Chromosome	1130	1131	lineage4.2.2.1	A	Euro-American	LAM7-TUR	None
Chromosome	4205	4206	lineage4.1.3	T	Euro-American	T;X;H	None
Chromosome	9943	9944	lineage4.2.2	C	Euro-American (Ural)	T;LAM7-TUR	None
Chromosome	10359	10360	lineage1.2.2.1	C	Indo-Oceanic	NA	RD239
Chromosome	10726	10727	La1.8	G	M.bovis	None	None
Chromosome	12203	12204	lineage3	A	East-African-Indian	CAS	RD750
Chromosome	12233	12234	lineage1.1.2	G	Indo-Oceanic	EAI3;EAI5	RD239
Chromosome	12554	12555	lineage4.5	T	Euro-American	H;T	RD122
Chromosome	13174	13175	lineage1.2.1.2	G	Indo-Oceanic	NA	RD239
Chromosome	13528	13529	lineage5.1.3	A	West-Africa 1	AFRI_2;AFRI_3	RD711
Chromosome	14250	14251	lineage4.3	A	Euro-American (LAM)	mainly-LAM	None
Chromosome	15035	15036	lineage4.4.1.1.1	G	Euro-American	S;Orphans	None
Chromosome	15176	15177	lineage1.1.3	G	Indo-Oceanic	EAI6	RD239
Chromosome	17664	17665	lineage4.6.5	A	Euro-American	T;LAM	None
Chromosome	17841	17842	lineage3.1.3	C	East-African-Indian	CAS	RD750
Chromosome	18090	18091	lineage4.6	A	Euro-American	T;LAM	None
Chromosome	19946	19947	lineage6.1.2	A	West-Africa 2	AFRI_1	RD702
Chromosome	20406	20407	lineage1.2.2	A	Indo-Oceanic	EAI1	RD239
Chromosome	22806	22807	lineage5.2	T	West-Africa 1	AFRI_2;AFRI_3	RD711
Chromosome	23296	23297	La1.3	T	M.bovis	None	None
Chromosome	25138	25139	lineage1.1.3.2	G	Indo-Oceanic	NA	RD239
Chromosome	25305	25306	La1.8.1	G	M.bovis	None	None
Chromosome	26299	26300	lineage4.1.1.2	C	Euro-American (X-type)	X1	None
Chromosome	28438	28439	lineage1.2.1.1	C	Indo-Oceanic	NA	RD239
Chromosome	30311	30312	lineage6.1.2	A	West-Africa 2	AFRI_1	RD702
Chromosome	32580	32581	lineage4.1.3	T	Euro-American	T;X;H	None
Chromosome	32772	32773	lineage1.2.2	A	Indo-Oceanic	EAI1	RD239
Chromosome	34604	34605	lineage3.1.2	A	East-African-Indian	CAS;CAS2	RD750
Chromosome	37240	37241	lineage6.2	A	West-Africa 2	AFRI_1	RD702
Chromosome	39157	39158	lineage2	G	East-Asian	Beijing	RD105
Chromosome	47698	47699	lineage4.3.2	A	Euro-American (LAM)	LAM3	None
Chromosome	47977	47978	lineage6.2.2	T	West-Africa 2	AFRI_1	RD702
Chromosome	49078	49079	lineage4.6.2	G	Euro-American	T;LAM	RD726
Chromosome	51458	51459	La1.5	C	M.bovis	None	None
Chromosome	54303	54304	lineage4.6	T	Euro-American	T;LAM	None
Chromosome	56603	56604	lineage4.4.1.2	A	Euro-American	T1	None
Chromosome	57161	57162	lineage5.1.5	T	West-Africa 1	AFRI_2;AFRI_3	RD711
Chromosome	58785	58786	lineage4.1.4	C	Euro-American	T;X;H	None
Chromosome	60296	60297	lineage1.2.2.1	C	Indo-Oceanic	NA	RD239
Chromosome	61841	61842	lineage1.2.2.2	C	Indo-Oceanic	NA	RD239
Chromosome	62656	62657	lineage4.1	A	Euro-American	T;X;H	None
Chromosome	65810	65811	lineage6.1.1	T	West-Africa 2	AFRI_1	RD702
Chromosome	67075	67076	La1.3	T	M.bovis	None	None
Chromosome	67812	67813	lineage1.2.1.1	A	Indo-Oceanic	NA	RD239
Chromosome	67968	67969	lineage1.1.3.3	T	Indo-Oceanic	NA	RD239
Chromosome	68226	68227	lineage6.3	T	West-Africa 2	AFRI_1	RD702
Chromosome	68687	68688	lineage4.4.1.1.1	T	Euro-American	S;Orphans	None
Chromosome	69341	69342	lineage4.6.2.2	A	Euro-American (Cameroon)	LAM10-CAM	RD726
Chromosome	69872	69873	lineage4.1.1.1	A	Euro-American (X-type)	X2	RD183
Chromosome	69983	69984	lineage3	A	East-African-Indian	CAS	RD750
Chromosome	71498	71499	lineage5.1.5	T	West-Africa 1	AFRI_2;AFRI_3	RD711
Chromosome	71635	71636	lineage5.1.2	T	West-Africa 1	AFRI_2;AFRI_3	RD711
Chromosome	74955	74956	lineage4.2.2	C	Euro-American (Ural)	T;LAM7-TUR	None
Chromosome	78092	78093	lineage6.3	A	West-Africa 2	AFRI_1	RD702
Chromosome	83841	83842	lineage4.1.2	A	Euro-American	T;H	None
Chromosome	85984	85985	lineage3.1.1	C	East-African-Indian	CAS1-Kili	RD750
Chromosome	88763	88764	lineage1.2.2.2	T	Indo-Oceanic	NA	RD239
Chromosome	90228	90229	lineage4.9.1	T	Euro-American (H37Rv-like)	T1	None
Chromosome	90369	90370	lineage4.1.4	T	Euro-American	T;X;H	None
Chromosome	93043	93044	lineage4.6.2.2	A	Euro-American (Cameroon)	LAM10-CAM	RD726
Chromosome	94018	94019	lineage5.1.5	C	West-Africa 1	AFRI_2;AFRI_3	RD711
Chromosome	97897	97898	lineage9	T	Lineage 9	None	None
Chromosome	98535	98536	lineage6.3	T	West-Africa 2	AFRI_1	RD702
Chromosome	103180	103181	lineage4.2	G	Euro-American	H;T;LAM	None
Chromosome	107793	107794	lineage4.1.2.1	T	Euro-American (Haarlem)	T1;H1	RD182
Chromosome	111850	111851	lineage4.6.3	A	Euro-American	T;LAM	None
Chromosome	112489	112490	lineage5.1.5	T	West-Africa 1	AFRI_2;AFRI_3	RD711
Chromosome	112957	112958	lineage4.1.2.1.1	A	Euro-American (Haarlem)	T1;H1	RD182
Chromosome	117294	117295	lineage1.1	A	Indo-Oceanic	EAI3;EAI4;EAI5;EAI6	RD239
Chromosome	118467	118468	La1.7	T	M.bovis	None	None
Chromosome	118468	118469	lineage4.6.2.2	A	Euro-American (Cameroon)	LAM10-CAM	RD726
Chromosome	119599	119600	lineage4.9.1	G	Euro-American (H37Rv-like)	T1	None
Chromosome	121462	121463	lineage4.2.2.1	T	Euro-American	LAM7-TUR	None
Chromosome	122793	122794	lineage4.6	G	Euro-American	T;LAM	None
Chromosome	128263	128264	La1.2.BCG	G	M.bovis	BCG	None
Chromosome	129851	129852	lineage4.1.4	T	Euro-American	T;X;H	None
Chromosome	130448	130449	lineage4.6.1.2	A	Euro-American	T2	RD724
Chromosome	135328	135329	lineage2.2.1	T	East-Asian (Beijing)	Beijing-RD181	RD105;RD207;RD181
Chromosome	135694	135695	lineage4.4.1.1.1	A	Euro-American	S;Orphans	None
Chromosome	136350	136351	lineage6.2.2	A	West-Africa 2	AFRI_1	RD702
Chromosome	136731	136732	lineage6.1.2	T	West-Africa 2	AFRI_1	RD702
Chromosome	138787	138788	lineage4.6.1.2	T	Euro-American	T2	RD724
Chromosome	142316	142317	lineage4.6.2.2	T	Euro-American (Cameroon)	LAM10-CAM	RD726
Chromosome	143534	143535	lineage9	T	Lineage 9	None	None
Chromosome	144389	144390	lineage4.1.1.3	A	Euro-American (X-type)	X1;X3	RD193
Chromosome	147654	147655	lineage4.3.2.1	C	Euro-American (LAM)	LAM3	RD761
Chromosome	152091	152092	lineage4.2.2.1	T	Euro-American	LAM7-TUR	None
Chromosome	154050	154051	lineage1.2.2	G	Indo-Oceanic	EAI1	RD239
Chromosome	154989	154990	lineage2.2.2	T	East-Asian (Beijing)	Beijing-RD105/RD207	RD105;RD207
Chromosome	155292	155293	lineage4.1.1.3	A	Euro-American (X-type)	X1;X3	RD193
Chromosome	155554	155555	lineage4.6.5	T	Euro-American	T;LAM	None
Chromosome	162580	162581	lineage4.3	A	Euro-American (LAM)	mainly-LAM	None
Chromosome	163704	163705	lineage2.2.1	T	East-Asian (Beijing)	Beijing-RD181	RD105;RD207;RD181
Chromosome	164681	164682	lineage1.1.3.2	T	Indo-Oceanic	NA	RD239
Chromosome	166347	166348	lineage4.6.2.2	C	Euro-American (Cameroon)	LAM10-CAM	RD726
Chromosome	176820	176821	lineage4.6.4	G	Euro-American	T;LAM	None
Chromosome	184253	184254	lineage4.1.3	C	Euro-American	T;X;H	None
Chromosome	187284	187285	lineage1.1.3.2	C	Indo-Oceanic	NA	RD239
Chromosome	187341	187342	lineage3.1.2.2	C	East-African-Indian	CAS	RD750
Chromosome	191217	191218	lineage5.1.3	C	West-Africa 1	AFRI_2;AFRI_3	RD711
Chromosome	193734	193735	lineage4.2.2	G	Euro-American (Ural)	T;LAM7-TUR	None
Chromosome	195681	195682	lineage2.2	G	East-Asian (Beijing)	Beijing-RD207	RD105;RD207
Chromosome	197046	197047	lineage4.3.4.1	G	Euro-American (LAM)	LAM1;LAM2	RD174
Chromosome	197396	197397	lineage4.4.1	C	Euro-American (S-type)	S;T	None
Chromosome	201122	201123	lineage4.1.1.1	C	Euro-American (X-type)	X2	RD183
Chromosome	201895	201896	lineage4.7	G	Euro-American (mainly T)	T1;T5	None
Chromosome	202714	202715	lineage6.2	G	West-Africa 2	AFRI_1	RD702
Chromosome	203213	203214	lineage6.1.3	C	West-Africa 2	AFRI_1	RD702
Chromosome	204723	204724	lineage1.2.2.1	A	Indo-Oceanic	NA	RD239
Chromosome	205401	205402	lineage4.3.1	T	Euro-American (LAM)	LAM9	None
Chromosome	206480	206481	lineage4	C	Euro-American	LAM;T;S;X;H	None
Chromosome	208709	208710	lineage4.4.1.1.1	A	Euro-American	S;Orphans	None
Chromosome	208781	208782	lineage2.1	C	East-Asian (non-Beijing)	None	None
Chromosome	211575	211576	lineage4.2.1.1	A	Euro-American (TUR)	H3;H4	None
Chromosome	212243	212244	lineage4.8	A	Euro-American (mainly T)	T1;T2;T3;T5	RD219
Chromosome	214035	214036	lineage4.8.3	T	Euro-American (mainly T)	T1;T2;T3;T5	RD219
Chromosome	215612	215613	lineage4.6.1.1	A	Euro-American	T2-Uganda	RD724
Chromosome	215976	215977	lineage2.2.1	T	East-Asian (Beijing)	Beijing-RD181	RD105;RD207;RD181
Chromosome	216468	216469	lineage2.1	T	East-Asian (non-Beijing)	None	None
Chromosome	217305	217306	lineage4.2	G	Euro-American	H;T;LAM	None
Chromosome	219754	219755	lineage9	T	Lineage 9	None	None
Chromosome	220103	220104	La1.8.X-unk6	T	M.bovis	None	None
Chromosome	221189	221190	lineage8	T	Lineage 8	None	None
Chromosome	223626	223627	lineage4.3.1.1	A	Euro-American (LAM)	LAM9	None
Chromosome	224900	224901	lineage4.4.1.1	G	Euro-American	S;Orphans	None
Chromosome	225038	225039	lineage1.1.2	A	Indo-Oceanic	EAI3;EAI5	RD239
Chromosome	225494	225495	lineage4.3.4.2.1	C	Euro-American (LAM)	LAM11	RD174
Chromosome	225656	225657	lineage5.3	A	West-Africa 1	AFRI_2;AFRI_3	RD711
Chromosome	230257	230258	lineage9	T	Lineage 9	None	None
Chromosome	231260	231261	lineage5.1.3	A	West-Africa 1	AFRI_2;AFRI_3	RD711
Chromosome	234694	234695	lineage4.1.3	T	Euro-American	T;X;H	None
Chromosome	240753	240754	lineage5.1.3	G	West-Africa 1	AFRI_2;AFRI_3	RD711
Chromosome	247551	247552	lineage6.1.2	A	West-Africa 2	AFRI_1	RD702
Chromosome	252494	252495	lineage4.6.3	A	Euro-American	T;LAM	None
Chromosome	252899	252900	lineage2.2.2	T	East-Asian (Beijing)	Beijing-RD105/RD207	RD105;RD207
Chromosome	253968	253969	lineage4.1.1.1	A	Euro-American (X-type)	X2	RD183
Chromosome	255224	255225	lineage4.1.2.1.1	A	Euro-American (Haarlem)	T1;H1	RD182
Chromosome	257040	257041	lineage4.9.1	T	Euro-American (H37Rv-like)	T1	None
Chromosome	260801	260802	lineage5.2	A	West-Africa 1	AFRI_2;AFRI_3	RD711
Chromosome	261627	261628	lineage5.3	C	West-Africa 1	AFRI_2;AFRI_3	RD711
Chromosome	262867	262868	lineage4.8.3	G	Euro-American (mainly T)	T1;T2;T3;T5	RD219
Chromosome	263056	263057	lineage1.2.1.2	G	Indo-Oceanic	NA	RD239
