactose mutarotase-like superfamily protein
Af0004			O	-	-	-	-	-		Ciclev10025125m	scaffold_7	8447414	8453714	C_unshiu_00290:mRNA_10.1	C_unshiu_00290	83615	110154	Hypothetical protein	AGI-02	2.847
Bf0142			O	-	-	-	-	-		Ciclev10024891m	scaffold_7	8508837	8516759	C_unshiu_00290:mRNA_16.1	C_unshiu_00290	151884	158772	Class III homeodomain leucine zipper protein	AGI-02	5.104
Cp1111		MDisagree by Marco analysis	-	-	-	-	-	-		Ciclev10024860m	scaffold_7	8603450	8610239	C_unshiu_00290:mRNA_28.1	C_unshiu_00290	241335	248051	Cell division protein ftsH, putative isoform 1	AGI-02	5.054
Tf0067		OOthers	O	-	-	-	-	-	SI033,SI187	Ciclev10025950m	scaffold_7	8438702	8442381	C_unshiu_00290:mRNA_9.1	C_unshiu_00290	74194	77624	Transcription factor	AGI-02	5.104
Wy0035		ULess informative for main cultivars	O	-	-	-	-	-		Ciclev10014857m	scaffold_2	31148849	31150616	C_unshiu_00292:mRNA_13.1	C_unshiu_00292	110620	112650	FAD-binding Berberine family protein	AGI-06	36.863
Bf0413			-	-	-	-	-	-						C_unshiu_00293:mRNA_16.1	C_unshiu_00293	231743	233897	Hypothetical protein	AGI-09	86.996
Bf0125			-	-	-	-	-	-		Ciclev10001956m	scaffold_5	15764937	15766976	C_unshiu_00293:mRNA_8.1	C_unshiu_00293	104196	105925	NAC transcription factor							NAT-03	8.920	RP-03	31.431
Tf0147			-	-	-	-	-	-		Ciclev10001956m	scaffold_5	15764937	15766976	C_unshiu_00293:mRNA_8.1	C_unshiu_00293	104196	105925	NAC transcription factor	AGI-02	22.436
Gn0067		OOthers	O	-	-	-	-	-	SI204,SI349	Ciclev10004730m	scaffold_9	22728310	22730086	C_unshiu_00295:mRNA_17.1	C_unshiu_00295	207257	208985	Lycopene beta-cyclase	AGI-03	46.274
Bf0205			O	-	-	-	-	-	SI236	Ciclev10025925m	scaffold_7	3541924	3543863	C_unshiu_00301:mRNA_11.1	C_unshiu_00301	55570	57462	WRKY
Af1379			-	-	-	-	-	-		Ciclev10026357m	scaffold_7	3456105	3460607	C_unshiu_00301:mRNA_21.2	C_unshiu_00301	134429	138770	CBS domain-containing protein CBSX1, chloroplastic	AGI-02	68.467
Tf0280			-	-	-	-	-	-	SI158,SI200	Ciclev10025566m	scaffold_7	3429964	3433239	C_unshiu_00301:mRNA_24.3	C_unshiu_00301	159835	163045	Floral homeotic protein APETALA 2	AGI-05	54.268
Cp1738		AAvailable marker	-	-	-	-	-	O	SI237,SI296	Ciclev10025941m	scaffold_7	5388458	5389981	C_unshiu_00303:mRNA_12.1	C_unshiu_00303	100918	102276	Putative clathrin assembly protein
Fb0223			-	-	-	-	-	-	SI240					C_unshiu_00303:mRNA_13.1	C_unshiu_00303	108935	110191	E3 ubiquitin-protein ligase ATL6									RP-08	15.967
Al0029		Bno homozygous cultivar with minor allele	O	-	-	-	-	-						C_unshiu_00305:mRNA_10.1	C_unshiu_00305	69938	73026	Basic helix-loop-helix transcription factor	AGI-01	37.357			JtR-01S	50.000
Cp0781		AAvailable marker	-	-	-	-	O	O		Ciclev10021469m	scaffold_3	41043663	41046480	C_unshiu_00305:mRNA_28.1	C_unshiu_00305	251599	254198	Thioredoxin-like 7 family protein	AGI-05	50.294
Bf0031			O	-	-	-	-	-		Ciclev10031547m	scaffold_4	4077557	4083819	C_unshiu_00306:mRNA_12.1	C_unshiu_00306	51707	57589	Chorismate synthase	AGI-07	32.590							RP-07	19.092
Af1498			-	-	-	-	-	-		Ciclev10006723m	scaffold_9	6766349	6768025	C_unshiu_00307:mRNA_26.2	C_unshiu_00307	212314	218407	Heterogeneous nuclear ribonucleoprotein 1	AGI-03	46.274
Al0619			-	-	-	-	-	-		Ciclev10005142m	scaffold_9	2234066	2238313	C_unshiu_00311:mRNA_12.1	C_unshiu_00311	55933	60057	TLP domain class transcription factor	AGI-01	57.863	KmG-01	39.698
Al0525		OOthers	O	-	-	-	-	-		Ciclev10026706m	scaffold_7	252320	254023	C_unshiu_00312:mRNA_20.2	C_unshiu_00312	114652	116351	High mobility group (HMG)-box protein	AGI-01	38.939	KmG-01	41.081
Tf0026			O	-	-	-	-	-	SI111,SI288	Ciclev10025369m	scaffold_7	285299	292550	C_unshiu_00312:mRNA_28.1	C_unshiu_00312	151229	158232	Ubiquilin	AGI-02	78.531
Al0228			-	-	-	-	-	-		Ciclev10009018m	scaffold_1	26206063	26208427	C_unshiu_00315:mRNA_25.1	C_unshiu_00315	212819	220361	Serine/threonine-protein kinase HT1					JtR-034	7.115
If0219		MDisagree by Marco analysis	-	-	-	-	-	-						C_unshiu_00318:mRNA_17.1	C_unshiu_00318	110550	117056	Esterase					JtR-05	13.922	NAT-05	28.283
Ov0316			-	-	-	-	-	-		Ciclev10020995m	scaffold_3	3963024	3966516	C_unshiu_00318:mRNA_19.1	C_unshiu_00318	155111	158235	Zinc finger CCCH domain-containing protein 43					JtR-05	31.749
Af1633			-	-	-	-	-	-		Ciclev10020304m	scaffold_3	3963024	3966516	C_unshiu_00318:mRNA_19.1	C_unshiu_00318	155111	158235	Zinc finger CCCH domain-containing protein 43	AGI-07	67.201
Tf0051			-	-	-	-	-	-	SI027,SI214	Ciclev10021952m	scaffold_3	3964036	3966516	C_unshiu_00318:mRNA_19.1	C_unshiu_00318	155111	158235	Zinc finger CCCH domain-containing protein 43	AGI-05	25.590
Cp2229		AAvailable marker	-	-	-	-	O	O		Ciclev10022058m	scaffold_3	4117485	4120274	C_unshiu_00318:mRNA_6.1	C_unshiu_00318	44376	47085	Nucleoside diphosphate kinase	AGI-05	27.135
Bf0024			O	-	-	-	-	-	SI093	Ciclev10002093m	scaffold_5	38134662	38138860	C_unshiu_00319:mRNA_24.1	C_unshiu_00319	167810	171973	Probable protein phosphatase 2C 11	AGI-05	39.006
Af2596			-	-	-	-	-	-		Ciclev10002840m	scaffold_5	38154975	38155769	C_unshiu_00319:mRNA_29.1	C_unshiu_00319	189073	189599	Basic blue protein	AGI-09	57.830
Al0324		MDisagree by Marco analysis	-	-	-	-	-	-		Ciclev10029315m	scaffold_8	20424287	20425903	C_unshiu_00320:mRNA_1.2	C_unshiu_00320	12758	14314	Hypothetical protein	AGI-08	41.127					NAT-082	31.019	RP-08	17.081
Ov0121		HDisagree on Clementine haploid genotype	-	-	-	-	-	-		Ciclev10028359m	scaffold_8	20352232	20354410	C_unshiu_00320:mRNA_8.1	C_unshiu_00320	86929	88531	Arogenate dehydratase							NAT-081
Ov0125		AAvailable marker	-	-	-	-	O	O		Ciclev10028359m	scaffold_8	20352232	20354410	C_unshiu_00320:mRNA_8.1	C_unshiu_00320	86929	88531	Arogenate dehydratase	AGI-08	41.398