Chromosome	264534	264535	lineage1.1.3.3	T	Indo-Oceanic	NA	RD239
Chromosome	265967	265968	lineage4.1.1	G	Euro-American (X-type)	X1;X2;X3	None
Chromosome	266114	266115	lineage4.1.1.2	T	Euro-American (X-type)	X1	None
Chromosome	270361	270362	lineage8	A	Lineage 8	None	None
Chromosome	272677	272678	lineage1	T	Indo-Oceanic	EAI	RD239
Chromosome	274929	274930	lineage4.1.1.2	A	Euro-American (X-type)	X1	None
Chromosome	276362	276363	lineage6.1.1	T	West-Africa 2	AFRI_1	RD702
Chromosome	278188	278189	lineage1.1.1	C	Indo-Oceanic	EAI4;EAI5	RD239
Chromosome	279802	279803	lineage5.1.1	T	West-Africa 1	AFRI_2;AFRI_3	RD711
Chromosome	281207	281208	lineage1.1	T	Indo-Oceanic	EAI3;EAI4;EAI5;EAI6	RD239
Chromosome	281315	281316	lineage4.5	T	Euro-American	H;T	RD122
Chromosome	281663	281664	lineage4.6.3	G	Euro-American	T;LAM	None
Chromosome	282485	282486	lineage1.2.1.1	A	Indo-Oceanic	NA	RD239
Chromosome	282891	282892	lineage2	T	East-Asian	Beijing	RD105
Chromosome	284622	284623	lineage4.1	A	Euro-American	T;X;H	None
Chromosome	285095	285096	lineage1.1.3.2	T	Indo-Oceanic	NA	RD239
Chromosome	286299	286300	lineage4.1.1.3.1	A	Euro-American (X-type)	X1;X3	RD193
Chromosome	288172	288173	lineage3.1.2.2	C	East-African-Indian	CAS	RD750
Chromosome	288951	288952	La1.8	T	M.bovis	None	None
Chromosome	292633	292634	lineage4.8.3	G	Euro-American (mainly T)	T1;T2;T3;T5	RD219
Chromosome	294595	294596	lineage2.2.2	G	East-Asian (Beijing)	Beijing-RD105/RD207	RD105;RD207
Chromosome	294934	294935	lineage6.2.3	A	West-Africa 2	AFRI_1	RD702
Chromosome	297395	297396	lineage1.2.1.2.1	A	Indo-Oceanic	NA	RD239
Chromosome	298595	298596	lineage6.3	C	West-Africa 2	AFRI_1	RD702
Chromosome	300110	300111	lineage2.1	G	East-Asian (non-Beijing)	None	None
Chromosome	302190	302191	lineage5.1.5	T	West-Africa 1	AFRI_2;AFRI_3	RD711
Chromosome	303110	303111	lineage6.3.1	A	West-Africa 2	AFRI_1	RD702
Chromosome	303413	303414	lineage1.2.1	T	Indo-Oceanic	EAI2	RD239
Chromosome	304049	304050	lineage1.1.3.1	C	Indo-Oceanic	NA	RD239
Chromosome	305345	305346	lineage4.1.4	T	Euro-American	T;X;H	None
Chromosome	305454	305455	lineage1.1.3.1	A	Indo-Oceanic	NA	RD239
Chromosome	306112	306113	lineage4.8.1	T	Euro-American (mainly T)	T1;T2;T3;T5	RD219
Chromosome	306638	306639	lineage4.2.1	C	Euro-American (TUR)	H3;H4	None
Chromosome	311379	311380	lineage6.2.2	C	West-Africa 2	AFRI_1	RD702
Chromosome	311612	311613	lineage4.9	G	Euro-American (H37Rv-like)	T1	None
Chromosome	312943	312944	lineage4.6	T	Euro-American	T;LAM	None
Chromosome	313424	313425	lineage1.1.1	T	Indo-Oceanic	EAI4;EAI5	RD239
Chromosome	313604	313605	La1.7.1	A	M.bovis	None	None
Chromosome	314337	314338	lineage4.2.1	G	Euro-American (TUR)	H3;H4	None
Chromosome	317044	317045	lineage1.1.3	A	Indo-Oceanic	EAI6	RD239
Chromosome	318067	318068	La1.2	T	M.bovis	None	None
Chromosome	321557	321558	lineage2.1	T	East-Asian (non-Beijing)	None	None
Chromosome	323525	323526	lineage1.1.3.2	G	Indo-Oceanic	NA	RD239
Chromosome	324661	324662	lineage4.3.1.1	T	Euro-American (LAM)	LAM9	None
Chromosome	325037	325038	lineage4.6	A	Euro-American	T;LAM	None
Chromosome	326038	326039	lineage4.3.2	T	Euro-American (LAM)	LAM3	None
Chromosome	327231	327232	La3	C	M.orygis	None	None
Chromosome	328640	328641	lineage4.1.1.3	T	Euro-American (X-type)	X1;X3	RD193
Chromosome	329078	329079	lineage6.3	G	West-Africa 2	AFRI_1	RD702
Chromosome	342200	342201	lineage4.4.1.2	G	Euro-American	T1	None
Chromosome	342339	342340	lineage4.1.2.1	T	Euro-American (Haarlem)	T1;H1	RD182
Chromosome	342872	342873	lineage3	T	East-African-Indian	CAS	RD750
Chromosome	343091	343092	lineage3.1.2.2	T	East-African-Indian	CAS	RD750
Chromosome	343313	343314	lineage8	T	Lineage 8	None	None
Chromosome	344287	344288	lineage1	G	Indo-Oceanic	EAI	RD239
Chromosome	344413	344414	lineage8	C	Lineage 8	None	None
Chromosome	345316	345317	lineage5	C	West-Africa 1	AFRI_2;AFRI_3	RD711
Chromosome	345696	345697	lineage4.4.1.2	T	Euro-American	T1	None
Chromosome	346692	346693	lineage2.2.2	T	East-Asian (Beijing)	Beijing-RD105/RD207	RD105;RD207
Chromosome	346897	346898	lineage3.1.2.2	T	East-African-Indian	CAS	RD750
Chromosome	347976	347977	lineage8	C	Lineage 8	None	None
Chromosome	349080	349081	lineage7	A	Lineage 7	None	None
Chromosome	352645	352646	lineage5	A	West-Africa 1	AFRI_2;AFRI_3	RD711
Chromosome	353765	353766	lineage4.2.2	C	Euro-American (Ural)	T;LAM7-TUR	None
Chromosome	353766	353767	lineage4.2.2	T	Euro-American (Ural)	T;LAM7-TUR	None
Chromosome	354233	354234	lineage5.2	A	West-Africa 1	AFRI_2;AFRI_3	RD711
Chromosome	355180	355181	lineage4.4.1.1	A	Euro-American	S;Orphans	None
Chromosome	361144	361145	lineage4.4.1.1	C	Euro-American	S;Orphans	None
Chromosome	363463	363464	lineage2.2	A	East-Asian (Beijing)	Beijing-RD207	RD105;RD207
Chromosome	383080	383081	lineage4.4.1.1	G	Euro-American	S;Orphans	None
Chromosome	393779	393780	lineage4.3.4.1	G	Euro-American (LAM)	LAM1;LAM2	RD174
Chromosome	394921	394922	lineage4.9.1	T	Euro-American (H37Rv-like)	T1	None
Chromosome	403480	403481	lineage1.1.3.1	T	Indo-Oceanic	NA	RD239
Chromosome	403919	403920	lineage4.3.3	T	Euro-American (LAM)	LAM;T	RD115
Chromosome	406388	406389	lineage1.1	A	Indo-Oceanic	EAI3;EAI4;EAI5;EAI6	RD239
Chromosome	415692	415693	lineage3.1.3	A	East-African-Indian	CAS	RD750
Chromosome	420007	420008	lineage4.9	A	Euro-American (H37Rv-like)	T1	None
Chromosome	420307	420308	lineage6.2	T	West-Africa 2	AFRI_1	RD702
Chromosome	422878	422879	lineage4.2.1	A	Euro-American (TUR)	H3;H4	None
Chromosome	423333	423334	lineage1.1	A	Indo-Oceanic	EAI3;EAI4;EAI5;EAI6	RD239
Chromosome	435189	435190	lineage4.1.2	T	Euro-American	T;H	None
Chromosome	435707	435708	lineage4.6.1	A	Euro-American (Uganda)	T2	RD724
Chromosome	436202	436203	lineage6.2.2	G	West-Africa 2	AFRI_1	RD702
Chromosome	438443	438444	La1.6	C	M.bovis	None	None
Chromosome	442071	442072	lineage8	A	Lineage 8	None	None
Chromosome	443276	443277	lineage4.1.2	C	Euro-American	T;H	None
Chromosome	446164	446165	lineage4.1.2	C	Euro-American	T;H	None
Chromosome	449193	449194	lineage2.2.2	A	East-Asian (Beijing)	Beijing-RD105/RD207	RD105;RD207
Chromosome	449703	449704	lineage4.8.1	T	Euro-American (mainly T)	T1;T2;T3;T5	RD219
Chromosome	455758	455759	lineage4.4.1.1.1	G	Euro-American	S;Orphans	None
Chromosome	457031	457032	lineage4.3.2.1	C	Euro-American (LAM)	LAM3	RD761
Chromosome	457391	457392	lineage3.1.3	A	East-African-Indian	CAS	RD750
Chromosome	458047	458048	lineage6.3.2	C	West-Africa 2	AFRI_1	RD702
Chromosome	461438	461439	lineage6.3.1	A	West-Africa 2	AFRI_1	RD702
Chromosome	464957	464958	lineage5.1	T	West-Africa 1	AFRI_2;AFRI_3	RD711
Chromosome	465299	465300	lineage2.2	T	East-Asian (Beijing)	Beijing-RD207	RD105;RD207
Chromosome	465836	465837	lineage1.2.1.1	A	Indo-Oceanic	NA	RD239
Chromosome	465863	465864	lineage6.2	T	West-Africa 2	AFRI_1	RD702
Chromosome	471575	471576	La1.4	C	M.bovis	None	None
Chromosome	472123	472124	lineage1.2.1.1	T	Indo-Oceanic	NA	RD239
Chromosome	472897	472898	lineage5.1.1	A	West-Africa 1	AFRI_2;AFRI_3	RD711
Chromosome	479631	479632	lineage4.3.3	T	Euro-American (LAM)	LAM;T	RD115
Chromosome	481568	481569	lineage4.2.1.1	A	Euro-American (TUR)	H3;H4	None
Chromosome	483488	483489	lineage1.2.2	A	Indo-Oceanic	EAI1	RD239
Chromosome	485433	485434	lineage4.1.4	A	Euro-American	T;X;H	None
Chromosome	488795	488796	lineage4.6.1	A	Euro-American (Uganda)	T2	RD724
Chromosome	489023	489024	lineage5.1	T	West-Africa 1	AFRI_2;AFRI_3	RD711
Chromosome	489239	489240	lineage2.1	G	East-Asian (non-Beijing)	None	None
Chromosome	490375	490376	lineage6.3.2	T	West-Africa 2	AFRI_1	RD702
Chromosome	492768	492769	lineage5.1.5	T	West-Africa 1	AFRI_2;AFRI_3	RD711
Chromosome	495103	495104	lineage4.1.1.2	T	Euro-American (X-type)	X1	None
Chromosome	495691	495692	lineage6.2.3	A	West-Africa 2	AFRI_1	RD702
Chromosome	497490	497491	lineage2	A	East-Asian	Beijing	RD105
Chromosome	498009	498010	lineage1.1.2	C	Indo-Oceanic	EAI3;EAI5	RD239
Chromosome	498530	498531	lineage4	A	Euro-American	LAM;T;S;X;H	None
Chromosome	506385	506386	lineage4.4.1.1	C	Euro-American	S;Orphans	None
Chromosome	511349	511350	lineage5.3	A	West-Africa 1	AFRI_2;AFRI_3	RD711
Chromosome	514244	514245	lineage4.1.1	T	Euro-American (X-type)	X1;X2;X3	None
Chromosome	522052	522053	lineage2.1	A	East-Asian (non-Beijing)	None	None
Chromosome	526895	526896	M.canetti	C	M.canetti	None	None
Chromosome	528780	528781	lineage1.2.1.2	A	Indo-Oceanic	NA	RD239
Chromosome	529362	529363	lineage1.1.1	T	Indo-Oceanic	EAI4;EAI5	RD239
Chromosome	533327	533328	La2	A	M.caprae	None	None
Chromosome	533546	533547	lineage2.2.1	G	East-Asian (Beijing)	Beijing-RD181	RD105;RD207;RD181
Chromosome	534204	534205	lineage5.1	T	West-Africa 1	AFRI_2;AFRI_3	RD711
Chromosome	534690	534691	lineage4.3	T	Euro-American (LAM)	mainly-LAM	None
Chromosome	535694	535695	lineage4.3.3	T	Euro-American (LAM)	LAM;T	RD115
Chromosome	540939	540940	La1.7	C	M.bovis	None	None
Chromosome	541047	541048	lineage4.1.1.2	G	Euro-American (X-type)	X1	None
Chromosome	541200	541201	lineage4.9	A	Euro-American (H37Rv-like)	T1	None
Chromosome	541868	541869	lineage6.2.2	T	West-Africa 2	AFRI_1	RD702
Chromosome	545116	545117	lineage4.8.1	A	Euro-American (mainly T)	T1;T2;T3;T5	RD219
Chromosome	545402	545403	La1.8.X-unk6	T	M.bovis	None	None
Chromosome	546356	546357	lineage4	A	Euro-American	LAM;T;S;X;H	None
Chromosome	550572	550573	lineage4.3.4.2.1	C	Euro-American (LAM)	LAM11	RD174
Chromosome	550975	550976	lineage5.1.2	G	West-Africa 1	AFRI_2;AFRI_3	RD711
Chromosome	551418	551419	lineage4.1.4	G	Euro-American	T;X;H	None
Chromosome	552360	552361	lineage1.2.2	A	Indo-Oceanic	EAI1	RD239
Chromosome	554492	554493	lineage5.1	A	West-Africa 1	AFRI_2;AFRI_3	RD711
Chromosome	556960	556961	lineage4.9.1	T	Euro-American (H37Rv-like)	T1	None
Chromosome	559349	559350	lineage1.1.2	A	Indo-Oceanic	EAI3;EAI5	RD239
Chromosome	561020	561021	lineage4.6.2	A	Euro-American	T;LAM	RD726