If0203		MDisagree by Marco analysis	-	-	-	-	-	-		Ciclev10022993m	scaffold_3	42229224	42231230	C_unshiu_00322:mRNA_21.1	C_unshiu_00322	121122	123131	Small ubiquitin-related modifier	AGI-05	51.293	KmG-05S	67.257	JtR-05	43.446
Lp0208			-	-	-	-	-	-		Ciclev10018482m	scaffold_3	45704361	45713084	C_unshiu_00326:mRNA_24.1	C_unshiu_00326	146528	154002	ABC transporter C family member 3	AGI-03	15.136					NAT-03	28.397
Cp1427		AAvailable marker	-	-	-	-	O	O		Ciclev10021746m	scaffold_3	45576863	45579197	C_unshiu_00326:mRNA_5.1	C_unshiu_00326	23073	25265	Bifunctional protein FolD	AGI-05	58.917
If0011		Bno homozygous cultivar with minor allele	-	-	-	-	-	-		Ciclev10013189m	scaffold_6	20522569	20523527	C_unshiu_00331:mRNA_8.1	C_unshiu_00331	122906	127189	PLASMODESMATA CALLOSE-BINDING PROTEIN 3
Lp0103		OOthers	-	-	-	-	-	-		Ciclev10012274m	scaffold_6	16393309	16395378	C_unshiu_00332:mRNA_15.1	C_unshiu_00332	142648	144673	Pyridoxal biosynthesis lyase pdxS									RP-04	11.437
Af1068			O	-	-	-	-	-		Ciclev10021732m	scaffold_3	40110008	40113420	C_unshiu_00335:mRNA_13.1	C_unshiu_00335	99790	103133	Protein vip1	AGI-05	48.750
Af1685			-	-	-	-	-	-		Ciclev10023782m	scaffold_3	40086985	40089114	C_unshiu_00335:mRNA_9.1	C_unshiu_00335	76164	77436	Hypothetical protein	AGI-05	56.481
Gn0005		MDisagree by Marco analysis	-	-	-	-	-	-		Ciclev10015934m	scaffold_2	35693249	35696515	C_unshiu_00337:mRNA_13.1	C_unshiu_00337	68883	71725	Fibrillin	AGI-06	16.857	KmG-06	63.840			NAT-06S	59.976
Vt0001		AAvailable marker	-	-	-	-	O	O		Ciclev10014290m	scaffold_2	35624935	35628855	C_unshiu_00337:mRNA_2.1	C_unshiu_00337	2684	6536	Subtilase family protein	AGI-06	16.327	KmG-06	68.041
Vt0011		AAvailable marker	-	-	-	-	O	O		Ciclev10021162m	scaffold_3	12984411	12986574	C_unshiu_00337:mRNA_2.1	C_unshiu_00337	2684	6536	Subtilase family protein	AGI-05	41.306			JtR-05	37.780
Fb0104		OOthers	O	-	-	-	-	-		Ciclev10016358m	scaffold_2	35758546	35760859	C_unshiu_00337:mRNA_24.1	C_unshiu_00337	135198	136991	Tropinone reductase like	AGI-06	16.857							RP-06.2	16.271
Cp0635		AAvailable marker	O	-	O	-	O	O						C_unshiu_00337:mRNA_4.1	C_unshiu_00337	11596	15307	50S ribosomal protein L4	AGI-06	17.029
Fb0237			-	-	-	-	-	-		Ciclev10007227m	scaffold_1	23487200	23497316	C_unshiu_00338:mRNA_20.1	C_unshiu_00338	134033	144369	Hypothetical protein	AGI-01	28.325
Tf0230			-	-	-	-	-	-	SI140	Ciclev10008206m	scaffold_1	23463843	23470911	C_unshiu_00338:mRNA_22.1	C_unshiu_00338	163174	169978	NAD-dependent protein deacetylase SRT1
Tf0406		Bno homozygous cultivar with minor allele	O	-	-	-	-	-		Ciclev10008206m	scaffold_1	23463843	23470911	C_unshiu_00338:mRNA_22.1	C_unshiu_00338	163174	169978	NAD-dependent protein deacetylase SRT1	AGI-01	28.515
Gn0011			-	-	-	-	-	-		Ciclev10007488m	scaffold_1	24814539	24819264	C_unshiu_00341:mRNA_12.1	C_unshiu_00341	85182	89905	Sucrose synthase			KmG-01	21.459
Tf0168		AAvailable marker	O	O	-	O	O	O	SI175	Ciclev10007563m	scaffold_1	24898769	24905716	C_unshiu_00341:mRNA_22.1	C_unshiu_00341	170777	178753	AT-rich interactive domain-containing protein 4	AGI-01	25.752
Ov0116			-	-	-	-	-	-		Ciclev10032931m	scaffold_4	3193875	3196468	C_unshiu_00342:mRNA_22.1	C_unshiu_00342	154980	164222	Hypothetical protein			KmG-02	53.208	JtR-02	27.051			RP-02.2	5.192
Fb0322			O	-	-	-	-	-		Ciclev10030532m	scaffold_4	3249710	3254808	C_unshiu_00342:mRNA_35.1	C_unshiu_00342	217525	222590	Splicing factor 3B subunit 3	AGI-07	14.580			JtR-07	64.384			RP-07	47.636
Tf0342			-	-	-	-	-	-	SI151	Ciclev10019088m	scaffold_3	1649410	1655963	C_unshiu_00343:mRNA_23.1	C_unshiu_00343	203038	209504	DNA repair helicase	AGI-05	5.510
Mf0039		AAvailable marker	O	-	-	-	O	O	SI016,SI147					C_unshiu_00343:mRNA_25.1	C_unshiu_00343	221381	224081	PLAC8 family protein	AGI-05	5.510	KmG-05S	5.643	JtR-05	10.014
Bf0033			-	-	-	-	-	-	SI356,SI379	Ciclev10007537m	scaffold_1	27204998	27211059	C_unshiu_00347:mRNA_22.1	C_unshiu_00347	166830	172467	NADPH--hemoprotein reductase	AGI-01	32.408							RP-01	85.146
Af1223			-	-	-	-	-	-		Ciclev10009839m	scaffold_1	27111412	27114276	C_unshiu_00347:mRNA_8.1	C_unshiu_00347	66555	79401	Flavin-binding kelch domain F box protein	AGI-09	97.668
Lp0105		Bno homozygous cultivar with minor allele	O	-	-	-	-	-	SI113,SI163,SI254	Ciclev10026412m	scaffold_7	815904	817239	C_unshiu_00353:mRNA_13.1	C_unshiu_00353	92033	93437	Hypothetical protein	AGI-02	75.939
Af1031			O	-	-	-	-	-		Ciclev10025711m	scaffold_7	718488	722516	C_unshiu_00353:mRNA_22.1	C_unshiu_00353	151145	154679	3-dehydroquinate synthase AroB	AGI-02	76.168
Gn0101			-	-	-	-	-	-		Ciclev10025706m	scaffold_7	662802	667420	C_unshiu_00353:mRNA_30.1	C_unshiu_00353	203269	207136	Protein MID1-COMPLEMENTING ACTIVITY 1	AGI-02	77.881
Tf0065			-	-	-	-	-	-	SI142	Ciclev10030696m	scaffold_4	13945795	13951313	C_unshiu_00357:mRNA_3.1	C_unshiu_00357	35189	39739	Auxin response factor	AGI-07	41.876
Al0517		AAvailable marker	-	-	-	-	O	O		Ciclev10028293m	scaffold_8	2572439	2574295	C_unshiu_00363:mRNA_1.1	C_unshiu_00363	5892	7583	Limonoid glucosyltransferase	AGI-08	74.016			JtR-08	15.435
Gn0033		MDisagree by Marco analysis	-	-	-	-	-	-		Ciclev10028247m	scaffold_8	2561845	2563605	C_unshiu_00363:mRNA_2.1	C_unshiu_00363	14663	16198	Limonoid UDP-glucosyltransferase-like protein	AGI-08	73.527	KmG-08	86.664			NAT-082	86.620
Fb0246			-	-	-	-	-	-		Ciclev10029680m	scaffold_8	2403492	2406922	C_unshiu_00363:mRNA_27.1	C_unshiu_00363	170901	174318	Hypothetical protein	AGI-08	80.078
Cp0603		MDisagree by Marco analysis	O	-	-	-	-	-		Ciclev10028998m	scaffold_8	2349655	2354496	C_unshiu_00363:mRNA_34.1	C_unshiu_00363	217631	222409	Hop-interacting protein THI043	AGI-08	75.684