Chromosome	567445	567446	lineage1.1.2	A	Indo-Oceanic	EAI3;EAI5	RD239
Chromosome	569044	569045	lineage1.1.2	T	Indo-Oceanic	EAI3;EAI5	RD239
Chromosome	571942	571943	lineage4.3.4	A	Euro-American (LAM)	LAM	RD174
Chromosome	576076	576077	lineage4.2.2	T	Euro-American (Ural)	T;LAM7-TUR	None
Chromosome	578031	578032	lineage4.6.1.2	T	Euro-American	T2	RD724
Chromosome	590249	590250	lineage4.1.4	T	Euro-American	T;X;H	None
Chromosome	590594	590595	lineage1.2.1.1	A	Indo-Oceanic	NA	RD239
Chromosome	594026	594027	lineage4.1.1.2	T	Euro-American (X-type)	X1	None
Chromosome	594056	594057	La1.5	A	M.bovis	None	None
Chromosome	596474	596475	lineage1.2.2.2	T	Indo-Oceanic	NA	RD239
Chromosome	599576	599577	lineage6.1.2	T	West-Africa 2	AFRI_1	RD702
Chromosome	599867	599868	lineage4	A	Euro-American	LAM;T;S;X;H	None
Chromosome	606375	606376	lineage4.6.3	A	Euro-American	T;LAM	None
Chromosome	608178	608179	lineage4.1.1.2	T	Euro-American (X-type)	X1	None
Chromosome	609253	609254	lineage4.2.1	T	Euro-American (TUR)	H3;H4	None
Chromosome	611462	611463	lineage4.2.2.2	A	Euro-American (Ural)	T;LAM7-TUR	None
Chromosome	615937	615938	lineage1	A	Indo-Oceanic	EAI	RD239
Chromosome	616407	616408	lineage4.8.3	G	Euro-American (mainly T)	T1;T2;T3;T5	RD219
Chromosome	617987	617988	lineage5.1.4	T	West-Africa 1	AFRI_2;AFRI_3	RD711
Chromosome	620028	620029	lineage4.5	T	Euro-American	H;T	RD122
Chromosome	622546	622547	lineage4.6.3	T	Euro-American	T;LAM	None
Chromosome	632329	632330	lineage4.3.4.2	T	Euro-American (LAM)	LAM1;LAM4;LAM11	RD174
Chromosome	633630	633631	lineage1.1.3.3	T	Indo-Oceanic	NA	RD239
Chromosome	636623	636624	La1.7.X-unk4	T	M.bovis	None	None
Chromosome	637729	637730	lineage4.1.2.1	T	Euro-American (Haarlem)	T1;H1	RD182
Chromosome	638211	638212	lineage4.2.1.1	T	Euro-American (TUR)	H3;H4	None
Chromosome	646242	646243	lineage4.3.2	C	Euro-American (LAM)	LAM3	None
Chromosome	646530	646531	lineage1	T	Indo-Oceanic	EAI	RD239
Chromosome	648464	648465	lineage2.1	G	East-Asian (non-Beijing)	None	None
Chromosome	651771	651772	lineage4.4.1	A	Euro-American (S-type)	S;T	None
Chromosome	652949	652950	lineage3	C	East-African-Indian	CAS	RD750
Chromosome	654995	654996	lineage1.2.1	T	Indo-Oceanic	EAI2	RD239
Chromosome	656297	656298	lineage6.2.3	G	West-Africa 2	AFRI_1	RD702
Chromosome	662910	662911	lineage4	T	Euro-American	LAM;T;S;X;H	None
Chromosome	663076	663077	lineage6.2.3	A	West-Africa 2	AFRI_1	RD702
Chromosome	665901	665902	lineage6.2	T	West-Africa 2	AFRI_1	RD702
Chromosome	666744	666745	lineage4.8.2	A	Euro-American (mainly T)	T1;T2;T3;T5	RD219
Chromosome	670803	670804	lineage6.3.2	A	West-Africa 2	AFRI_1	RD702
Chromosome	671384	671385	lineage2.2.1.1	G	East-Asian (Beijing)	Beijing-RD150	RD105;RD207;RD181;RD150
Chromosome	681312	681313	lineage4.8.2	T	Euro-American (mainly T)	T1;T2;T3;T5	RD219
Chromosome	685577	685578	lineage1.1.3.1	A	Indo-Oceanic	NA	RD239
Chromosome	685868	685869	lineage4.6.1	A	Euro-American (Uganda)	T2	RD724
Chromosome	687188	687189	lineage4.1.3	G	Euro-American	T;X;H	None
Chromosome	693520	693521	lineage9	T	Lineage 9	None	None
Chromosome	701866	701867	lineage1.1.1	T	Indo-Oceanic	EAI4;EAI5	RD239
Chromosome	703721	703722	lineage4.1.1.3.1	G	Euro-American (X-type)	X1;X3	RD193
Chromosome	705061	705062	lineage4.4.1.1	C	Euro-American	S;Orphans	None
Chromosome	705569	705570	lineage1.1	T	Indo-Oceanic	EAI3;EAI4;EAI5;EAI6	RD239
Chromosome	705594	705595	lineage4.3.2	T	Euro-American (LAM)	LAM3	None
Chromosome	707485	707486	M.canetti	C	M.canetti	None	None
Chromosome	709492	709493	lineage4.8.3	T	Euro-American (mainly T)	T1;T2;T3;T5	RD219
Chromosome	709656	709657	lineage5.1.4	C	West-Africa 1	AFRI_2;AFRI_3	RD711
Chromosome	711154	711155	lineage1.1.2	A	Indo-Oceanic	EAI3;EAI5	RD239
Chromosome	715516	715517	lineage5.1.1	T	West-Africa 1	AFRI_2;AFRI_3	RD711
Chromosome	716917	716918	lineage4.7	A	Euro-American (mainly T)	T1;T5	None
Chromosome	717878	717879	lineage1.2.2.1	A	Indo-Oceanic	NA	RD239
Chromosome	721580	721581	lineage5.1.2	G	West-Africa 1	AFRI_2;AFRI_3	RD711
Chromosome	723564	723565	lineage4.1.3	C	Euro-American	T;X;H	None
Chromosome	724338	724339	lineage4.1.3	T	Euro-American	T;X;H	None
Chromosome	729356	729357	lineage1.2.2.2	T	Indo-Oceanic	NA	RD239
Chromosome	731014	731015	lineage2.2.1.1	G	East-Asian (Beijing)	Beijing-RD150	RD105;RD207;RD181;RD150
Chromosome	732060	732061	lineage5.1.5	T	West-Africa 1	AFRI_2;AFRI_3	RD711
Chromosome	734561	734562	lineage4.6.3	A	Euro-American	T;LAM	None
Chromosome	738602	738603	lineage1.1.3.1	T	Indo-Oceanic	NA	RD239
Chromosome	738836	738837	lineage2.2.1.2	T	East-Asian (Beijing)	Beijing-RD142	RD105;RD207;RD181;RD142
Chromosome	740854	740855	lineage4.1.2.1.1	C	Euro-American (Haarlem)	T1;H1	RD182
Chromosome	742269	742270	lineage8	T	Lineage 8	None	None
Chromosome	745875	745876	lineage1.1	G	Indo-Oceanic	EAI3;EAI4;EAI5;EAI6	RD239
Chromosome	748922	748923	lineage4.8.3	T	Euro-American (mainly T)	T1;T2;T3;T5	RD219
Chromosome	753087	753088	lineage4.4	T	Euro-American	S;T	None
Chromosome	756567	756568	lineage6.2	A	West-Africa 2	AFRI_1	RD702
Chromosome	758121	758122	lineage4.6.3	T	Euro-American	T;LAM	None
Chromosome	764151	764152	M.canetti	T	M.canetti	None	None
Chromosome	771653	771654	lineage5.3	G	West-Africa 1	AFRI_2;AFRI_3	RD711
Chromosome	771722	771723	lineage6.3.2	A	West-Africa 2	AFRI_1	RD702
Chromosome	772739	772740	La1.7	T	M.bovis	None	None
Chromosome	772802	772803	lineage4.3.1.1	G	Euro-American (LAM)	LAM9	None
Chromosome	773808	773809	lineage4.3	A	Euro-American (LAM)	mainly-LAM	None
Chromosome	778297	778298	lineage4.6.2	T	Euro-American	T;LAM	RD726
Chromosome	783600	783601	lineage4.2.1	C	Euro-American (TUR)	H3;H4	None
Chromosome	784142	784143	lineage7	C	Lineage 7	None	None
Chromosome	784439	784440	lineage4.3.4.2	T	Euro-American (LAM)	LAM1;LAM4;LAM11	RD174
Chromosome	784580	784581	lineage4.3.2.1	C	Euro-American (LAM)	LAM3	RD761
Chromosome	791670	791671	lineage3.1.2.1	C	East-African-Indian	CAS2	RD750
Chromosome	794734	794735	lineage3.1.3	A	East-African-Indian	CAS	RD750
Chromosome	795562	795563	lineage4.1.4	T	Euro-American	T;X;H	None
Chromosome	796875	796876	lineage4.7	G	Euro-American (mainly T)	T1;T5	None
Chromosome	797735	797736	lineage2.2.1	T	East-Asian (Beijing)	Beijing-RD181	RD105;RD207;RD181
Chromosome	801958	801959	lineage5	T	West-Africa 1	AFRI_2;AFRI_3	RD711
Chromosome	806604	806605	lineage4.2.1.1	T	Euro-American (TUR)	H3;H4	None
Chromosome	809980	809981	lineage5.2	A	West-Africa 1	AFRI_2;AFRI_3	RD711
Chromosome	811491	811492	lineage1	G	Indo-Oceanic	EAI	RD239
Chromosome	811641	811642	lineage7	T	Lineage 7	None	None
Chromosome	811752	811753	lineage2	T	East-Asian	Beijing	RD105
Chromosome	812501	812502	lineage1	T	Indo-Oceanic	EAI	RD239
Chromosome	812807	812808	lineage4.3.3	A	Euro-American (LAM)	LAM;T	RD115
Chromosome	818797	818798	lineage4.6.1.2	T	Euro-American	T2	RD724
Chromosome	821101	821102	lineage4.4.1	T	Euro-American (S-type)	S;T	None
Chromosome	821436	821437	lineage5.1.1	A	West-Africa 1	AFRI_2;AFRI_3	RD711
Chromosome	825584	825585	lineage4.3.1	C	Euro-American (LAM)	LAM9	None
Chromosome	831205	831206	lineage4.3.4.1	T	Euro-American (LAM)	LAM1;LAM2	RD174
Chromosome	832071	832072	lineage1.1.3	C	Indo-Oceanic	EAI6	RD239
Chromosome	832707	832708	lineage4.1.2	C	Euro-American	T;H	None
Chromosome	851796	851797	lineage1.1.1.1	A	Indo-Oceanic	EAI4;ZERO	RD239
Chromosome	852640	852641	lineage1.1.3	T	Indo-Oceanic	EAI6	RD239
Chromosome	853468	853469	lineage4.3.2	A	Euro-American (LAM)	LAM3	None
Chromosome	860033	860034	lineage6.3.2	A	West-Africa 2	AFRI_1	RD702
Chromosome	863339	863340	lineage4.6.2	C	Euro-American	T;LAM	RD726
Chromosome	864165	864166	lineage1.2.1	T	Indo-Oceanic	EAI2	RD239
Chromosome	865760	865761	lineage1	T	Indo-Oceanic	EAI	RD239
Chromosome	868005	868006	lineage4.6.2	T	Euro-American	T;LAM	RD726
Chromosome	869439	869440	lineage4.1.1	T	Euro-American (X-type)	X1;X2;X3	None
Chromosome	870111	870112	lineage1.1.1	T	Indo-Oceanic	EAI4;EAI5	RD239
Chromosome	870186	870187	lineage4.2.1.1	T	Euro-American (TUR)	H3;H4	None
Chromosome	870309	870310	lineage6.1.3	G	West-Africa 2	AFRI_1	RD702
Chromosome	874118	874119	lineage6.1.3	A	West-Africa 2	AFRI_1	RD702
Chromosome	875033	875034	lineage3.1.2.2	A	East-African-Indian	CAS	RD750
Chromosome	876377	876378	lineage4.6.1.1	C	Euro-American	T2-Uganda	RD724
Chromosome	877054	877055	lineage1.1.3	C	Indo-Oceanic	EAI6	RD239
Chromosome	885633	885634	lineage6.2.3	A	West-Africa 2	AFRI_1	RD702
Chromosome	888213	888214	lineage4.9.1	A	Euro-American (H37Rv-like)	T1	None
Chromosome	891755	891756	lineage4.1.2	G	Euro-American	T;H	None
Chromosome	892415	892416	lineage2.2	T	East-Asian (Beijing)	Beijing-RD207	RD105;RD207
Chromosome	894078	894079	lineage4.1.1.1	T	Euro-American (X-type)	X2	RD183
Chromosome	895562	895563	lineage6.3.1	A	West-Africa 2	AFRI_1	RD702
Chromosome	896118	896119	lineage4.6.2.1	T	Euro-American	T3	RD726
Chromosome	896151	896152	lineage8	T	Lineage 8	None	None
Chromosome	896355	896356	lineage4.1.1.3	T	Euro-American (X-type)	X1;X3	RD193
Chromosome	896430	896431	lineage7	A	Lineage 7	None	None
Chromosome	898136	898137	lineage6.2.2	T	West-Africa 2	AFRI_1	RD702
Chromosome	899318	899319	lineage4.2.1.1	G	Euro-American (TUR)	H3;H4	None
Chromosome	902412	902413	lineage4.1	T	Euro-American	T;X;H	None
Chromosome	903225	903226	lineage6.2.3	T	West-Africa 2	AFRI_1	RD702
Chromosome	903261	903262	lineage8	A	Lineage 8	None	None
Chromosome	903912	903913	lineage4.9	T	Euro-American (H37Rv-like)	T1	None
Chromosome	912544	912545	lineage4.6.3	G	Euro-American	T;LAM	None
Chromosome	917595	917596	lineage2.2.2	A	East-Asian (Beijing)	Beijing-RD105/RD207	RD105;RD207
Chromosome	918645	918646	lineage6.2.1	A	West-Africa 2	AFRI_1	RD702
Chromosome	919392	919393	lineage4.3.3	C	Euro-American (LAM)	LAM;T	RD115
Chromosome	923064	923065	lineage4.1	A	Euro-American	T;X;H	None
Chromosome	931122	931123	lineage4	T	Euro-American	LAM;T;S;X;H	None