Al0206		AAvailable marker	-	-	-	-	O	O		Ciclev10032727m	scaffold_4	12309480	12311438	C_unshiu_00365:mRNA_26.1	C_unshiu_00365	192643	194502	NADPH-dependent codeinone reductase-like protein	AGI-07	38.565			JtR-07	52.611			RP-07	29.935
Af1415			-	-	-	-	-	-		Ciclev10005717m	scaffold_9	2603134	2605405	C_unshiu_00366:mRNA_20.1	C_unshiu_00366	130993	132913	Transmembrane BAX inhibitor motif-containing protein 4	AGI-03	16.667
Gn0052			-	-	-	-	-	-		Ciclev10005365m	scaffold_9	10357084	10359834	C_unshiu_00367:mRNA_10.1	C_unshiu_00367	100255	102997	Male sterility MS5 family protein			KmG-032	15.450	JtR-031	12.830
Wy0032		OOthers	O	-	-	-	O	O		Ciclev10005365m	scaffold_9	10357084	10359834	C_unshiu_00367:mRNA_10.1	C_unshiu_00367	100255	102997	Male sterility MS5 family protein	AGI-03	46.121	KmG-032	14.572	JtR-031	12.840
Al0234		OOthers	-	-	-	-	-	-		Ciclev10005909m	scaffold_9	1372972	1374927	C_unshiu_00369:mRNA_20.1	C_unshiu_00369	74034	74546	Ribosomal protein L19			KmG-031	6.974			NAT-03	47.094	RP-03	3.219
Af1060			O	-	-	-	-	-		Ciclev10000400m	scaffold_5	42918371	42923480	C_unshiu_00370:mRNA_16.1	C_unshiu_00370	75283	79772	Tonoplast monosaccharide transporter 2	AGI-09	23.647
Fb0326			O	-	-	-	-	-		Ciclev10002506m	scaffold_5	43051579	43053394	C_unshiu_00370:mRNA_38.1	C_unshiu_00370	207050	209216	Cell division control protein 2	AGI-09	8.959							RP-09	78.225
Bf0164		ULess informative for main cultivars	O	-	-	-	-	-	SI263	Ciclev10000615m	scaffold_5	43060442	43066562	C_unshiu_00370:mRNA_39.2	C_unshiu_00370	217887	223455	Pyrophosphate-dependent phosphofructokinase alpha subunit	AGI-09	21.471					NAT-09	111.981	RP-09	94.065
Tf0454		AAvailable marker	O	-	-	-	O	O		Ciclev10027306m	scaffold_7	16108723	16113463	C_unshiu_00371:mRNA_10.1	C_unshiu_00371	121418	127245	GATA transcription factor	AGI-02	21.099
Al0239		Bno homozygous cultivar with minor allele	-	-	-	-	-	-		Ciclev10026364m	scaffold_7	16185818	16187223	C_unshiu_00371:mRNA_7.1	C_unshiu_00371	54653	56423	B-box type zinc finger protein, putative
Af3023			-	-	-	-	-	-		Ciclev10026364m	scaffold_7	16185818	16187223	C_unshiu_00371:mRNA_7.1	C_unshiu_00371	54653	56423	B-box type zinc finger protein, putative	AGI-02	21.337
Gn0097			-	-	-	-	-	-		Ciclev10005133m	scaffold_9	10246239	10248409	C_unshiu_00372:mRNA_8.1	C_unshiu_00372	77039	79209	Naringenin-chalcone synthase	AGI-02
Vs0014		Bno homozygous cultivar with minor allele	-	-	-	-	-	-						C_unshiu_00375:mRNA_10.1	C_unshiu_00375	50515	51680	Metallothionein
Fb0159		AAvailable marker	O	-	-	-	O	O	SI227	Ciclev10028241m	scaffold_8	23456630	23459052	C_unshiu_00375:mRNA_4.1	C_unshiu_00375	27952	30443	O-Glycosyl hydrolases family 17 protein	AGI-08	13.499	KmG-08	9.978					RP-08	2.327
Bf0019			-	-	-	-	-	-		Ciclev10028586m	scaffold_8	232123	235806	C_unshiu_00376:mRNA_8.1	C_unshiu_00376	72474	76027	Putative serine/threonine-protein kinase Cx32									RP-04
Vt0032			O	-	-	-	-	-	SI024	Ciclev10024737m	scaffold_7	17901487	17905433	C_unshiu_00382:mRNA_15.1	C_unshiu_00382	163577	167662	Leucine-rich repeat receptor-like serine/threonine-protein kinase BAM1	AGI-02	25.601							RP-02	6.081
Wy0012			O	-	-	-	-	O		Ciclev10004385m	scaffold_9	4888531	4892972	C_unshiu_00386:mRNA_17.1	C_unshiu_00386	142436	145911	Ethylene receptor			KmG-032	11.250	JtR-031	4.898	NAT-03	11.970
Af1414			-	-	-	-	-	-		Ciclev10004385m	scaffold_9	4888531	4892972	C_unshiu_00386:mRNA_17.1	C_unshiu_00386	142436	145911	Ethylene receptor	AGI-03	50.895
Tf0240			-	-	-	-	-	-	SI184	Ciclev10018505m	scaffold_3	42718991	42733040	C_unshiu_00386:mRNA_19.1	C_unshiu_00386	164396	178993	Myosin 2
Bf0003		ULess informative for main cultivars	O	-	-	-	-	-	SI354	Ciclev10011720m	scaffold_6	16246773	16250769	C_unshiu_00390:mRNA_6.1	C_unshiu_00390	75799	78947	Vacuolar cation/proton exchanger 3									RP-04	10.253
Al0419		OOthers	O	-	-	-	-	-		Ciclev10005894m	scaffold_9	2452853	2455181	C_unshiu_00394:mRNA_25.1	C_unshiu_00394	150531	152208	Hypothetical protein	AGI-03	17.378	KmG-09	9.593	JtR-09S	7.976
Cp1031		AAvailable marker	-	O	-	-	O	O		Ciclev10005224m	scaffold_9	2324313	2328666	C_unshiu_00394:mRNA_4.1	C_unshiu_00394	11970	16480	Putative E3 ubiquitin-protein ligase MARCH10	AGI-03	18.610
Fb0827			O	-	-	-	-	-	SI215,SI301	Ciclev10004432m	scaffold_9	2353442	2357780	C_unshiu_00394:mRNA_9.1	C_unshiu_00394	41719	45690	Chloroplast 1-deoxy-D-xylulose-5-phosphate synthase	AGI-03	19.017	KmG-031	16.544	JtR-034
Tf0058			-	-	-	-	-	-	SI257	Ciclev10009065m	scaffold_1	20885102	20889283	C_unshiu_00395:mRNA_8.2	C_unshiu_00395	50978	54866	Fertilization-independent endosperm protein	AGI-01	46.623
Tf0203			-	-	-	-	-	-	SI121	Ciclev10014039m	scaffold_2	10459593	10472483	C_unshiu_00403:mRNA_13.1	C_unshiu_00403	88988	102135	Homeodomain transcriptional regulator
Bf0218			O	-	-	-	-	-	SI232	Ciclev10000452m	scaffold_5	36036990	36048487	C_unshiu_00406:mRNA_20.1	C_unshiu_00406	134274	145322	Isoamylase	AGI-09	53.205	KmG-09	37.847					RP-09	70.349
Cp0973		OOthers	-	-	-	-	-	-		Ciclev10013409m	scaffold_6	8193393	8195764	C_unshiu_00407:mRNA_4.1	C_unshiu_00407	55425	57717	Thioredoxin F-type, chloroplastic
Tf0256		AtAvailable marker	O	-	-	-	O	O		Ciclev10021699m	scaffold_3	43420187	43422432	C_unshiu_00411:mRNA_13.1	C_unshiu_00411	116444	118424	Myb-related protein Myb4	AGI-05	52.314
Al0319		Bno homozygous cultivar with minor allele	O	-	-	-	-	-		Ciclev10022720m	scaffold_3	43447942	43449920	C_unshiu_00411:mRNA_15.1	C_unshiu_00411	140821	145311	Actin-depolymerizing factor 2	AGI-03	46.274	KmG-05S	65.273	JtR-05	42.339			RP-05	72.912
Tf0351			-	-	-	-	-	-	SI122	Ciclev10021622m	scaffold_3	43472094	43473220	C_unshiu_00411:mRNA_17.1	C_unshiu_00411	160316	161284	Ethylene-responsive transcription factor 1B	AGI-05	52.655
Af1091			O	-	-	-	-	-		Ciclev10021043m	scaffold_3	43316046	43317909	C_unshiu_00411:mRNA_2.1	C_unshiu_00411	11510	13352	Arabinose 5-phosphate isomerase	AGI-05	52.655
Cp1585		MDisagree by Marco analysis	-	-	-	-	-	-		Ciclev10021651m	scaffold_3	6602994	6605239	C_unshiu_00412:mRNA_10.1	C_unshiu_00412	80300	82171	Stay green protein
Tf0083			-	-	-	-	-	-	SI129	Ciclev10021651m	scaffold_3	6602994	6605239	C_unshiu_00412:mRNA_10.1	C_unshiu_00412	80300	82171	Stay green protein	AGI-05	37.103
Tf0420		AAvailable marker	O	O	O	-	O	O		Ciclev10022018m	scaffold_3	6602994	6605239	C_unshiu_00412:mRNA_10.1	C_unshiu_00412	80300	82171	Stay green protein	AGI-05	37.103
Ov0311			-	-	-	-	-	-		Ciclev10022001m	scaffold_3	18341166	18342395	C_unshiu_00417:mRNA_9.1	C_unshiu_00417	93426	94543	Kunitz trypsin inhibitor			KmG-04	10.598			NAT-09	82.730
Al0329		AAvailable marker	O	-	-	-	O	O	SI185	Ciclev10025866m	scaffold_7	17201236	17204282	C_unshiu_00421:mRNA_21.2	C_unshiu_00421	196945	199790	Actin	AGI-02	25.162	KmG-02	11.218	JtR-02	7.174	NAT-02S	5.552	RP-02	8.191
Mf0090		AAvailable marker	-	O	-	-	O	O		Ciclev10025866m	scaffold_7	17201236	17204282	C_unshiu_00421:mRNA_21.2	C_unshiu_00421	196945	199790	Actin	AGI-02	25.869	KmG-02	11.182	JtR-02	3.182			RP-02	8.191
Tf0199			-	-	-	-	-	-	SI023,SI157	Ciclev10000697m	scaffold_5	30994812	30999834	C_unshiu_00422:mRNA_12.1	C_unshiu_00422	116754	121159	Serine/threonine-protein kinase isoform 2
Bf0195			-	-	-	-	-	-	SI369	Ciclev10000780m	scaffold_5	31069237	31075092	C_unshiu_00422:mRNA_5.1	C_unshiu_00422	35322	40511	Sodium/hydrogen exchanger 2	AGI-09	74.076
Gn0058			-	-	-	-	-	-		Ciclev10029531m	scaffold_8	11297754	11299510	C_unshiu_00424:mRNA_23.1	C_unshiu_00424	213541	217268	Hypothetical protein	AGI-08	59.107
Al0001			-	-	-	-	-	-						C_unshiu_00424:mRNA_23.1	C_unshiu_00424	213541	217268	Hypothetical protein	AGI-03	62.228			JtR-031	17.616
Af1036			O	-	-	-	-	-		Ciclev10021080m	scaffold_3	7016831	7019863	C_unshiu_00425:mRNA_11.1	C_unshiu_00425	65596	68473	Replication factor C subunit 2	AGI-05	43.118
Tf0079		MDisagree by Marco analysis	O	-	-	O	-	-	SI270,SI294	Ciclev10021287m	scaffold_3	7047024	7049430	C_unshiu_00425:mRNA_7.1	C_unshiu_00425	35608	38027	Heat stress transcription factor B-4	AGI-05	45.092
Bf0138		MDisagree by Marco analysis	O	-	-	-	-	-		Ciclev10019462m	scaffold_3	6072460	6076187	C_unshiu_00428:mRNA_16.2	C_unshiu_00428	119232	121021	Oxygen-evolving enhancer protein 2, chloroplastic							NAT-05	14.555	RP-05	24.995
Bf0182			O	-	-	-	-	-		Ciclev10009454m	scaffold_1	17831333	17834889	C_unshiu_00429:mRNA_12.1	C_unshiu_00429	90883	94296	3-deoxy-D-manno-octulosonate cytidylyltransferase	AGI-01	47.439
Tf0360			-	-	-	-	-	-	SI112	Ciclev10000627m	scaffold_5	38669123	38672110	C_unshiu_00430:mRNA_12.1	C_unshiu_00430	98615	101120	Trihelix transcription factor GT-2	AGI-09	43.140
Cp1627		AAvailable marker	-	-	-	-	O	O		Ciclev10022024m	scaffold_3	13309398	13310636	C_unshiu_00431:mRNA_6.1	C_unshiu_00431	44507	45451	Chloroplast small heat shock protein	AGI-05	41.272
Ov0512		OOthers	O	-	-	-	-	-		Ciclev10006241m	scaffold_9	27198508	27199642	C_unshiu_00433:mRNA_19.1	C_unshiu_00433	116730	118286	Small heat shock protein	AGI-03	40.361	KmG-032	25.743	JtR-031		NAT-03
Fb0233			O	-	-	-	-	-	SI025,SI079,SI169	Ciclev10025557m	scaffold_7	6535522	6540965	C_unshiu_00437:mRNA_15.1	C_unshiu_00437	131524	136642	WD-40 repeat-containing protein MSI4	AGI-02	47.382
Ov0520		OOthers	O	-	-	-	-	-		Ciclev10029053m	scaffold_8	4712393	4713689	C_unshiu_00438:mRNA_3.1	C_unshiu_00438	34343	35619	BURP domain-containing protein	AGI-08	33.144			JtR-08	26.748
Wy0018		AAvailable marker	-	-	-	-	O	O		Ciclev10021374m	scaffold_3	5318874	5321054	C_unshiu_00442:mRNA_14.1	C_unshiu_00442	123398	125451	Homeobox-leucine zipper protein HAT3	AGI-05	29.033	KmG-05S	20.128	JtR-05	19.008
Tf0301			-	-	-	-	-	-	SI182	Ciclev10021374m	scaffold_3	5318874	5321054	C_unshiu_00442:mRNA_14.1	C_unshiu_00442	123398	125451	Homeobox-leucine zipper protein HAT3
Ov0301		Bno homozygous cultivar with minor allele	-	-	-	-	-	-	SI078	Ciclev10021068m	scaffold_3	5360113	5362918	C_unshiu_00442:mRNA_18.1	C_unshiu_00442	163615	166153	Transcription factor			KmG-05S	23.526	JtR-05	19.932			RP-05	21.590
Ov0302	Ov0301.2		-	-	-	-	-	-		Ciclev10021068m	scaffold_3	5360113	5362918	C_unshiu_00442:mRNA_18.1	C_unshiu_00442	163615	166153	Transcription factor
Tf0017			-	-	-	-	-	-	SI285	Ciclev10021068m	scaffold_3	5360113	5362918	C_unshiu_00442:mRNA_18.1	C_unshiu_00442	163615	166153	Transcription factor	AGI-05	28.617
Ov0006		Bno homozygous cultivar with minor allele	O	-	-	-	-	-		Ciclev10021068m	scaffold_3	5360113	5362918	C_unshiu_00442:mRNA_18.1	C_unshiu_00442	163615	166153	Transcription factor			KmG-05S	25.587	JtR-08	27.669
Tf0307		Bno homozygous cultivar with minor allele	O	-	-	-	-	-		Ciclev10009286m	scaffold_1	25395688	25397278	C_unshiu_00442:mRNA_24.1	C_unshiu_00442	209015	209831	Myb domain protein 5	AGI-01	23.266
Tf0028			-	-	-	-	-	-	SI377	Ciclev10022572m	scaffold_3	19780711	19782241	C_unshiu_00443:mRNA_20.1	C_unshiu_00443	195567	202424	MADS-box transcription factor
Al0326		AAvailable marker	-	-	-	O	O	-	SI065,SI344	Ciclev10022558m	scaffold_3	6409311	6411254	C_unshiu_00443:mRNA_7.1	C_unshiu_00443	62532	64193	Zinc finger A20 and AN1 domain-containing stress-associated protein 8	AGI-05	42.609	KmG-05S	32.841	JtR-05	16.025			RP-05	27.235
Tf0059			-	-	-	-	-	-	SI101	Ciclev10007297m	scaffold_1	12883722	12897805	C_unshiu_00450:mRNA_3.1	C_unshiu_00450	36956	58462	AGC family Serine/Threonine kinase family protein	AGI-01	56.416