Chromosome	938152	938153	lineage3.1.3	G	East-African-Indian	CAS	RD750
Chromosome	951566	951567	lineage6.1.3	G	West-Africa 2	AFRI_1	RD702
Chromosome	953396	953397	lineage4.8.2	T	Euro-American (mainly T)	T1;T2;T3;T5	RD219
Chromosome	958361	958362	lineage3.1	G	East-African-Indian	Non-CAS1-Delhi	RD750
Chromosome	961597	961598	lineage3.1.2.1	G	East-African-Indian	CAS2	RD750
Chromosome	963021	963022	lineage5.2	C	West-Africa 1	AFRI_2;AFRI_3	RD711
Chromosome	964098	964099	lineage4.4.1.1	C	Euro-American	S;Orphans	None
Chromosome	973289	973290	lineage4.5	A	Euro-American	H;T	RD122
Chromosome	979313	979314	lineage4.6.1	T	Euro-American (Uganda)	T2	RD724
Chromosome	979858	979859	lineage4.1.1.3	C	Euro-American (X-type)	X1;X3	RD193
Chromosome	982362	982363	lineage6	T	West-Africa 2	AFRI_1	RD702
Chromosome	985286	985287	lineage4.4.2	A	Euro-American	T1;T2	None
Chromosome	990382	990383	lineage1.2.1	A	Indo-Oceanic	EAI2	RD239
Chromosome	990532	990533	lineage4.3.4.2	C	Euro-American (LAM)	LAM1;LAM4;LAM11	RD174
Chromosome	993015	993016	lineage3.1.2	A	East-African-Indian	CAS;CAS2	RD750
Chromosome	996870	996871	lineage4.6.1.1	A	Euro-American	T2-Uganda	RD724
Chromosome	1006079	1006080	lineage4.1.1.1	A	Euro-American (X-type)	X2	RD183
Chromosome	1010531	1010532	lineage4.6.2	A	Euro-American	T;LAM	RD726
Chromosome	1011205	1011206	lineage5.3	G	West-Africa 1	AFRI_2;AFRI_3	RD711
Chromosome	1014057	1014058	lineage5.1.2	A	West-Africa 1	AFRI_2;AFRI_3	RD711
Chromosome	1014721	1014722	lineage5.3	T	West-Africa 1	AFRI_2;AFRI_3	RD711
Chromosome	1017835	1017836	lineage4.2.1	C	Euro-American (TUR)	H3;H4	None
Chromosome	1018810	1018811	lineage1.2.2	A	Indo-Oceanic	EAI1	RD239
Chromosome	1020731	1020732	La1.7.X-unk5	C	M.bovis	None	None
Chromosome	1025613	1025614	lineage4.1.2.1.1	T	Euro-American (Haarlem)	T1;H1	RD182
Chromosome	1028943	1028944	lineage4.1.1.3	T	Euro-American (X-type)	X1;X3	RD193
Chromosome	1030367	1030368	lineage4.6.2.1	G	Euro-American	T3	RD726
Chromosome	1037354	1037355	lineage4.3.4	C	Euro-American (LAM)	LAM	RD174
Chromosome	1038107	1038108	lineage3.1.2.1	G	East-African-Indian	CAS2	RD750
Chromosome	1039980	1039981	lineage1.1.1	C	Indo-Oceanic	EAI4;EAI5	RD239
Chromosome	1049904	1049905	lineage5.3	T	West-Africa 1	AFRI_2;AFRI_3	RD711
Chromosome	1051948	1051949	lineage4.4.1	A	Euro-American (S-type)	S;T	None
Chromosome	1052898	1052899	lineage4.4	T	Euro-American	S;T	None
Chromosome	1053307	1053308	lineage4.2.2.1	T	Euro-American	LAM7-TUR	None
Chromosome	1055671	1055672	lineage4.3.2.1	A	Euro-American (LAM)	LAM3	RD761
Chromosome	1060877	1060878	lineage1.1.3.1	T	Indo-Oceanic	NA	RD239
Chromosome	1064933	1064934	lineage5.1.4	G	West-Africa 1	AFRI_2;AFRI_3	RD711
Chromosome	1065610	1065611	La1.4	A	M.bovis	None	None
Chromosome	1069145	1069146	lineage6	T	West-Africa 2	AFRI_1	RD702
Chromosome	1072627	1072628	lineage1.2.2	A	Indo-Oceanic	EAI1	RD239
Chromosome	1074928	1074929	lineage4.9.1	C	Euro-American (H37Rv-like)	T1	None
Chromosome	1082444	1082445	lineage4.8	A	Euro-American (mainly T)	T1;T2;T3;T5	RD219
Chromosome	1082982	1082983	lineage4.1.2.1.1	A	Euro-American (Haarlem)	T1;H1	RD182
Chromosome	1083081	1083082	lineage4.3.1.1	T	Euro-American (LAM)	LAM9	None
Chromosome	1098697	1098698	lineage4.6.1.2	G	Euro-American	T2	RD724
Chromosome	1099211	1099212	lineage1.2.1	T	Indo-Oceanic	EAI2	RD239
Chromosome	1102467	1102468	lineage2	A	East-Asian	Beijing	RD105
Chromosome	1106648	1106649	lineage4.3.4.1	C	Euro-American (LAM)	LAM1;LAM2	RD174
Chromosome	1107319	1107320	lineage5.3	A	West-Africa 1	AFRI_2;AFRI_3	RD711
Chromosome	1109534	1109535	lineage4.1.1.2	A	Euro-American (X-type)	X1	None
Chromosome	1111468	1111469	lineage1.1.1.1	T	Indo-Oceanic	EAI4;ZERO	RD239
Chromosome	1111924	1111925	lineage4.1.2	G	Euro-American	T;H	None
Chromosome	1115795	1115796	lineage4.2.1.1	A	Euro-American (TUR)	H3;H4	None
Chromosome	1120158	1120159	lineage6.2.2	A	West-Africa 2	AFRI_1	RD702
Chromosome	1125893	1125894	lineage7	C	Lineage 7	None	None
Chromosome	1126894	1126895	lineage4.4.1.1.1	A	Euro-American	S;Orphans	None
Chromosome	1129157	1129158	lineage4.8.3	G	Euro-American (mainly T)	T1;T2;T3;T5	RD219
Chromosome	1130525	1130526	lineage4.8	A	Euro-American (mainly T)	T1;T2;T3;T5	RD219
Chromosome	1132367	1132368	lineage4.3.4.2	T	Euro-American (LAM)	LAM1;LAM4;LAM11	RD174
Chromosome	1132436	1132437	lineage4.8.1	T	Euro-American (mainly T)	T1;T2;T3;T5	RD219
Chromosome	1134958	1134959	lineage6.1.3	C	West-Africa 2	AFRI_1	RD702
Chromosome	1135797	1135798	lineage2.1	T	East-Asian (non-Beijing)	None	None
Chromosome	1136016	1136017	lineage1.2.1	G	Indo-Oceanic	EAI2	RD239
Chromosome	1137517	1137518	lineage7	A	Lineage 7	None	None
Chromosome	1142265	1142266	lineage4.3	C	Euro-American (LAM)	mainly-LAM	None
Chromosome	1144220	1144221	lineage1.1.3	A	Indo-Oceanic	EAI6	RD239
Chromosome	1147707	1147708	lineage4.6.5	A	Euro-American	T;LAM	None
Chromosome	1153213	1153214	lineage5.3	A	West-Africa 1	AFRI_2;AFRI_3	RD711
Chromosome	1153675	1153676	lineage4.1.2	G	Euro-American	T;H	None
Chromosome	1154367	1154368	lineage4.8.3	C	Euro-American (mainly T)	T1;T2;T3;T5	RD219
Chromosome	1155867	1155868	lineage4.8.1	T	Euro-American (mainly T)	T1;T2;T3;T5	RD219
Chromosome	1158433	1158434	La1.7.X-unk4	A	M.bovis	None	None
Chromosome	1169027	1169028	lineage4.3.1	A	Euro-American (LAM)	LAM9	None
Chromosome	1172078	1172079	lineage4.3.1	G	Euro-American (LAM)	LAM9	None
Chromosome	1184797	1184798	lineage1.1.3	T	Indo-Oceanic	EAI6	RD239
Chromosome	1193667	1193668	lineage1.1.3.3	A	Indo-Oceanic	NA	RD239
Chromosome	1204545	1204546	lineage4.8.2	G	Euro-American (mainly T)	T1;T2;T3;T5	RD219
Chromosome	1208651	1208652	lineage4.4.1	A	Euro-American (S-type)	S;T	None
Chromosome	1221278	1221279	lineage6.3	T	West-Africa 2	AFRI_1	RD702
Chromosome	1221478	1221479	lineage4.4.1.1.1	T	Euro-American	S;Orphans	None
Chromosome	1227216	1227217	lineage4.8	T	Euro-American (mainly T)	T1;T2;T3;T5	RD219
Chromosome	1227517	1227518	lineage8	A	Lineage 8	None	None
Chromosome	1228066	1228067	lineage1.2.2.2	A	Indo-Oceanic	NA	RD239
Chromosome	1229122	1229123	lineage6.3.3	G	West-Africa 2	AFRI_1	RD702
Chromosome	1229179	1229180	lineage3.1.2.2	A	East-African-Indian	CAS	RD750
Chromosome	1232495	1232496	lineage4.3.2.1	C	Euro-American (LAM)	LAM3	RD761
Chromosome	1233284	1233285	lineage4.2.2.2	A	Euro-American (Ural)	T;LAM7-TUR	None
Chromosome	1233416	1233417	lineage4.1.1.3.1	G	Euro-American (X-type)	X1;X3	RD193
Chromosome	1234998	1234999	lineage4.4.1.1.1	A	Euro-American	S;Orphans	None
Chromosome	1237817	1237818	lineage3.1.2.1	G	East-African-Indian	CAS2	RD750
Chromosome	1239077	1239078	lineage4.3.4.2.1	A	Euro-American (LAM)	LAM11	RD174
Chromosome	1244258	1244259	lineage3.1.3	C	East-African-Indian	CAS	RD750
Chromosome	1245274	1245275	lineage1.2.2.1	T	Indo-Oceanic	NA	RD239
Chromosome	1249770	1249771	lineage1.1.3.1	A	Indo-Oceanic	NA	RD239
Chromosome	1250339	1250340	lineage4	A	Euro-American	LAM;T;S;X;H	None
Chromosome	1251954	1251955	lineage4.3.4.1	T	Euro-American (LAM)	LAM1;LAM2	RD174
Chromosome	1256805	1256806	lineage4.1.1	T	Euro-American (X-type)	X1;X2;X3	None
Chromosome	1261055	1261056	lineage1.1.1	T	Indo-Oceanic	EAI4;EAI5	RD239
Chromosome	1267405	1267406	lineage6.1.1	T	West-Africa 2	AFRI_1	RD702
Chromosome	1273070	1273071	lineage4.8	C	Euro-American (mainly T)	T1;T2;T3;T5	RD219
Chromosome	1274334	1274335	lineage4.3.4.1	A	Euro-American (LAM)	LAM1;LAM2	RD174
Chromosome	1286665	1286666	lineage4.1.1.2	A	Euro-American (X-type)	X1	None
Chromosome	1288125	1288126	La1.8.X-unk6	C	M.bovis	None	None
Chromosome	1288697	1288698	lineage2.2	A	East-Asian (Beijing)	Beijing-RD207	RD105;RD207
Chromosome	1289554	1289555	lineage4.6.2	G	Euro-American	T;LAM	RD726
Chromosome	1293120	1293121	lineage1.1.3	T	Indo-Oceanic	EAI6	RD239
Chromosome	1297083	1297084	lineage7	A	Lineage 7	None	None
Chromosome	1297326	1297327	lineage4.3.4	A	Euro-American (LAM)	LAM	RD174
Chromosome	1297980	1297981	lineage4.4.1.2	C	Euro-American	T1	None
Chromosome	1301570	1301571	lineage5.1.3	T	West-Africa 1	AFRI_2;AFRI_3	RD711
Chromosome	1311085	1311086	lineage4.3.1	G	Euro-American (LAM)	LAM9	None
Chromosome	1311442	1311443	lineage5.1.4	T	West-Africa 1	AFRI_2;AFRI_3	RD711
Chromosome	1315745	1315746	lineage1.2.1	A	Indo-Oceanic	EAI2	RD239
Chromosome	1317654	1317655	lineage2	T	East-Asian	Beijing	RD105
Chromosome	1317795	1317796	lineage5.1.2	T	West-Africa 1	AFRI_2;AFRI_3	RD711
Chromosome	1321209	1321210	lineage4.4.1.1	T	Euro-American	S;Orphans	None
Chromosome	1331186	1331187	lineage4.6.5	C	Euro-American	T;LAM	None
Chromosome	1334259	1334260	lineage4.3.2.1	A	Euro-American (LAM)	LAM3	RD761
Chromosome	1335912	1335913	lineage4.4.1.1.1	G	Euro-American	S;Orphans	None
Chromosome	1345103	1345104	lineage1.1.3.1	A	Indo-Oceanic	NA	RD239
Chromosome	1352349	1352350	lineage4.6.2.2	T	Euro-American (Cameroon)	LAM10-CAM	RD726
Chromosome	1353772	1353773	lineage1.1.3.1	G	Indo-Oceanic	NA	RD239
Chromosome	1358196	1358197	lineage4.6.5	T	Euro-American	T;LAM	None
Chromosome	1358421	1358422	La1.8.2	T	M.bovis	None	None
Chromosome	1361219	1361220	lineage3.1.3	T	East-African-Indian	CAS	RD750
Chromosome	1363193	1363194	lineage1.2.1	A	Indo-Oceanic	EAI2	RD239
Chromosome	1363985	1363986	lineage4.3.1.1	T	Euro-American (LAM)	LAM9	None
Chromosome	1364433	1364434	lineage4.3.4.1	T	Euro-American (LAM)	LAM1;LAM2	RD174
Chromosome	1365429	1365430	lineage1.2.2	C	Indo-Oceanic	EAI1	RD239
Chromosome	1365894	1365895	lineage7	A	Lineage 7	None	None
Chromosome	1369926	1369927	lineage1.1.1.1	T	Indo-Oceanic	EAI4;ZERO	RD239
Chromosome	1372001	1372002	lineage6	T	West-Africa 2	AFRI_1	RD702
Chromosome	1378724	1378725	lineage3.1.1	C	East-African-Indian	CAS1-Kili	RD750
Chromosome	1391867	1391868	lineage4.6.1.2	A	Euro-American	T2	RD724
Chromosome	1396921	1396922	lineage4.9	T	Euro-American (H37Rv-like)	T1	None
Chromosome	1401049	1401050	La1.7.X-unk4	T	M.bovis	None	None