Af1100			-	-	-	-	-	-		Ciclev10026703m	scaffold_7	10853487	10855215	C_unshiu_00451:mRNA_17.1	C_unshiu_00451	120744	122474	Ran BP2/NZF zinc finger-like superfamily protein isoform 1	AGI-02	13.326
Cp0249			-	-	-	-	-	-		Ciclev10001084m	scaffold_5	39480647	39484776	C_unshiu_00457:mRNA_14.1	C_unshiu_00457	96540	99356	Acetyltransferase component of pyruvate dehydrogenase complex	AGI-09	41.336
If0220		AAvailable marker	-	-	-	-	-	O		Ciclev10001084m	scaffold_5	39480647	39484776	C_unshiu_00457:mRNA_15.1	C_unshiu_00457	99488	99913	Hypothetical protein
Lp0135			-	-	-	-	-	-		Ciclev10002870m	scaffold_5	39412819	39414334	C_unshiu_00457:mRNA_3.1	C_unshiu_00457	27521	28982	Xylem serinease 1-like protein					JtR-05	41.854
Wy0039		AAvailable marker	-	-	-	-	O	O		Ciclev10028965m	scaffold_8	18824262	18825514	C_unshiu_00459:mRNA_4.1	C_unshiu_00459	34475	34918	Hypothetical protein	AGI-08	45.276			JtR-08	16.276
Cp1279		AAvailable marker	-	-	-	-	O	O		Ciclev10031414m	scaffold_4	12900777	12903692	C_unshiu_00461:mRNA_17.1	C_unshiu_00461	144878	147555	Ornithine aminotransferase	AGI-07	40.184
Gn0002			-	-	-	-	-	-		Ciclev10032697m	scaffold_4	3335945	3338632	C_unshiu_00465:mRNA_12.1	C_unshiu_00465	149021	153095	Hypothetical protein	AGI-07	90.233			JtR-07	64.361
Fb0301		AAvailable marker	-	-	-	-	O	O	SI053	Ciclev10014804m	scaffold_2	14143537	14146003	C_unshiu_00466:mRNA_1.1	C_unshiu_00466	13811	16178	4-coumarate:coenzyme A ligase 4	AGI-06	92.727	KmG-06						RP-06.1	16.627
Vs0006		ULess informative for main cultivars	-	-	-	-	-	-		Ciclev10025343m	scaffold_7	19024295	19026021	C_unshiu_00468:mRNA_22.1	C_unshiu_00468	132124	133922	Cytochrome P450 78A4	AGI-02	27.491			JtR-02	50.216	NAT-02S	3.328
Cp0026			-	-	-	-	-	-		Ciclev10014741m	scaffold_2	24938686	24943643	C_unshiu_00472:mRNA_8.1	C_unshiu_00472	85278	89618	Putative ADP-glucose pyrophosphorylase small subunit	AGI-06	72.449
Tf0167			-	-	-	-	-	-	SI230,SI241,SI247	Ciclev10030998m	scaffold_4	17143350	17147918	C_unshiu_00478:mRNA_2.1	C_unshiu_00478	19232	27824	Sigma factor	AGI-07	46.244
Tf0241		Bno homozygous cultivar with minor allele	O	-	-	-	-	-		Ciclev10027798m	scaffold_8	22106872	22114471	C_unshiu_00481:mRNA_18.1	C_unshiu_00481	121975	128680	Zinc finger CCCH domain-containing protein 24	AGI-08	27.618
Cp0237			-	-	-	-	-	-		Ciclev10033007m	scaffold_4	10652381	10655082	C_unshiu_00483:mRNA_11.1	C_unshiu_00483	100177	109515	Protein LSD1	AGI-07	35.506
Bf0115			O	-	-	-	-	-	SI054,SI295	Ciclev10029066m	scaffold_8	6317205	6322458	C_unshiu_00484:mRNA_11.3	C_unshiu_00484	48216	54250	Squalene synthase	AGI-08	58.587					NAT-081	17.717
Bf0026			-	-	-	-	-	-		Ciclev10008765m	scaffold_1	21082902	21086082	C_unshiu_00487:mRNA_12.1	C_unshiu_00487	113166	115416	Thiazole biosynthetic enzyme	AGI-01	43.164							RP-01	56.137
Tf0221			-	-	-	-	-	-	SI057,SI225	Ciclev10025996m	scaffold_7	490750	492882	C_unshiu_00488:mRNA_7.1	C_unshiu_00488	44813	48259	Ankyrin repeat domain-containing protein, chloroplastic	AGI-02	81.212
Tf0317			-	-	-	-	-	-	SI145	Ciclev10021941m	scaffold_3	2106810	2109266	C_unshiu_00490:mRNA_19.1	C_unshiu_00490	159122	161521	Transcription factor bHLH47
Vs0004			-	-	-	-	-	-		Ciclev10021761m	scaffold_3	2078691	2083111	C_unshiu_00490:mRNA_23.1	C_unshiu_00490	182148	190847	Nucleosome assembly protein			KmG-06	51.244
Ks9003		AAvailable marker	-	-	-	-	-	O		Ciclev10014733m	scaffold_2	8436110	8440408	C_unshiu_00494:mRNA_1.1	C_unshiu_00494	7014	11146	Ascorbate oxidase			KmG-09	19.560	JtR-09S	5.836
Lp0220			O	-	-	-	-	-		Ciclev10000749m	scaffold_5	39221210	39227401	C_unshiu_00495:mRNA_21.1	C_unshiu_00495	125230	136174	Hypothetical protein	AGI-07	14.968
Tf0172			O	-	-	-	-	-		Ciclev10026400m	scaffold_7	9976621	9980176	C_unshiu_00496:mRNA_5.1	C_unshiu_00496	48069	50951	Auxin-induced protein IAA6	AGI-02	10.638
Gn0042			-	-	-	-	-	-		Ciclev10009742m	scaffold_1	25370176	25371445	C_unshiu_00498:mRNA_21.1	C_unshiu_00498	140388	142383	Deficiens					JtR-08	6.490
Bf0411		MDisagree by Marco analysis	-	-	-	-	-	-		Ciclev10028317m	scaffold_8	21869065	21874083	C_unshiu_00500:mRNA_13.1	C_unshiu_00500	128482	133656	Sulfotransferase
Tf0029			-	-	-	-	-	-		Ciclev10027901m	scaffold_8	21887372	21893128	C_unshiu_00500:mRNA_16.1	C_unshiu_00500	147319	151840	Auxin response factor	AGI-08	27.318
Cp0532			-	-	-	-	-	-		Ciclev10020319m	scaffold_3	30393811	30398972	C_unshiu_00501:mRNA_15.1	C_unshiu_00501	133280	137847	Solanesyl diphosphate synthase	AGI-05	42.168
Tf0012		AAvailable marker	-	-	-	-	O	O		Ciclev10018673m	scaffold_3	37601493	37607586	C_unshiu_00502:mRNA_21.1	C_unshiu_00502	155419	162660	Protein NLP8	AGI-05	47.173
Af1052			O	-	-	-	-	-		Ciclev10004444m	scaffold_9	12808154	12820311	C_unshiu_00508:mRNA_9.1	C_unshiu_00508	40385	58179	Hypothetical protein	AGI-08	56.724
Tf0328			-	-	-	-	-	-	SI039,SI180	Ciclev10021606m	scaffold_3	2530708	2533942	C_unshiu_00509:mRNA_27.1	C_unshiu_00509	178211	181426	Transcription factor bHLH79
Af1043			-	-	-	-	-	-		Ciclev10026060m	scaffold_7	20049936	20052008	C_unshiu_00519:mRNA_19.1	C_unshiu_00519	110187	111261	Ribonucleoside-diphosphate reductase subunit M2	AGI-02	44.231
Af1396			-	-	-	-	-	-		Ciclev10022545m	scaffold_3	4920662	4923421	C_unshiu_00520:mRNA_16.2	C_unshiu_00520	166824	167867	Ribosomal protein L19 family protein	AGI-05	28.041
Bf0233		MDisagree by Marco analysis	O	-	-	-	-	-	SI359	Ciclev10019826m	scaffold_3	6502231	6504139	C_unshiu_00521:mRNA_1.1	C_unshiu_00521	2449	4274	Cytochrome P450 76C2	AGI-05	42.581							RP-05	27.235
Tf0411		OOthers	O	-	-	-	-	-		Ciclev10020263m	scaffold_3	38111191	38116265	C_unshiu_00523:mRNA_15.1	C_unshiu_00523	100297	104594	Putative transcription factor PosF21	AGI-05	48.613
Af1003			O	-	-	-	-	-		Ciclev10001093m	scaffold_5	15605852	15610028	C_unshiu_00533:mRNA_20.1	C_unshiu_00533	131430	141111	Glutamyl-tRNA(Gln) amidotransferase subunit A, chloroplastic/mitochondrial	AGI-02	22.436
Lp0021		AtAvailable marker	O	-	-	-	-	O		Ciclev10021502m	scaffold_3	1771668	1774647	C_unshiu_00534:mRNA_8.2	C_unshiu_00534	53508	55845	Aquaporin
Tf0212			-	-	-	-	-	-	SI196	Ciclev10030538m	scaffold_4	19816800	19825304	C_unshiu_00535:mRNA_20.1	C_unshiu_00535	166525	174142	Putative nuclear matrix constituent protein 1-like protein	AGI-07	56.586
Ov0312			-	-	-	-	-	-		Ciclev10018858m	scaffold_3	1344192	1349935	C_unshiu_00541:mRNA_19.1	C_unshiu_00541	170170	175878	Spastin									SA-09	8.022
Fb0364		AAvailable marker	-	-	-	-	O	O	SI373	Ciclev10022215m	scaffold_3	13810497	13813004	C_unshiu_00542:mRNA_3.1	C_unshiu_00542	15940	18433	Nascent polypeptide-associated complex subunit alpha-like protein	AGI-05	41.306	KmG-05S	55.482	JtR-05	39.609			RP-05	56.834
Fb0995		OOthers	O	-	-	-	-	-	SI026	Ciclev10024677m	scaffold_7	1180019	1202408	C_unshiu_00544:mRNA_10.1	C_unshiu_00544	97318	121662	FAT domain-containing protein	AGI-02	74.555	KmG-02	82.954	JtR-02	10.215
Tf0309			-	-	-	-	-	-	SI190	Ciclev10020466m	scaffold_3	45314016	45316651	C_unshiu_00546:mRNA_23.1	C_unshiu_00546	158416	160829	TLP domain class transcription factor	AGI-05	57.948
Tf0184		AAvailable marker	O	-	-	-	O	O		Ciclev10019968m	scaffold_3	45393857	45398298	C_unshiu_00546:mRNA_8.1	C_unshiu_00546	75023	78260	Zinc finger CCCH domain-containing protein 3	AGI-05	57.948
Bf0011		AAvailable marker	O	-	-	-	O	O	SI218	Ciclev10008900m	scaffold_1	4722889	4726339	C_unshiu_00547:mRNA_9.1	C_unshiu_00547	54556	57654	NADH-cytochrome b5 reductase	AGI-01	67.331							RP-01	23.653
Tf0245			-	-	-	-	-	-	SI021	Ciclev10008628m	scaffold_1	18298599	18300295	C_unshiu_00548:mRNA_21.1	C_unshiu_00548	168151	169460	Hypothetical protein
Al0209		HDisagree on Clementine haploid genotype	-	-	-	-	-	-		Ciclev10008628m	scaffold_1	18298599	18300295	C_unshiu_00548:mRNA_21.1	C_unshiu_00548	168151	169460	Hypothetical protein			KmG-01	37.230	JtR-01S	88.382
Gn0064		ULess informative for main cultivars	O	-	-	-	-	-	SI144,SI380	Ciclev10019364m	scaffold_3	29351854	29354190	C_unshiu_00549:mRNA_6.1	C_unshiu_00549	39588	41921	9-cis-epoxycarotenoid dioxygenase 1	AGI-05	42.191							RP-05	51.531
Wy0063	Wy0063.em		-	-	-	-	-	-		Ciclev10021336m	scaffold_3	29395094	29402560	C_unshiu_00549:mRNA_8.1	C_unshiu_00549	83149	90542	Splicing regulatory glutamine/lysine-rich protein 1	AGI-01	33.445
Wy0064	Wy0064.em		-	-	-	-	-	-		Ciclev10021336m	scaffold_3	29395094	29402560	C_unshiu_00549:mRNA_8.1	C_unshiu_00549	83149	90542	Splicing regulatory glutamine/lysine-rich protein 1
Ov0427			-	-	-	-	-	-		Ciclev10009427m	scaffold_1	2156679	2158871	C_unshiu_00553:mRNA_14.1	C_unshiu_00553	110847	134434	Hypothetical protein			KmG-05S	36.268
Ov0013		OOthers	-	-	-	-	-	-		Ciclev10005251m	scaffold_9	18058387	18060752	C_unshiu_00556:mRNA_14.1	C_unshiu_00556	103101	105466	Caffeic acid 3-O-methyltransferase	AGI-03	50.691	KmG-032	18.852	JtR-031	11.918			RP-03	38.986
Bf0029		MDisagree by Marco analysis	-	-	-	O	-	-	SI193,SI283					C_unshiu_00564:mRNA_19.1	C_unshiu_00564	138967	142178	Limonene synthase	AGI-09	84.912	KmG-09	24.379	JtR-09S	5.526
Fb0313			-	-	-	-	-	-		Ciclev10002602m	scaffold_5	29803196	29804310	C_unshiu_00570:mRNA_7.1	C_unshiu_00570	69328	70168	Mitochondrial import inner membrane translocase subunit tim23									RP-07	9.871
Tf0081			-	-	-	-	-	-	SI038,SI324	Ciclev10021980m	scaffold_3	38214468	38216861	C_unshiu_00575:mRNA_8.1	C_unshiu_00575	47693	51431	Leucine-rich repeat disease resistance protein-like	AGI-05	48.590
Gmom29			-	-	-	-	-	-		Ciclev10000654m	scaffold_5	12677414	12680761	C_unshiu_00578:mRNA_7.1	C_unshiu_00578	77446	80730	Putative WRKY transcription factor 33	AGI-02	22.436
Af1370			-	-	-	-	-	-		Ciclev10009015m	scaffold_1	8822834	8826308	C_unshiu_00579:mRNA_6.1	C_unshiu_00579	46507	50108	Plasma membrane	AGI-01	56.590
Tf0001.2		AAvailable marker	O	O	O	-	O	O		Ciclev10020248m	scaffold_3	8647529	8652282	C_unshiu_00580:mRNA_10.1	C_unshiu_00580	75118	81473	Transcription factor BIM1	AGI-05	41.893
Cp1791		Bno homozygous cultivar with minor allele	-	-	-	-	-	-		Ciclev10027428m	scaffold_7	11604464	11607028	C_unshiu_00582:mRNA_4.1	C_unshiu_00582	10067	11470	NBS-LRR type disease resistance protein	AGI-02	12.969
Ov0027	Ov0027.em		-	-	-	-	-	-		Ciclev10009797m	scaffold_1	8417158	8419377	C_unshiu_00584:mRNA_9.1	C_unshiu_00584	74089	76266	60S ribosomal protein L28	AGI-03	51.749
Ov0503		AtAvailable marker	O	-	-	-	-	O		Ciclev10020582m	scaffold_3	28382218	28386683	C_unshiu_00585:mRNA_5.1	C_unshiu_00585	31636	34824	60S ribosomal protein L5							NAT-05	19.042
Gn0056			-	-	-	-	-	-		Ciclev10020582m	scaffold_3	28382218	28386683	C_unshiu_00585:mRNA_5.1	C_unshiu_00585	31636	34824	60S ribosomal protein L5	AGI-05	39.424
Af1416			-	-	-	-	-	-		Ciclev10029140m	scaffold_8	3738607	3741747	C_unshiu_00589:mRNA_10.1	C_unshiu_00589	131180	134227	Embryo defective 1273, putative isoform 1	AGI-08	68.834
Tf0077			O	-	-	-	-	-	SI135	Ciclev10008135m	scaffold_1	28433972	28437921	C_unshiu_00590:mRNA_15.1	C_unshiu_00590	86430	90131	WRKY	AGI-01	34.814
Cp0671		AAvailable marker	-	-	-	-	O	O		Ciclev10009489m	scaffold_1	28353948	28356507	C_unshiu_00590:mRNA_26.1	C_unshiu_00590	165626	168046	UPF0133 protein	AGI-01	36.113
Af1568			-	-	-	-	-	-						C_unshiu_00591:mRNA_15.1	C_unshiu_00591	108974	112318	Putative elongation factor 2-like	AGI-01	24.954
Al0215		OOthers	-	-	-	-	-	-		Ciclev10007304m	scaffold_1	21918726	21922966	C_unshiu_00595:mRNA_18.1	C_unshiu_00595	85575	88636	Disease resistance protein	AGI-01	38.255