Chromosome	1405847	1405848	lineage3.1.3	T	East-African-Indian	CAS	RD750
Chromosome	1406311	1406312	lineage1.2.1.2.1	G	Indo-Oceanic	NA	RD239
Chromosome	1421108	1421109	lineage4.3.1	G	Euro-American (LAM)	LAM9	None
Chromosome	1427066	1427067	La1.7.X-unk5	G	M.bovis	None	None
Chromosome	1434318	1434319	lineage5.1.3	T	West-Africa 1	AFRI_2;AFRI_3	RD711
Chromosome	1435762	1435763	lineage4.5	T	Euro-American	H;T	RD122
Chromosome	1436229	1436230	lineage6.1.3	G	West-Africa 2	AFRI_1	RD702
Chromosome	1436781	1436782	lineage3.1.3	A	East-African-Indian	CAS	RD750
Chromosome	1439331	1439332	lineage4.6.1.1	T	Euro-American	T2-Uganda	RD724
Chromosome	1442108	1442109	lineage4.6.4	T	Euro-American	T;LAM	None
Chromosome	1444654	1444655	lineage4.8.2	T	Euro-American (mainly T)	T1;T2;T3;T5	RD219
Chromosome	1449010	1449011	lineage6.2.2	A	West-Africa 2	AFRI_1	RD702
Chromosome	1450315	1450316	lineage3	T	East-African-Indian	CAS	RD750
Chromosome	1450462	1450463	lineage6.1.1	T	West-Africa 2	AFRI_1	RD702
Chromosome	1451541	1451542	lineage4.3.2.1	T	Euro-American (LAM)	LAM3	RD761
Chromosome	1452070	1452071	lineage4.3	A	Euro-American (LAM)	mainly-LAM	None
Chromosome	1454191	1454192	lineage6.2.1	G	West-Africa 2	AFRI_1	RD702
Chromosome	1455779	1455780	lineage4.2.2.1	C	Euro-American	LAM7-TUR	None
Chromosome	1459256	1459257	lineage6.2.2	T	West-Africa 2	AFRI_1	RD702
Chromosome	1463775	1463776	lineage7	T	Lineage 7	None	None
Chromosome	1466778	1466779	lineage4.2	T	Euro-American	H;T;LAM	None
Chromosome	1467752	1467753	lineage4.6.2	A	Euro-American	T;LAM	RD726
Chromosome	1478221	1478222	lineage1.2.1	G	Indo-Oceanic	EAI2	RD239
Chromosome	1487795	1487796	lineage4.2.2	A	Euro-American (Ural)	T;LAM7-TUR	None
Chromosome	1491274	1491275	lineage1.1.3	A	Indo-Oceanic	EAI6	RD239
Chromosome	1492048	1492049	lineage1.2.2.2	T	Indo-Oceanic	NA	RD239
Chromosome	1492960	1492961	lineage5.1.4	A	West-Africa 1	AFRI_2;AFRI_3	RD711
Chromosome	1494230	1494231	lineage4.4.1.2	A	Euro-American	T1	None
Chromosome	1498303	1498304	lineage4.6.5	C	Euro-American	T;LAM	None
Chromosome	1501714	1501715	lineage5.1	T	West-Africa 1	AFRI_2;AFRI_3	RD711
Chromosome	1501741	1501742	lineage5.1	A	West-Africa 1	AFRI_2;AFRI_3	RD711
Chromosome	1505805	1505806	lineage5	T	West-Africa 1	AFRI_2;AFRI_3	RD711
Chromosome	1511459	1511460	lineage2.2.2	T	East-Asian (Beijing)	Beijing-RD105/RD207	RD105;RD207
Chromosome	1523574	1523575	lineage3.1.1	G	East-African-Indian	CAS1-Kili	RD750
Chromosome	1526099	1526100	lineage1.1.1.1	G	Indo-Oceanic	EAI4;ZERO	RD239
Chromosome	1526838	1526839	lineage4.2.1.1	A	Euro-American (TUR)	H3;H4	None
Chromosome	1534537	1534538	lineage4.6.2	T	Euro-American	T;LAM	RD726
Chromosome	1534928	1534929	La1.8.1	T	M.bovis	None	None
Chromosome	1539298	1539299	lineage6.3.3	T	West-Africa 2	AFRI_1	RD702
Chromosome	1541213	1541214	lineage4.3.1	C	Euro-American (LAM)	LAM9	None
Chromosome	1543873	1543874	lineage5.1.2	T	West-Africa 1	AFRI_2;AFRI_3	RD711
Chromosome	1547497	1547498	lineage4.8.1	A	Euro-American (mainly T)	T1;T2;T3;T5	RD219
Chromosome	1551193	1551194	lineage6.2.3	A	West-Africa 2	AFRI_1	RD702
Chromosome	1552836	1552837	La1.5	T	M.bovis	None	None
Chromosome	1553854	1553855	lineage1.2.1	T	Indo-Oceanic	EAI2	RD239
Chromosome	1553875	1553876	lineage4.6.5	G	Euro-American	T;LAM	None
Chromosome	1555431	1555432	lineage5	T	West-Africa 1	AFRI_2;AFRI_3	RD711
Chromosome	1556017	1556018	lineage5.1.5	T	West-Africa 1	AFRI_2;AFRI_3	RD711
Chromosome	1556429	1556430	lineage3.1.1	G	East-African-Indian	CAS1-Kili	RD750
Chromosome	1560776	1560777	lineage5.1.3	A	West-Africa 1	AFRI_2;AFRI_3	RD711
Chromosome	1560911	1560912	lineage1	A	Indo-Oceanic	EAI	RD239
Chromosome	1561244	1561245	lineage7	T	Lineage 7	None	None
Chromosome	1564798	1564799	lineage4.1.3	T	Euro-American	T;X;H	None
Chromosome	1565424	1565425	M.canetti	A	M.canetti	None	None
Chromosome	1565565	1565566	lineage2.2.2	T	East-Asian (Beijing)	Beijing-RD105/RD207	RD105;RD207
Chromosome	1567984	1567985	lineage1.2.1.2	G	Indo-Oceanic	NA	RD239
Chromosome	1568017	1568018	lineage4.2	T	Euro-American	H;T;LAM	None
Chromosome	1577240	1577241	lineage2	A	East-Asian	Beijing	RD105
Chromosome	1577845	1577846	lineage6.2	A	West-Africa 2	AFRI_1	RD702
Chromosome	1578211	1578212	lineage5	C	West-Africa 1	AFRI_2;AFRI_3	RD711
Chromosome	1581703	1581704	lineage4.6.5	C	Euro-American	T;LAM	None
Chromosome	1588745	1588746	lineage6.3.2	T	West-Africa 2	AFRI_1	RD702
Chromosome	1588886	1588887	lineage4.6.2.1	C	Euro-American	T3	RD726
Chromosome	1590554	1590555	lineage1	T	Indo-Oceanic	EAI	RD239
Chromosome	1591544	1591545	lineage3.1.1	T	East-African-Indian	CAS1-Kili	RD750
Chromosome	1592014	1592015	lineage4.3.2.1	T	Euro-American (LAM)	LAM3	RD761
Chromosome	1594847	1594848	lineage4.8.1	A	Euro-American (mainly T)	T1;T2;T3;T5	RD219
Chromosome	1597404	1597405	lineage4.6.1	A	Euro-American (Uganda)	T2	RD724
Chromosome	1597695	1597696	lineage4.6.1.1	A	Euro-American	T2-Uganda	RD724
Chromosome	1599075	1599076	lineage5.1.2	T	West-Africa 1	AFRI_2;AFRI_3	RD711
Chromosome	1599995	1599996	lineage1.1.3.1	T	Indo-Oceanic	NA	RD239
Chromosome	1601415	1601416	lineage6.3.3	T	West-Africa 2	AFRI_1	RD702
Chromosome	1619840	1619841	lineage1.2.2.2	A	Indo-Oceanic	NA	RD239
Chromosome	1620581	1620582	lineage4.3.1.1	C	Euro-American (LAM)	LAM9	None
Chromosome	1623788	1623789	lineage1.2.1.2.1	T	Indo-Oceanic	NA	RD239
Chromosome	1625768	1625769	lineage4.6.2.1	A	Euro-American	T3	RD726
Chromosome	1626589	1626590	lineage6.2	A	West-Africa 2	AFRI_1	RD702
Chromosome	1639225	1639226	lineage3.1.1	T	East-African-Indian	CAS1-Kili	RD750
Chromosome	1645598	1645599	lineage4.5	T	Euro-American	H;T	RD122
Chromosome	1645619	1645620	lineage6.3.2	A	West-Africa 2	AFRI_1	RD702
Chromosome	1647806	1647807	lineage4.3.1.1	C	Euro-American (LAM)	LAM9	None
Chromosome	1649264	1649265	lineage5	A	West-Africa 1	AFRI_2;AFRI_3	RD711
Chromosome	1651062	1651063	lineage1.2.2.1	G	Indo-Oceanic	NA	RD239
Chromosome	1652215	1652216	lineage4.2.1.1	G	Euro-American (TUR)	H3;H4	None
Chromosome	1659665	1659666	lineage4.6.4	A	Euro-American	T;LAM	None
Chromosome	1660439	1660440	lineage4.2.1.1	A	Euro-American (TUR)	H3;H4	None
Chromosome	1667069	1667070	lineage6.3.3	A	West-Africa 2	AFRI_1	RD702
Chromosome	1670813	1670814	lineage4.2	T	Euro-American	H;T;LAM	None
Chromosome	1672807	1672808	lineage1.2.2.2	A	Indo-Oceanic	NA	RD239
Chromosome	1692068	1692069	lineage2.2.1.2	G	East-Asian (Beijing)	Beijing-RD142	RD105;RD207;RD181;RD142
Chromosome	1692639	1692640	lineage5.1.1	T	West-Africa 1	AFRI_2;AFRI_3	RD711
Chromosome	1695036	1695037	lineage2.2	A	East-Asian (Beijing)	Beijing-RD207	RD105;RD207
Chromosome	1695790	1695791	lineage5.1.1	T	West-Africa 1	AFRI_2;AFRI_3	RD711
Chromosome	1697459	1697460	lineage1.1.3	T	Indo-Oceanic	EAI6	RD239
Chromosome	1701476	1701477	lineage4.1.2.1.1	G	Euro-American (Haarlem)	T1;H1	RD182
Chromosome	1715827	1715828	lineage4.3.1	C	Euro-American (LAM)	LAM9	None
Chromosome	1724119	1724120	lineage4.3.4.2	A	Euro-American (LAM)	LAM1;LAM4;LAM11	RD174
Chromosome	1726540	1726541	lineage4.6.1.2	A	Euro-American	T2	RD724
Chromosome	1733617	1733618	lineage5.1	T	West-Africa 1	AFRI_2;AFRI_3	RD711
Chromosome	1740534	1740535	lineage4.3.4.2.1	A	Euro-American (LAM)	LAM11	RD174
Chromosome	1741099	1741100	lineage5.1.3	A	West-Africa 1	AFRI_2;AFRI_3	RD711
Chromosome	1750464	1750465	lineage1.1.1.1	C	Indo-Oceanic	EAI4;ZERO	RD239
Chromosome	1759251	1759252	lineage4.9	G	Euro-American (H37Rv-like)	T1	None
Chromosome	1764224	1764225	lineage3	T	East-African-Indian	CAS	RD750
Chromosome	1764807	1764808	lineage4.8.2	T	Euro-American (mainly T)	T1;T2;T3;T5	RD219
Chromosome	1765766	1765767	La1.7.X-unk4	C	M.bovis	None	None
Chromosome	1771319	1771320	lineage4.3.4.2	A	Euro-American (LAM)	LAM1;LAM4;LAM11	RD174
Chromosome	1775673	1775674	lineage6.2	T	West-Africa 2	AFRI_1	RD702
Chromosome	1778556	1778557	lineage4.3.2	T	Euro-American (LAM)	LAM3	None
Chromosome	1798560	1798561	lineage4.6.4	T	Euro-American	T;LAM	None
Chromosome	1799177	1799178	lineage1.1.3.3	A	Indo-Oceanic	NA	RD239
Chromosome	1799920	1799921	lineage5	A	West-Africa 1	AFRI_2;AFRI_3	RD711
Chromosome	1803958	1803959	lineage4.4.1.2	T	Euro-American	T1	None
Chromosome	1808123	1808124	lineage4.4.1.2	C	Euro-American	T1	None
Chromosome	1811963	1811964	lineage6	A	West-Africa 2	AFRI_1	RD702
Chromosome	1819030	1819031	lineage5.1.4	C	West-Africa 1	AFRI_2;AFRI_3	RD711
Chromosome	1821773	1821774	lineage1.2.2.1	T	Indo-Oceanic	NA	RD239
Chromosome	1841960	1841961	lineage6.3.2	A	West-Africa 2	AFRI_1	RD702
Chromosome	1842236	1842237	lineage6.3.2	G	West-Africa 2	AFRI_1	RD702
Chromosome	1846091	1846092	lineage5.1	T	West-Africa 1	AFRI_2;AFRI_3	RD711
Chromosome	1847810	1847811	lineage4.3.4	C	Euro-American (LAM)	LAM	RD174
Chromosome	1849050	1849051	lineage2.2	T	East-Asian (Beijing)	Beijing-RD207	RD105;RD207
Chromosome	1850118	1850119	lineage4.1.1.1	T	Euro-American (X-type)	X2	RD183
Chromosome	1853673	1853674	lineage4.4.1.1.1	A	Euro-American	S;Orphans	None
Chromosome	1862120	1862121	lineage3.1.2.2	T	East-African-Indian	CAS	RD750
Chromosome	1867706	1867707	lineage6	T	West-Africa 2	AFRI_1	RD702
Chromosome	1870172	1870173	lineage6.3	A	West-Africa 2	AFRI_1	RD702
Chromosome	1872210	1872211	lineage4.2	A	Euro-American	H;T;LAM	None
Chromosome	1875206	1875207	lineage4.1	T	Euro-American	T;X;H	None
Chromosome	1877861	1877862	lineage4.1.2.1.1	T	Euro-American (Haarlem)	T1;H1	RD182
Chromosome	1879700	1879701	lineage5.1.2	C	West-Africa 1	AFRI_2;AFRI_3	RD711
Chromosome	1880849	1880850	lineage4.2.2.2	A	Euro-American (Ural)	T;LAM7-TUR	None
Chromosome	1882572	1882573	lineage4.9.1	G	Euro-American (H37Rv-like)	T1	None
Chromosome	1882816	1882817	lineage6.1	A	West-Africa 2	AFRI_1	RD702
Chromosome	1885494	1885495	lineage1.2.2.1	A	Indo-Oceanic	NA	RD239
Chromosome	1891255	1891256	lineage5.1.1	G	West-Africa 1	AFRI_2;AFRI_3	RD711