Fb0329			-	-	-	-	-	-		Ciclev10004180m	scaffold_9	29237838	29242883	C_unshiu_00606:mRNA_2.1	C_unshiu_00606	13693	18703	Methyltransferase MT-A70 family protein isoform 1	AGI-03	60.686
Tf0010			-	-	-	-	-	-		Ciclev10021038m	scaffold_3	1054257	1056078	C_unshiu_00609:mRNA_18.1	C_unshiu_00609	77883	79313	Putative WRKY transcription factor 41	AGI-05
Gn0018			-	-	-	-	-	-		Ciclev10030969m	scaffold_4	5053540	5061039	C_unshiu_00616:mRNA_15.1	C_unshiu_00616	99349	106841	V-type H+-transporting ATPase subunit A	AGI-08	84.345	KmG-02	16.986
Vt0003			-	-	-	-	-	-		Ciclev10027667m	scaffold_8	8153660	8174407	C_unshiu_00616:mRNA_3.1	C_unshiu_00616	10808	18470	Hypothetical protein	AGI-08	56.724
Bf0409			-	-	-	-	-	-						C_unshiu_00616:mRNA_6.1	C_unshiu_00616	72171	79153	Disease resistance protein (CC-NBS-LRR class) family protein	AGI-08	57.386
Cp0190		OOthers	-	-	-	-	-	-		Ciclev10023646m	scaffold_3	18648426	18650443	C_unshiu_00618:mRNA_5.1	C_unshiu_00618	20273	22297	UPF0426 protein, chloroplastic	AGI-06	27.617
Wy0030		AAvailable marker	O	-	-	-	O	O		Ciclev10001854m	scaffold_5	36229310	36230518	C_unshiu_00619:mRNA_10.1	C_unshiu_00619	87213	88404	EXORDIUM like 2	AGI-09	53.205	KmG-09	44.154	JtR-09S	63.577	NAT-09	65.585
Gmom13			-	-	-	-	-	-		Ciclev10005787m	scaffold_9	13223034	13225922	C_unshiu_00620:mRNA_11.2	C_unshiu_00620	118042	120892	Ethylene-responsive transcription factor ERF114	AGI-08	56.724
Lp0019		MDisagree by Marco analysis	-	-	-	-	-	-		Ciclev10026623m	scaffold_7	20922631	20924709	C_unshiu_00622:mRNA_2.1	C_unshiu_00622	28630	30583	50S ribosomal protein L29, chloroplastic			KmG-02	4.377	JtR-02	-6.938
Cp1709		AAvailable marker	-	-	-	-	-	O		Ciclev10025382m	scaffold_7	1450748	1452915	C_unshiu_00624:mRNA_14.1	C_unshiu_00624	137579	139378	Cytochrome P450 84A1
Bf0030			O	-	-	-	-	-		Ciclev10022841m	scaffold_3	46452893	46453717	C_unshiu_00627:mRNA_10.1	C_unshiu_00627	45215	45931	Calvin cycle protein CP12									RP-05	58.661
Af1207			-	-	-	-	-	-		Ciclev10025335m	scaffold_7	15605065	15607345	C_unshiu_00628:mRNA_20.1	C_unshiu_00628	144683	146646	Flavonoid 3'-monooxygenase	AGI-02	21.344
Wy0006			O	-	-	-	-	-		Ciclev10021901m	scaffold_3	4903592	4905871	C_unshiu_00628:mRNA_6.1	C_unshiu_00628	38419	40239	Bax inhibitor 1			KmG-05S	19.072	JtR-05	19.698	NAT-05	21.803
Bf0165			-	-	-	-	-	-	SI280	Ciclev10021901m	scaffold_3	4903592	4905871	C_unshiu_00628:mRNA_6.1	C_unshiu_00628	38419	40239	Bax inhibitor 1	AGI-05	29.035					NAT-05	23.083	RP-05	19.690
Cp0975		MDisagree by Marco analysis	-	-	-	-	-	-		Ciclev10012312m	scaffold_6	7924189	7928192	C_unshiu_00631:mRNA_15.1	C_unshiu_00631	149702	153660	Isopentenyl pyrophosphate isomerase	AGI-07	29.152
Al0416		OOthers	-	-	-	-	-	-		Ciclev10028443m	scaffold_8	22316999	22319482	C_unshiu_00639:mRNA_12.1	C_unshiu_00639	90698	99467	Elongation factor 1-alpha	AGI-08	23.023			JtR-07	60.405	NAT-082	21.126
Tf0345			-	-	-	-	-	-	SI011	Ciclev10027918m	scaffold_8	22248129	22254029	C_unshiu_00639:mRNA_3.1	C_unshiu_00639	31842	37665	Auxin response factor
Lp0031			-	-	-	-	-	-		Ciclev10027944m	scaffold_8	22261408	22266208	C_unshiu_00639:mRNA_5.1	C_unshiu_00639	45321	49901	N-terminal isoform 1	AGI-08	9.183
Bf0415			-	-	-	-	-	-						C_unshiu_00643:mRNA_7.1	C_unshiu_00643	115076	117637	BEL1-like homeodomain protein 1	AGI-08	46.736
Ov0004			-	-	-	-	-	-		Ciclev10025545m	scaffold_7	20360086	20363290	C_unshiu_00650:mRNA_9.1	C_unshiu_00650	86670	89289	Myo-inositol-1 phosphate synthase			KmG-02	17.680			NAT-02S
Al0621		Bno homozygous cultivar with minor allele	O	-	-	-	-	-		Ciclev10025875m	scaffold_7	4575503	4577125	C_unshiu_00656:mRNA_8.1	C_unshiu_00656	32940	34329	Hypothetical protein	AGI-02	60.566	KmG-02	47.196	JtR-02	28.472
Af1482			-	-	-	-	-	-		Ciclev10001945m	scaffold_5	36550507	36552800	C_unshiu_00657:mRNA_2.2	C_unshiu_00657	28541	30831	DRE binding transcription factor	AGI-09	49.255
Cp0257			-	-	-	-	-	-		Ciclev10001536m	scaffold_5	36526073	36528589	C_unshiu_00657:mRNA_4.1	C_unshiu_00657	52199	54744	Trehalose-phosphatase	AGI-09	48.390
Cp0748			-	-	-	-	-	-		Ciclev10022288m	scaffold_3	34673451	34674900	C_unshiu_00669:mRNA_14.1	C_unshiu_00669	103814	104779	Light-dependent short hypocotyls protein	AGI-01	33.562
Tf0353		MDisagree by Marco analysis	O	-	-	-	-	-	SI087	Ciclev10018691m	scaffold_3	34696661	34702240	C_unshiu_00669:mRNA_17.2	C_unshiu_00669	126539	133312	Cell division cycle 5-like protein	AGI-08	53.069
Cp2154			-	-	-	-	-	-	SI164	Ciclev10009584m	scaffold_1	20462860	20465557	C_unshiu_00670:mRNA_8.1	C_unshiu_00670	44502	47121	50S ribosomal protein L24, chloroplastic
Lp0032		Bno homozygous cultivar with minor allele	-	-	-	-	-	-	SI286					C_unshiu_00679:mRNA_13.1	C_unshiu_00679	124222	132199	CwfJ-like family protein, putative isoform 1
Tf0144			-	-	-	-	-	-	SI125,SI189,SI192	Ciclev10028782m	scaffold_8	8009000	8012045	C_unshiu_00682:mRNA_12.1	C_unshiu_00682	86334	89311	Transcription factor bHLH121	AGI-08	56.439
Al0240		AAvailable marker	-	-	-	-	O	O		Ciclev10028497m	scaffold_8	8033465	8038415	C_unshiu_00682:mRNA_9.1	C_unshiu_00682	59786	63447	Hypothetical protein	AGI-08	53.867
Cp1483			-	-	-	-	-	-		Ciclev10020574m	scaffold_3	20762974	20770394	C_unshiu_00692:mRNA_14.1	C_unshiu_00692	122321	129331	Abhydrolase domain-containing protein 11	AGI-05	41.162
Tf0350		OOthers	O	-	-	-	-	-	SI132	Ciclev10019034m	scaffold_3	8914744	8921411	C_unshiu_00695:mRNA_7.1	C_unshiu_00695	71483	77987	Acetyl-coenzyme A synthetase	AGI-05	43.295
Gn0004			-	-	-	-	-	-		Ciclev10026028m	scaffold_7	6011523	6014015	C_unshiu_00696:mRNA_14.1	C_unshiu_00696	122646	125456	Flavonol synthase	AGI-02	49.699	KmG-02	38.471	JtR-02	15.126
Lp0004		OOthers	-	-	-	-	-	-		Ciclev10026144m	scaffold_7	15376818	15378771	C_unshiu_00703:mRNA_1.1	C_unshiu_00703	2793	4693	C6HC-type zinc finger RING/U-box protein	AGI-02	20.292	KmG-02	15.368					RP-02	11.119
Wy0023			-	-	-	-	-	-	SI037	Ciclev10025834m	scaffold_7	70855	73880	C_unshiu_00706:mRNA_12.1	C_unshiu_00706	76103	78923	Thioredoxin-disulfide reductase
Al0627		HDisagree on Clementine haploid genotype	O	-	-	-	-	-		Ciclev10025602m	scaffold_7	128539	131642	C_unshiu_00706:mRNA_3.1	C_unshiu_00706	16590	18098	Trigalactosyldiacylglycerol 1 isoform 1	AGI-02	78.531
Tf0032		AAvailable marker	O	-	-	-	O	O		Ciclev10026014m	scaffold_7	94155	97631	C_unshiu_00706:mRNA_8.1	C_unshiu_00706	51525	54837	AT-hook motif nuclear-localized protein 10	AGI-02	78.531
Cp0974			-	-	-	-	-	-		Ciclev10011578m	scaffold_6	8029488	8035109	C_unshiu_00711:mRNA_6.1	C_unshiu_00711	128510	138133	Hypothetical protein	AGI-04	107.018
Mf0060			-	-	-	-	-	-						C_unshiu_00715:mRNA_6.1	C_unshiu_00715	29601	30242	Hypothetical protein					JtR-07	56.497
Ov0314		AAvailable marker	O	-	-	-	O	O	SI107	Ciclev10029386m	scaffold_8	8176371	8177435	C_unshiu_00728:mRNA_1.1	C_unshiu_00728	4070	4922	Mannan polymerase complex subunit mnn9	AGI-08	56.724	KmG-08	58.356	JtR-08	21.829			RP-08	41.217
Bf0116			-	-	-	-	-	-	SI260	Ciclev10015490m	scaffold_2	7662753	7667440	C_unshiu_00729:mRNA_11.1	C_unshiu_00729	81415	86474	Aminotransferase 2	AGI-06	133.800							RP-06.1	28.601
Ov0404		AAvailable marker	-	-	-	-	-	O		Ciclev10002415m	scaffold_5	29768091	29769281	C_unshiu_00731:mRNA_6.3	C_unshiu_00731	26598	28767	Hydroxycinnamoyl-CoA shikimate/quinate hydroxycinnamoyl transferase			KmG-09	29.016	JtR-09S	31.495			RP-09	29.347
Gn0063		OOthers	O	-	-	-	-	-		Ciclev10019925m	scaffold_3	40937725	40942854	C_unshiu_00735:mRNA_14.1	C_unshiu_00735	99621	103733	Violaxanthin de-epoxidase	AGI-08	60.140	KmG-07	31.750
Cp0047		HDisagree on Clementine haploid genotype	-	-	-	-	-	-		Ciclev10021599m	scaffold_3	40918148	40922656	C_unshiu_00735:mRNA_16.1	C_unshiu_00735	120088	124350	Hypothetical protein	AGI-05	48.590
Tf0368		AAvailable marker	O	-	-	-	O	O	SI102	Ciclev10020717m	scaffold_3	40963774	40965744	C_unshiu_00735:mRNA_9.1	C_unshiu_00735	76673	78652	NAC transcription factor 29	AGI-05	48.590
Cp0106		MDisagree by Marco analysis	-	-	-	-	-	-		Ciclev10020606m	scaffold_3	11867765	11869679	C_unshiu_00741:mRNA_6.1	C_unshiu_00741	44989	55203	Wall associated kinase-like 6, putative	AGI-03	40.566
Cp2210		AAvailable marker	-	-	-	-	-	O		Ciclev10007886m	scaffold_1	8125279	8130885	C_unshiu_00744:mRNA_3.1	C_unshiu_00744	19836	25320	6-phosphofructokinase isoform 1
Mf0096		OOthers	-	-	-	-	-	-	SI249,SI333	Ciclev10018252m	scaffold_2	27774863	27778271	C_unshiu_00745:mRNA_6.1	C_unshiu_00745	48150	62370	Hypothetical protein	AGI-06	60.007	KmG-06	22.141	JtR-06S	5.708	NAT-06S	10.082
Af1593			-	-	-	-	-	-		Ciclev10015971m	scaffold_2	27738397	27741912	C_unshiu_00745:mRNA_8.1	C_unshiu_00745	82265	85742	Prolactin regulatory element-binding protein, putative	AGI-06	61.501
Cp0419		AAvailable marker	-	O	-	-	O	O		Ciclev10002215m	scaffold_5	28815314	28816638	C_unshiu_00758:mRNA_1.1	C_unshiu_00758	794	4329	ATP-dependent Clp protease, proteolytic subunit ClpP	AGI-09	88.739							SA-09	44.226
Lp0102		MDisagree by Marco analysis	O	-	-	-	-	-	SI080,SI319,SI360,SI378	Ciclev10020840m	scaffold_3	30648732	30651259	C_unshiu_00759:mRNA_1.1	C_unshiu_00759	917	3353	Senescence-related gene 1	AGI-05	42.737	KmG-05S	41.895	JtR-05	28.682	NAT-05	37.917	RP-05	51.879
Cp1736			-	-	-	-	-	-		Ciclev10026179m	scaffold_7	5640058	5643125	C_unshiu_00761:mRNA_15.2	C_unshiu_00761	89991	92755	Protein CbbY	AGI-02	50.716
Lp0108		AAvailable marker	-	-	-	-	-	O		Ciclev10026340m	scaffold_7	5554619	5556993	C_unshiu_00761:mRNA_5.1	C_unshiu_00761	18704	21072	40S ribosomal protein S6			KmG-02	41.508	JtR-02	18.351
Tf0061			-	-	-	-	-	-	SI150,SI186	Ciclev10001592m	scaffold_5	35159690	35164384	C_unshiu_00764:mRNA_4.1	C_unshiu_00764	30899	36628	Auxin-responsive protein IAA8	AGI-09	61.651
Cp1533			-	-	-	-	-	-		Ciclev10021868m	scaffold_3	4831751	4834270	C_unshiu_00768:mRNA_14.1	C_unshiu_00768	110682	113065	Lil3 protein	AGI-05	29.039
Ov0407		AAvailable marker	-	-	-	-	O	O		Ciclev10000563m	scaffold_5	37043417	37051080	C_unshiu_00773:mRNA_1.1	C_unshiu_00773	7888	15416	OSBP(Oxysterol binding protein)-related protein 1C isoform 3	AGI-09	46.097	KmG-09	48.606	JtR-09S	66.176			RP-09	76.027
Tf0232			-	-	-	-	-	-	SI258,SI261	Ciclev10001105m	scaffold_5	37066208	37070717	C_unshiu_00773:mRNA_3.1	C_unshiu_00773	31351	35269	Histone-lysine N-methyltransferase ASHR1
Af1096			-	-	-	-	-	-		Ciclev10020597m	scaffold_3	42061488	42063267	C_unshiu_00778:mRNA_10.1	C_unshiu_00778	89741	91509	Cytochrome P450 82A4	AGI-05	51.052
Tf0311		AAvailable marker	O	-	-	-	O	O		Ciclev10011596m	scaffold_6	15932016	15936176	C_unshiu_00779:mRNA_8.1	C_unshiu_00779	78105	81377	Auxin transporter-like protein 2	AGI-08	91.890
Tf0096			O	-	-	-	-	-		Ciclev10028804m	scaffold_8	21369373	21370728	C_unshiu_00784:mRNA_1.1	C_unshiu_00784	297	1652	Transcription factor RAX3	AGI-08	34.042
Tf0027			-	-	-	-	-	-	SI046	Ciclev10026602m	scaffold_7	13911684	13912447	C_unshiu_00792:mRNA_11.1	C_unshiu_00792	92331	93069	Ethylene-responsive transcription factor ERF003	AGI-07	38.916
Bf0158			-	O	-	O	-	-	SI376	Ciclev10021285m	scaffold_3	5253281	5254755	C_unshiu_00795:mRNA_3.1	C_unshiu_00795	22534	23534	Ethylene responsive element binding factor, putative	AGI-05	29.035					NAT-05	21.258	RP-05	20.825
Lp0126		AAvailable marker	O	-	-	-	O	O		Ciclev10025164m	scaffold_7	3946818	3949964

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Target: Genome/map	Scaffold/LG