Chromosome	1891387	1891388	lineage2.2.1.1	G	East-Asian (Beijing)	Beijing-RD150	RD105;RD207;RD181;RD150
Chromosome	1897937	1897938	lineage1.2.1.2.1	A	Indo-Oceanic	NA	RD239
Chromosome	1901923	1901924	lineage4.5	C	Euro-American	H;T	RD122
Chromosome	1903049	1903050	lineage1.2.1.2.1	T	Indo-Oceanic	NA	RD239
Chromosome	1903546	1903547	lineage5.1.3	T	West-Africa 1	AFRI_2;AFRI_3	RD711
Chromosome	1906077	1906078	lineage2.2.1	G	East-Asian (Beijing)	Beijing-RD181	RD105;RD207;RD181
Chromosome	1907295	1907296	lineage4.9	G	Euro-American (H37Rv-like)	T1	None
Chromosome	1908786	1908787	lineage6.2.3	A	West-Africa 2	AFRI_1	RD702
Chromosome	1912267	1912268	lineage5.1.1	C	West-Africa 1	AFRI_2;AFRI_3	RD711
Chromosome	1914216	1914217	lineage3.1.2	A	East-African-Indian	CAS;CAS2	RD750
Chromosome	1919626	1919627	lineage3.1.3	A	East-African-Indian	CAS	RD750
Chromosome	1919735	1919736	lineage4.2.2.1	G	Euro-American	LAM7-TUR	None
Chromosome	1924764	1924765	lineage1.1.1	C	Indo-Oceanic	EAI4;EAI5	RD239
Chromosome	1925135	1925136	lineage3	A	East-African-Indian	CAS	RD750
Chromosome	1931218	1931219	lineage4.1.2.1	A	Euro-American (Haarlem)	T1;H1	RD182
Chromosome	1940610	1940611	lineage4.9.1	C	Euro-American (H37Rv-like)	T1	None
Chromosome	1947281	1947282	lineage2.2.1.1	G	East-Asian (Beijing)	Beijing-RD150	RD105;RD207;RD181;RD150
Chromosome	1952600	1952601	lineage4.1.1	T	Euro-American (X-type)	X1;X2;X3	None
Chromosome	1965132	1965133	lineage4.4.2	T	Euro-American	T1;T2	None
Chromosome	1976013	1976014	lineage1.1.3.3	T	Indo-Oceanic	NA	RD239
Chromosome	1978430	1978431	La1.7.X-unk5	T	M.bovis	None	None
Chromosome	1980651	1980652	lineage2	T	East-Asian	Beijing	RD105
Chromosome	1980870	1980871	lineage4.5	C	Euro-American	H;T	RD122
Chromosome	1985033	1985034	La1.2	C	M.bovis	None	None
Chromosome	1985572	1985573	lineage4.2.2.1	A	Euro-American	LAM7-TUR	None
Chromosome	2016285	2016286	lineage1.1.3.3	A	Indo-Oceanic	NA	RD239
Chromosome	2020119	2020120	lineage3.1.2.1	T	East-African-Indian	CAS2	RD750
Chromosome	2020143	2020144	lineage4.1	A	Euro-American	T;X;H	None
Chromosome	2022125	2022126	lineage4.4.1.1	C	Euro-American	S;Orphans	None
Chromosome	2022867	2022868	lineage4.9	T	Euro-American (H37Rv-like)	T1	None
Chromosome	2024412	2024413	lineage6.3.1	T	West-Africa 2	AFRI_1	RD702
Chromosome	2027616	2027617	La1.2.BCG	A	M.bovis	BCG	None
Chromosome	2033747	2033748	lineage4.6.1	C	Euro-American (Uganda)	T2	RD724
Chromosome	2033889	2033890	lineage4.4.1	T	Euro-American (S-type)	S;T	None
Chromosome	2043079	2043080	M.canetti	G	M.canetti	None	None
Chromosome	2053681	2053682	lineage4.3	T	Euro-American (LAM)	mainly-LAM	None
Chromosome	2054804	2054805	lineage4.1.1.3	A	Euro-American (X-type)	X1;X3	RD193
Chromosome	2058446	2058447	lineage4.6.1.2	A	Euro-American	T2	RD724
Chromosome	2063105	2063106	lineage1.1.1	T	Indo-Oceanic	EAI4;EAI5	RD239
Chromosome	2066473	2066474	lineage1.1.3.3	C	Indo-Oceanic	NA	RD239
Chromosome	2066632	2066633	lineage4.1.2	G	Euro-American	T;H	None
Chromosome	2073604	2073605	lineage4.8.2	C	Euro-American (mainly T)	T1;T2;T3;T5	RD219
Chromosome	2077252	2077253	lineage4.3.3	A	Euro-American (LAM)	LAM;T	RD115
Chromosome	2078023	2078024	lineage1.1.1	A	Indo-Oceanic	EAI4;EAI5	RD239
Chromosome	2078245	2078246	lineage2.2.1	G	East-Asian (Beijing)	Beijing-RD181	RD105;RD207;RD181
Chromosome	2080940	2080941	lineage4.1.1.1	A	Euro-American (X-type)	X2	RD183
Chromosome	2083682	2083683	lineage5.2	T	West-Africa 1	AFRI_2;AFRI_3	RD711
Chromosome	2091596	2091597	lineage5.2	T	West-Africa 1	AFRI_2;AFRI_3	RD711
Chromosome	2093997	2093998	lineage4.5	T	Euro-American	H;T	RD122
Chromosome	2105064	2105065	lineage4.6.2.1	T	Euro-American	T3	RD726
Chromosome	2108385	2108386	lineage5.2	T	West-Africa 1	AFRI_2;AFRI_3	RD711
Chromosome	2112831	2112832	lineage2.2	C	East-Asian (Beijing)	Beijing-RD207	RD105;RD207
Chromosome	2116662	2116663	lineage4.3.1.1	T	Euro-American (LAM)	LAM9	None
Chromosome	2153245	2153246	lineage4.2.2.2	G	Euro-American (Ural)	T;LAM7-TUR	None
Chromosome	2156846	2156847	lineage4.2.2.2	A	Euro-American (Ural)	T;LAM7-TUR	None
Chromosome	2158581	2158582	lineage4.1.1	A	Euro-American (X-type)	X1;X2;X3	None
Chromosome	2173057	2173058	lineage5.1.5	A	West-Africa 1	AFRI_2;AFRI_3	RD711
Chromosome	2183680	2183681	La1.4	A	M.bovis	None	None
Chromosome	2184780	2184781	lineage4.6.1	T	Euro-American (Uganda)	T2	RD724
Chromosome	2185537	2185538	lineage3.1.2.1	A	East-African-Indian	CAS2	RD750
Chromosome	2191656	2191657	lineage4.4.2	T	Euro-American	T1;T2	None
Chromosome	2194203	2194204	La2	G	M.caprae	None	None
Chromosome	2198181	2198182	lineage6.3.1	T	West-Africa 2	AFRI_1	RD702
Chromosome	2199683	2199684	lineage4.3.4.1	A	Euro-American (LAM)	LAM1;LAM2	RD174
Chromosome	2202499	2202500	lineage2.2	T	East-Asian (Beijing)	Beijing-RD207	RD105;RD207
Chromosome	2208142	2208143	lineage4.1.1.3.1	C	Euro-American (X-type)	X1;X3	RD193
Chromosome	2212761	2212762	lineage4.8	T	Euro-American (mainly T)	T1;T2;T3;T5	RD219
Chromosome	2215711	2215712	lineage1.2.1.2.1	A	Indo-Oceanic	NA	RD239
Chromosome	2225514	2225515	lineage4.6.2.1	A	Euro-American	T3	RD726
Chromosome	2239383	2239384	lineage6.3.3	A	West-Africa 2	AFRI_1	RD702
Chromosome	2240715	2240716	lineage5.2	A	West-Africa 1	AFRI_2;AFRI_3	RD711
Chromosome	2243434	2243435	La1.8.X-unk6	A	M.bovis	None	None
Chromosome	2244769	2244770	lineage4.1.2.1	A	Euro-American (Haarlem)	T1;H1	RD182
Chromosome	2245074	2245075	lineage4.4.2	T	Euro-American	T1;T2	None
Chromosome	2245498	2245499	lineage3.1.2.1	T	East-African-Indian	CAS2	RD750
Chromosome	2248162	2248163	lineage6.3.3	C	West-Africa 2	AFRI_1	RD702
Chromosome	2249402	2249403	lineage4.3.2	T	Euro-American (LAM)	LAM3	None
Chromosome	2253452	2253453	lineage4.1	C	Euro-American	T;X;H	None
Chromosome	2259578	2259579	lineage2.2.1.2	G	East-Asian (Beijing)	Beijing-RD142	RD105;RD207;RD181;RD142
Chromosome	2271142	2271143	lineage3.1.2.1	A	East-African-Indian	CAS2	RD750
Chromosome	2271442	2271443	lineage5.1.2	G	West-Africa 1	AFRI_2;AFRI_3	RD711
Chromosome	2271554	2271555	La1.1	A	M.bovis	None	None
Chromosome	2273626	2273627	lineage4.6.1	T	Euro-American (Uganda)	T2	RD724
Chromosome	2291556	2291557	La1.7.X-unk5	G	M.bovis	None	None
Chromosome	2311356	2311357	lineage1.1.1.1	A	Indo-Oceanic	EAI4;ZERO	RD239
Chromosome	2315589	2315590	lineage5.1.2	T	West-Africa 1	AFRI_2;AFRI_3	RD711
Chromosome	2326191	2326192	lineage1.1.1.1	T	Indo-Oceanic	EAI4;ZERO	RD239
Chromosome	2331060	2331061	lineage4.6.1.1	T	Euro-American	T2-Uganda	RD724
Chromosome	2356011	2356012	lineage4.4	A	Euro-American	S;T	None
Chromosome	2358915	2358916	lineage4.4	T	Euro-American	S;T	None
Chromosome	2369117	2369118	lineage4.6.2.2	A	Euro-American (Cameroon)	LAM10-CAM	RD726
Chromosome	2369186	2369187	lineage1.1.3.2	T	Indo-Oceanic	NA	RD239
Chromosome	2369459	2369460	lineage1.1.3.2	A	Indo-Oceanic	NA	RD239
Chromosome	2369970	2369971	lineage4.6	G	Euro-American	T;LAM	None
Chromosome	2377784	2377785	lineage4.6.1.1	T	Euro-American	T2-Uganda	RD724
Chromosome	2378812	2378813	lineage4.7	G	Euro-American (mainly T)	T1;T5	None
Chromosome	2382644	2382645	lineage5.1	A	West-Africa 1	AFRI_2;AFRI_3	RD711
Chromosome	2382829	2382830	La2	A	M.caprae	None	None
Chromosome	2408441	2408442	lineage6.1.2	A	West-Africa 2	AFRI_1	RD702
Chromosome	2410937	2410938	lineage4.4.1.2	T	Euro-American	T1	None
Chromosome	2412583	2412584	lineage1.1.1.1	A	Indo-Oceanic	EAI4;ZERO	RD239
Chromosome	2415041	2415042	lineage3.1.2.2	T	East-African-Indian	CAS	RD750
Chromosome	2416148	2416149	lineage5.2	G	West-Africa 1	AFRI_2;AFRI_3	RD711
Chromosome	2417280	2417281	lineage4.8.2	A	Euro-American (mainly T)	T1;T2;T3;T5	RD219
Chromosome	2418553	2418554	lineage1.1.3.2	A	Indo-Oceanic	NA	RD239
Chromosome	2420502	2420503	lineage4.2.2	G	Euro-American (Ural)	T;LAM7-TUR	None
Chromosome	2428077	2428078	La1.4	G	M.bovis	None	None
Chromosome	2428822	2428823	lineage5.1.5	T	West-Africa 1	AFRI_2;AFRI_3	RD711
Chromosome	2440952	2440953	lineage4.6.1	T	Euro-American (Uganda)	T2	RD724
Chromosome	2443187	2443188	lineage4.3.4.2	A	Euro-American (LAM)	LAM1;LAM4;LAM11	RD174
Chromosome	2450244	2450245	lineage4.1.3	A	Euro-American	T;X;H	None
Chromosome	2454855	2454856	lineage4.1.1.3	T	Euro-American (X-type)	X1;X3	RD193
Chromosome	2467097	2467098	lineage3.1.1	C	East-African-Indian	CAS1-Kili	RD750
Chromosome	2470626	2470627	lineage4.3.2.1	A	Euro-American (LAM)	LAM3	RD761
Chromosome	2470933	2470934	lineage1.1.1.1	A	Indo-Oceanic	EAI4;ZERO	RD239
Chromosome	2473698	2473699	lineage4.1.2.1	T	Euro-American (Haarlem)	T1;H1	RD182
Chromosome	2475887	2475888	La1	G	M.bovis	None	None
Chromosome	2478057	2478058	lineage5.1.3	T	West-Africa 1	AFRI_2;AFRI_3	RD711
Chromosome	2482887	2482888	lineage4.2.2	A	Euro-American (Ural)	T;LAM7-TUR	None
Chromosome	2485233	2485234	lineage6.1.3	T	West-Africa 2	AFRI_1	RD702
Chromosome	2485955	2485956	lineage5	A	West-Africa 1	AFRI_2;AFRI_3	RD711
Chromosome	2486341	2486342	lineage1.2.1.2.1	T	Indo-Oceanic	NA	RD239
Chromosome	2488723	2488724	lineage4.1.2.1.1	G	Euro-American (Haarlem)	T1;H1	RD182
Chromosome	2494262	2494263	lineage4.6.1.2	A	Euro-American	T2	RD724
Chromosome	2503624	2503625	lineage4.3	T	Euro-American (LAM)	mainly-LAM	None
Chromosome	2505084	2505085	lineage2.2	A	East-Asian (Beijing)	Beijing-RD207	RD105;RD207
Chromosome	2516157	2516158	lineage4.6.3	G	Euro-American	T;LAM	None
Chromosome	2516364	2516365	lineage4.6.3	C	Euro-American	T;LAM	None
Chromosome	2527675	2527676	lineage4.3.4	A	Euro-American (LAM)	LAM	RD174
Chromosome	2546349	2546350	lineage6.3.3	T	West-Africa 2	AFRI_1	RD702
Chromosome	2553394	2553395	La1.7.1	A	M.bovis	None	None
Chromosome	2563400	2563401	lineage6.1.1	G	West-Africa 2	AFRI_1	RD702
Chromosome	2565445	2565446	lineage5.1.4	A	West-Africa 1	AFRI_2;AFRI_3	RD711
Chromosome	2574021	2574022	lineage4.1	T	Euro-American	T;X;H	None
Chromosome	2585857	2585858	lineage4.1.1.1	A	Euro-American (X-type)	X2	RD183
Chromosome	2594631	2594632	La1.8.2	A	M.bovis	None	None
Chromosome	2597695	2597696	lineage4.5	T	Euro-American	H;T	RD122
Chromosome	2599820	2599821	lineage4.3.4	A	Euro-American (LAM)	LAM	RD174
Chromosome	2602159	2602160	lineage6.3.1	A	West-Africa 2	AFRI_1	RD702
Chromosome	2603796	2603797	lineage4.1.1	A	Euro-American (X-type)	X1;X2;X3	None
Chromosome	2612299	2612300	La1	T	M.bovis	None	None
Chromosome	2614030	2614031	lineage4.3.1.1	G	Euro-American (LAM)	LAM9	None
Chromosome	2622401	2622402	lineage1.1.2	A	Indo-Oceanic	EAI3;EAI5	RD239
Chromosome	2639867	2639868	lineage1.2.1.2	G	Indo-Oceanic	NA	RD239
Chromosome	2640368	2640369	lineage4.1.2.1.1	A	Euro-American (Haarlem)	T1;H1	RD182
Chromosome	2640806	2640807	lineage2.2.2	A	East-Asian (Beijing)	Beijing-RD105/RD207	RD105;RD207
Chromosome	2640959	2640960	lineage1.2.1.1	T	Indo-Oceanic	NA	RD239
Chromosome	2641657	2641658	lineage6.3.1	C	West-Africa 2	AFRI_1	RD702
Chromosome	2649854	2649855	lineage4.3.2	A	Euro-American (LAM)	LAM3	None
Chromosome	2655823	2655824	La1.6	C	M.bovis	None	None
Chromosome	2669114	2669115	La1.5	A	M.bovis	None	None
Chromosome	2671060	2671061	lineage4.1	A	Euro-American	T;X;H	None
Chromosome	2671676	2671677	lineage6.3.1	T	West-Africa 2	AFRI_1	RD702
Chromosome	2701537	2701538	La2	A	M.caprae	None	None
Chromosome	2702177	2702178	La1.7.1	A	M.bovis	None	None
Chromosome	2715124	2715125	La1.8	C	M.bovis	None	None
Chromosome	2724781	2724782	lineage4.1.2.1	T	Euro-American (Haarlem)	T1;H1	RD182
Chromosome	2729452	2729453	lineage4.3.4.2.1	A	Euro-American (LAM)	LAM11	RD174
Chromosome	2729453	2729454	lineage3.1.2	T	East-African-Indian	CAS;CAS2	RD750
Chromosome	2731554	2731555	La2	C	M.caprae	None	None
Chromosome	2737200	2737201	lineage1.2.1.2.1	C	Indo-Oceanic	NA	RD239
Chromosome	2737452	2737453	lineage2.1	C	East-Asian (non-Beijing)	None	None
Chromosome	2738220	2738221	lineage3	A	East-African-Indian	CAS	RD750
Chromosome	2738351	2738352	lineage1.1.3.3	T	Indo-Oceanic	NA	RD239
Chromosome	2739086	2739087	lineage4.1.1.3.1	T	Euro-American (X-type)	X1;X3	RD193
Chromosome	2744387	2744388	lineage3.1.1	A	East-African-Indian	CAS1-Kili	RD750
Chromosome	2748086	2748087	lineage4.2	A	Euro-American	H;T;LAM	None
Chromosome	2749451	2749452	lineage6.2	A	West-Africa 2	AFRI_1	RD702
Chromosome	2750051	2750052	lineage9	A	Lineage 9	None	None
Chromosome	2752853	2752854	lineage4.1.1	A	Euro-American (X-type)	X1;X2;X3	None
Chromosome	2755468	2755469	lineage4.6.4	A	Euro-American	T;LAM	None
Chromosome	2758267	2758268	lineage6.3	T	West-Africa 2	AFRI_1	RD702
Chromosome	2763623	2763624	lineage1.2.2	A	Indo-Oceanic	EAI1	RD239
Chromosome	2781383	2781384	lineage4.6.2.1	G	Euro-American	T3	RD726
Chromosome	2782139	2782140	lineage4.8.3	A	Euro-American (mainly T)	T1;T2;T3;T5	RD219
Chromosome	2782497	2782498	lineage3	A	East-African-Indian	CAS	RD750
Chromosome	2807763	2807764	La1.7.X-unk4	A	M.bovis	None	None
Chromosome	2809249	2809250	lineage4.8	T	Euro-American (mainly T)	T1;T2;T3;T5	RD219
Chromosome	2814960	2814961	lineage4.3.3	A	Euro-American (LAM)	LAM;T	RD115
Chromosome	2824838	2824839	lineage4.1.1.1	T	Euro-American (X-type)	X2	RD183
Chromosome	2825465	2825466	lineage4	G	Euro-American	LAM;T;S;X;H	None
Chromosome	2825580	2825581	lineage2.2.1	G	East-Asian (Beijing)	Beijing-RD181	RD105;RD207;RD181
Chromosome	2826038	2826039	lineage2.2.1.2	C	East-Asian (Beijing)	Beijing-RD142	RD105;RD207;RD181;RD142
Chromosome	2834423	2834424	La1.2.BCG	A	M.bovis	BCG	None
Chromosome	2840848	2840849	lineage1.2.1.2	C	Indo-Oceanic	NA	RD239
Chromosome	2844013	2844014	lineage4.1.4	A	Euro-American	T;X;H	None
Chromosome	2844688	2844689	lineage4.3.2.1	C	Euro-American (LAM)	LAM3	RD761
Chromosome	2847190	2847191	lineage1.2.1.1	A	Indo-Oceanic	NA	RD239
Chromosome	2847736	2847737	lineage6	A	West-Africa 2	AFRI_1	RD702
Chromosome	2848134	2848135	La1.6	A	M.bovis	None	None
Chromosome	2853154	2853155	La1.8	A	M.bovis	None	None
Chromosome	2859146	2859147	lineage5	T	West-Africa 1	AFRI_2;AFRI_3	RD711
Chromosome	2868924	2868925	lineage4.4	A	Euro-American	S;T	None
Chromosome	2871250	2871251	lineage4.1.2.1	A	Euro-American (Haarlem)	T1;H1	RD182
Chromosome	2873373	2873374	lineage4.3.4.2.1	A	Euro-American (LAM)	LAM11	RD174
Chromosome	2874343	2874344	lineage3.1.2.2	A	East-African-Indian	CAS	RD750
Chromosome	2875882	2875883	lineage4.6.2.2	T	Euro-American (Cameroon)	LAM10-CAM	RD726
Chromosome	2877697	2877698	lineage6.3.1	T	West-Africa 2	AFRI_1	RD702
Chromosome	2882342	2882343	lineage4.2.1	A	Euro-American (TUR)	H3;H4	None
Chromosome	2890667	2890668	La1.8.1	T	M.bovis	None	None
Chromosome	2891378	2891379	lineage2.2.1.1	C	East-Asian (Beijing)	Beijing-RD150	RD105;RD207;RD181;RD150
Chromosome	2892167	2892168	lineage4.7	A	Euro-American (mainly T)	T1;T5	None
Chromosome	2893700	2893701	lineage4.6.4	A	Euro-American	T;LAM	None
Chromosome	2897527	2897528	lineage1	A	Indo-Oceanic	EAI	RD239
Chromosome	2897683	2897684	lineage4.6.2.1	G	Euro-American	T3	RD726
Chromosome	2905504	2905505	lineage4.4.1	A	Euro-American (S-type)	S;T	None
Chromosome	2906977	2906978	lineage4.1	T	Euro-American	T;X;H	None
Chromosome	2907628	2907629	lineage4.3.2	A	Euro-American (LAM)	LAM3	None
Chromosome	2912515	2912516	La1	A	M.bovis	None	None
Chromosome	2912745	2912746	lineage4.8.2	T	Euro-American (mainly T)	T1;T2;T3;T5	RD219
Chromosome	2913090	2913091	lineage4.4.2	T	Euro-American	T1;T2	None
Chromosome	2914905	2914906	lineage4.8.1	C	Euro-American (mainly T)	T1;T2;T3;T5	RD219
Chromosome	2919531	2919532	lineage4.6.4	G	Euro-American	T;LAM	None
Chromosome	2923263	2923264	lineage4.2.2.2	A	Euro-American (Ural)	T;LAM7-TUR	None
Chromosome	2940051	2940052	lineage5.3	A	West-Africa 1	AFRI_2;AFRI_3	RD711
Chromosome	2948296	2948297	La1.7.X-unk5	C	M.bovis	None	None
Chromosome	2958569	2958570	lineage1.2.1.2.1	A	Indo-Oceanic	NA	RD239
Chromosome	2963596	2963597	La1.7	A	M.bovis	None	None
Chromosome	2980974	2980975	lineage4.1.1.3.1	A	Euro-American (X-type)	X1;X3	RD193
Chromosome	2989190	2989191	La1.8.2	C	M.bovis	None	None
Chromosome	2989682	2989683	lineage1.1	T	Indo-Oceanic	EAI3;EAI4;EAI5;EAI6	RD239
Chromosome	2994186	2994187	lineage4	T	Euro-American	LAM;T;S;X;H	None
Chromosome	2994963	2994964	lineage1.1.1.1	T	Indo-Oceanic	EAI4;ZERO	RD239
Chromosome	3007523	3007524	lineage4.2.2.1	A	Euro-American	LAM7-TUR	None
Chromosome	3015965	3015966	lineage4.6	A	Euro-American	T;LAM	None
Chromosome	3023683	3023684	lineage3.1.1	A	East-African-Indian	CAS1-Kili	RD750
Chromosome	3028657	3028658	lineage4.6.1.1	A	Euro-American	T2-Uganda	RD724
Chromosome	3033643	3033644	La1.2	C	M.bovis	None	None
Chromosome	3037135	3037136	lineage4.3.1	A	Euro-American (LAM)	LAM9	None
Chromosome	3038565	3038566	La1.5	A	M.bovis	None	None
Chromosome	3048840	3048841	lineage4.6.4	A	Euro-American	T;LAM	None
Chromosome	3072871	3072872	La1.6	A	M.bovis	None	None
Chromosome	3093940	3093941	lineage6.3.1	G	West-Africa 2	AFRI_1	RD702
Chromosome	3094576	3094577	lineage9	A	Lineage 9	None	None
Chromosome	3095341	3095342	La1.2.BCG	C	M.bovis	BCG	None
Chromosome	3097222	3097223	lineage5.1.4	T	West-Africa 1	AFRI_2;AFRI_3	RD711
Chromosome	3108168	3108169	lineage6.2.1	A	West-Africa 2	AFRI_1	RD702
Chromosome	3129358	3129359	lineage4.1.1	T	Euro-American (X-type)	X1;X2;X3	None
Chromosome	3141826	3141827	lineage4.2.2.2	G	Euro-American (Ural)	T;LAM7-TUR	None
Chromosome	3147315	3147316	lineage1.2.2.2	A	Indo-Oceanic	NA	RD239
Chromosome	3147375	3147376	lineage4.4.1	A	Euro-American (S-type)	S;T	None
Chromosome	3147510	3147511	lineage2.2.2	G	East-Asian (Beijing)	Beijing-RD105/RD207	RD105;RD207
Chromosome	3147741	3147742	lineage4.1.2	G	Euro-American	T;H	None
Chromosome	3148166	3148167	M.canetti	G	M.canetti	None	None
Chromosome	3153182	3153183	lineage6.3	G	West-Africa 2	AFRI_1	RD702
Chromosome	3168966	3168967	lineage4.8	A	Euro-American (mainly T)	T1;T2;T3;T5	RD219
Chromosome	3170459	3170460	lineage4.6	T	Euro-American	T;LAM	None
Chromosome	3191026	3191027	lineage4.3	A	Euro-American (LAM)	mainly-LAM	None
Chromosome	3193574	3193575	lineage5.1	T	West-Africa 1	AFRI_2;AFRI_3	RD711
Chromosome	3198495	3198496	lineage4.2	A	Euro-American	H;T;LAM	None
Chromosome	3213254	3213255	lineage6	T	West-Africa 2	AFRI_1	RD702
Chromosome	3213614	3213615	lineage4.1.1.2	A	Euro-American (X-type)	X1	None
Chromosome	3220221	3220222	lineage4.7	A	Euro-American (mainly T)	T1;T5	None
Chromosome	3231090	3231091	lineage4.1.1	A	Euro-American (X-type)	X1;X2;X3	None
Chromosome	3238747	3238748	lineage4.6.2.1	A	Euro-American	T3	RD726
Chromosome	3244323	3244324	La1.3	G	M.bovis	None	None
Chromosome	3244673	3244674	lineage4.3.4.1	A	Euro-American (LAM)	LAM1;LAM2	RD174
Chromosome	3253570	3253571	lineage4.1.1.3.1	T	Euro-American (X-type)	X1;X3	RD193
Chromosome	3259271	3259272	lineage4.2.2.1	C	Euro-American	LAM7-TUR	None
Chromosome	3270288	3270289	lineage4.7	A	Euro-American (mainly T)	T1;T5	None
Chromosome	3285944	3285945	lineage4.3.4.1	G	Euro-American (LAM)	LAM1;LAM2	RD174
Chromosome	3287787	3287788	M.canetti	G	M.canetti	None	None
Chromosome	3293314	3293315	lineage4.6.2.1	T	Euro-American	T3	RD726
Chromosome	3323664	3323665	lineage1.2.2.1	A	Indo-Oceanic	NA	RD239
Chromosome	3332625	3332626	lineage4.6.1.2	T	Euro-American	T2	RD724
Chromosome	3337584	3337585	lineage1.1.3.3	A	Indo-Oceanic	NA	RD239
Chromosome	3347069	3347070	La1.8.1	T	M.bovis	None	None
Chromosome	3347479	3347480	lineage4.4.1.1	A	Euro-American	S;Orphans	None
Chromosome	3348127	3348128	lineage6.3.3	T	West-Africa 2	AFRI_1	RD702
Chromosome	3348869	3348870	lineage4.8.1	A	Euro-American (mainly T)	T1;T2;T3;T5	RD219
Chromosome	3349092	3349093	lineage4.4.1.2	C	Euro-American	T1	None
Chromosome	3354624	3354625	lineage4.6.2.2	A	Euro-American (Cameroon)	LAM10-CAM	RD726
Chromosome	3360031	3360032	lineage4.3.1.1	A	Euro-American (LAM)	LAM9	None
Chromosome	3360151	3360152	lineage4.6.2.2	A	Euro-American (Cameroon)	LAM10-CAM	RD726
Chromosome	3363400	3363401	lineage6.3.3	A	West-Africa 2	AFRI_1	RD702
Chromosome	3367416	3367417	M.canetti	A	M.canetti	None	None
Chromosome	3367764	3367765	lineage4.9	G	Euro-American (H37Rv-like)	T1	None
Chromosome	3368283	3368284	lineage5.1.1	T	West-Africa 1	AFRI_2;AFRI_3	RD711
Chromosome	3368414	3368415	lineage6.2.2	A	West-Africa 2	AFRI_1	RD702
Chromosome	3370804	3370805	lineage9	C	Lineage 9	None	None
Chromosome	3383965	3383966	lineage4.2.2	C	Euro-American (Ural)	T;LAM7-TUR	None
Chromosome	3387251	3387252	lineage1.2.1.1	A	Indo-Oceanic	NA	RD239
Chromosome	3389921	3389922	lineage4.8.1	G	Euro-American (mainly T)	T1;T2;T3;T5	RD219
Chromosome	3396568	3396569	La3	A	M.orygis	None	None
Chromosome	3402589	3402590	lineage6.1.2	A	West-Africa 2	AFRI_1	RD702
Chromosome	3404882	3404883	lineage4.8.2	A	Euro-American (mainly T)	T1;T2;T3;T5	RD219
Chromosome	3414552	3414553	lineage9	A	Lineage 9	None	None
Chromosome	3414790	3414791	lineage4.3.2	C	Euro-American (LAM)	LAM3	None
Chromosome	3416733	3416734	lineage4.2.2.2	A	Euro-American (Ural)	T;LAM7-TUR	None
Chromosome	3418329	3418330	lineage4.3	A	Euro-American (LAM)	mainly-LAM	None
Chromosome	3419559	3419560	lineage4.4	T	Euro-American	S;T	None
Chromosome	3423183	3423184	lineage4.3.3	T	Euro-American (LAM)	LAM;T	RD115
Chromosome	3423938	3423939	La1.2.BCG	A	M.bovis	BCG	None
Chromosome	3433139	3433140	lineage6.3.3	A	West-Africa 2	AFRI_1	RD702
Chromosome	3464052	3464053	lineage4.1.1.1	A	Euro-American (X-type)	X2	RD183
Chromosome	3469693	3469694	lineage4.2	T	Euro-American	H;T;LAM	None
Chromosome	3471150	3471151	lineage4.2.1	A	Euro-American (TUR)	H3;H4	None
Chromosome	3488811	3488812	lineage6.1.1	T	West-Africa 2	AFRI_1	RD702
Chromosome	3497368	3497369	lineage4.2.2.2	A	Euro-American (Ural)	T;LAM7-TUR	None
Chromosome	3498197	3498198	lineage2.2.1	T	East-Asian (Beijing)	Beijing-RD181	RD105;RD207;RD181
Chromosome	3504929	3504930	lineage4.3.4.2	T	Euro-American (LAM)	LAM1;LAM4;LAM11	RD174
Chromosome	3557910	3557911	lineage3.1.2.1	T	East-African-Indian	CAS2	RD750
Chromosome	3562269	3562270	lineage4.6.1.1	C	Euro-American	T2-Uganda	RD724
Chromosome	3575551	3575552	lineage4.1.1.3.1	A	Euro-American (X-type)	X1;X3	RD193
Chromosome	3577778	3577779	La3	A	M.orygis	None	None
Chromosome	3579165	3579166	lineage4.2.2.1	G	Euro-American	LAM7-TUR	None
Chromosome	3580669	3580670	lineage5.1.1	T	West-Africa 1	AFRI_2;AFRI_3	RD711
Chromosome	3581186	3581187	La1.1	A	M.bovis	None	None
Chromosome	3603864	3603865	lineage6.1.2	T	West-Africa 2	AFRI_1	RD702
Chromosome	3608513	3608514	lineage4.4	A	Euro-American	S;T	None
Chromosome	3612008	3612009	lineage4.3.4	T	Euro-American (LAM)	LAM	RD174
Chromosome	3619853	3619854	lineage1.2.1.2.1	G	Indo-Oceanic	NA	RD239
Chromosome	3629290	3629291	lineage3.1.2.2	G	East-African-Indian	CAS	RD750
Chromosome	3629611	3629612	lineage1.2.1.2	A	Indo-Oceanic	NA	RD239
Chromosome	3643391	3643392	lineage4.3.3	T	Euro-American (LAM)	LAM;T	RD115
Chromosome	3646963	3646964	lineage4.2.1	G	Euro-American (TUR)	H3;H4	None
Chromosome	3664134	3664135	lineage4.4.1	A	Euro-American (S-type)	S;T	None
Chromosome	3666904	3666905	lineage4.2	T	Euro-American	H;T;LAM	None
Chromosome	3676092	3676093	La1.8.X-unk6	T	M.bovis	None	None
Chromosome	3720206	3720207	La1.7.1	T	M.bovis	None	None
Chromosome	3722701	3722702	lineage3.1.2	C	East-African-Indian	CAS;CAS2	RD750
Chromosome	3770448	3770449	La3	A	M.orygis	None	None
Chromosome	3787155	3787156	lineage1.2.2.1	A	Indo-Oceanic	NA	RD239
Chromosome	3813472	3813473	lineage4.4.1	A	Euro-American (S-type)	S;T	None
Chromosome	3823158	3823159	lineage4.9	A	Euro-American (H37Rv-like)	T1	None
Chromosome	3830347	3830348	La3	C	M.orygis	None	None
Chromosome	3830694	3830695	lineage4	A	Euro-American	LAM;T;S;X;H	None
Chromosome	3836738	3836739	lineage4.8	A	Euro-American (mainly T)	T1;T2;T3;T5	RD219
Chromosome	3849393	3849394	La1.4	A	M.bovis	None	None
Chromosome	3855302	3855303	lineage9	A	Lineage 9	None	None
Chromosome	3862147	3862148	lineage6	A	West-Africa 2	AFRI_1	RD702
Chromosome	3862180	3862181	lineage1.2.1.2	T	Indo-Oceanic	NA	RD239
Chromosome	3863544	3863545	lineage4.8.3	A	Euro-American (mainly T)	T1;T2;T3;T5	RD219
Chromosome	3865538	3865539	lineage4.1.1.3.1	C	Euro-American (X-type)	X1;X3	RD193
Chromosome	3877255	3877256	La1	T	M.bovis	None	None
Chromosome	3879881	3879882	lineage1.1.2	A	Indo-Oceanic	EAI3;EAI5	RD239
Chromosome	3886877	3886878	lineage4.4.2	C	Euro-American	T1;T2	None
Chromosome	3893138	3893139	lineage5.1.4	A	West-Africa 1	AFRI_2;AFRI_3	RD711
Chromosome	3918066	3918067	lineage6.1.1	C	West-Africa 2	AFRI_1	RD702
Chromosome	3955403	3955404	lineage6.1.1	A	West-Africa 2	AFRI_1	RD702
Chromosome	4000017	4000018	M.canetti	G	M.canetti	None	None
Chromosome	4001040	4001041	lineage6.2.1	A	West-Africa 2	AFRI_1	RD702
Chromosome	4004035	4004036	lineage4.4	T	Euro-American	S;T	None
Chromosome	4024367	4024368	lineage1.2.1.2	T	Indo-Oceanic	NA	RD239
Chromosome	4028291	4028292	lineage4.8	T	Euro-American (mainly T)	T1;T2;T3;T5	RD219
Chromosome	4030258	4030259	La1.8.1	G	M.bovis	None	None
Chromosome	4043364	4043365	lineage4.3.4.2	T	Euro-American (LAM)	LAM1;LAM4;LAM11	RD174
Chromosome	4047842	4047843	lineage4.3.1	T	Euro-American (LAM)	LAM9	None
Chromosome	4051662	4051663	lineage4.6.4	T	Euro-American	T;LAM	None
Chromosome	4053712	4053713	lineage3.1.2.1	G	East-African-Indian	CAS2	RD750
Chromosome	4054363	4054364	lineage1.1	T	Indo-Oceanic	EAI3;EAI4;EAI5;EAI6	RD239
Chromosome	4055216	4055217	lineage6.1.3	A	West-Africa 2	AFRI_1	RD702
Chromosome	4064551	4064552	lineage6.1.2	G	West-Africa 2	AFRI_1	RD702
Chromosome	4065299	4065300	lineage3.1.1	T	East-African-Indian	CAS1-Kili	RD750
Chromosome	4080524	4080525	lineage2.2.1.1	T	East-Asian (Beijing)	Beijing-RD150	RD105;RD207;RD181;RD150
Chromosome	4084404	4084405	lineage1.1.3.2	A	Indo-Oceanic	NA	RD239
Chromosome	4086696	4086697	lineage6	T	West-Africa 2	AFRI_1	RD702
Chromosome	4112594	4112595	lineage4.7	A	Euro-American (mainly T)	T1;T5	None
Chromosome	4114818	4114819	La1.7.1	C	M.bovis	None	None
Chromosome	4127645	4127646	lineage6.1.3	A	West-Africa 2	AFRI_1	RD702
Chromosome	4132948	4132949	lineage3.1.2	T	East-African-Indian	CAS;CAS2	RD750
Chromosome	4154050	4154051	lineage4.1.1.3	A	Euro-American (X-type)	X1;X3	RD193
Chromosome	4154815	4154816	lineage1.1.3.2	A	Indo-Oceanic	NA	RD239
Chromosome	4155798	4155799	La1.1	A	M.bovis	None	None
Chromosome	4157258	4157259	lineage1.1.2	A	Indo-Oceanic	EAI3;EAI5	RD239
Chromosome	4158492	4158493	lineage2.2.1	T	East-Asian (Beijing)	Beijing-RD181	RD105;RD207;RD181
Chromosome	4165204	4165205	lineage4.9.1	T	Euro-American (H37Rv-like)	T1	None
Chromosome	4165480	4165481	lineage2.1	C	East-Asian (non-Beijing)	None	None
Chromosome	4170989	4170990	lineage6.2.3	A	West-Africa 2	AFRI_1	RD702
Chromosome	4192676	4192677	lineage6.1.1	A	West-Africa 2	AFRI_1	RD702
Chromosome	4193068	4193069	La1.3	A	M.bovis	None	None
Chromosome	4198059	4198060	lineage6.1.3	C	West-Africa 2	AFRI_1	RD702
Chromosome	4199738	4199739	lineage4.2.1	T	Euro-American (TUR)	H3;H4	None
Chromosome	4200992	4200993	lineage1.2.2.2	G	Indo-Oceanic	NA	RD239
Chromosome	4204695	4204696	La1.8.2	A	M.bovis	None	None
Chromosome	4228100	4228101	lineage4.1.3	T	Euro-American	T;X;H	None
Chromosome	4229086	4229087	lineage4.1.1.3	T	Euro-American (X-type)	X1;X3	RD193
Chromosome	4231381	4231382	M.canetti	G	M.canetti	None	None
Chromosome	4236890	4236891	lineage6	A	West-Africa 2	AFRI_1	RD702
Chromosome	4236902	4236903	lineage4.6.4	A	Euro-American	T;LAM	None
Chromosome	4237382	4237383	lineage1.2.1.2	A	Indo-Oceanic	NA	RD239
Chromosome	4238119	4238120	lineage1.2.2	A	Indo-Oceanic	EAI1	RD239
Chromosome	4238962	4238963	lineage4.4	T	Euro-American	S;T	None
Chromosome	4254430	4254431	lineage2	A	East-Asian	Beijing	RD105
Chromosome	4256757	4256758	lineage4.1.2.1	C	Euro-American (Haarlem)	T1;H1	RD182
Chromosome	4260267	4260268	lineage4.6.1	C	Euro-American (Uganda)	T2	RD724
Chromosome	4260741	4260742	lineage4.6.2	A	Euro-American	T;LAM	RD726
Chromosome	4268185	4268186	lineage6.3.2	A	West-Africa 2	AFRI_1	RD702
Chromosome	4268476	4268477	lineage6.3	A	West-Africa 2	AFRI_1	RD702
Chromosome	4268524	4268525	lineage6.1.2	G	West-Africa 2	AFRI_1	RD702
Chromosome	4269539	4269540	lineage4.1.1.3.1	A	Euro-American (X-type)	X1;X3	RD193
Chromosome	4273841	4273842	lineage4.3.4.2.1	C	Euro-American (LAM)	LAM11	RD174
Chromosome	4286155	4286156	lineage1.1	C	Indo-Oceanic	EAI3;EAI4;EAI5;EAI6	RD239
Chromosome	4294319	4294320	lineage6.1.1	G	West-Africa 2	AFRI_1	RD702
Chromosome	4297209	4297210	La1.8.2	G	M.bovis	None	None
Chromosome	4298105	4298106	lineage4.2.2.2	A	Euro-American (Ural)	T;LAM7-TUR	None
Chromosome	4307885	4307886	lineage4.4	A	Euro-American	S;T	None
Chromosome	4308394	4308395	lineage2	A	East-Asian	Beijing	RD105
Chromosome	4309280	4309281	La1.2	T	M.bovis	None	None
Chromosome	4331584	4331585	lineage4.1.2.1	A	Euro-American (Haarlem)	T1;H1	RD182
Chromosome	4332754	4332755	lineage6.2.3	T	West-Africa 2	AFRI_1	RD702
Chromosome	4357502	4357503	La1.1	G	M.bovis	None	None
Chromosome	4373474	4373475	lineage4.3.4.2	G	Euro-American (LAM)	LAM1;LAM4;LAM11	RD174
Chromosome	4380235	4380236	lineage4.3.4.2.1	G	Euro-American (LAM)	LAM11	RD174
Chromosome	4382533	4382534	lineage5.1.4	C	West-Africa 1	AFRI_2;AFRI_3	RD711
Chromosome	4390752	4390753	lineage4.3.3	G	Euro-American (LAM)	LAM;T	RD115
Chromosome	4391578	4391579	lineage4.7	G	Euro-American (mainly T)	T1;T5	None
Chromosome	4391662	4391663	lineage4.1.4	A	Euro-American	T;X;H	None
Chromosome	4392119	4392120	lineage4.4.1.2	A	Euro-American	T1	None
Chromosome	4396494	4396495	lineage3	A	East-African-Indian	CAS	RD750
Chromosome	4402047	4402048	lineage1.2.1.1	T	Indo-Oceanic	NA	RD239
Chromosome	4404246	4404247	lineage1.1	A	Indo-Oceanic	EAI3;EAI4;EAI5;EAI6	RD239
Chromosome	4404312	4404313	lineage4.1.2.1.1	A	Euro-American (Haarlem)	T1;H1	RD182
Chromosome	4406748	4406749	lineage4.6.1.1	A	Euro-American	T2-Uganda	RD724
