r-bioc-iranges 2.12.0-2 / usr / lib / R / site-library / IRanges / extdata / hs_b36v3_chrY.agp

This file is indexed.

/usr/lib/R/site-library/IRanges/extdata/hs_b36v3_chrY.agp is in r-bioc-iranges 2.12.0-2.

This file is owned by root:root, with mode 0o644.

The actual contents of the file can be viewed below. 

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#
# Homo sapiens chromosome Y, reference assembly, complete sequence
#
# This file provides assembly instructions for sequence NC_000024
# included in reference assembly of NCBI build 36 (HGSC Finished Genome v4.0).
#
#chrom	chr_start	chr_stop	part_no	part_type	comp_id/gap_len	comp_type/gap_type	comp_end/linkage	orientation/empty
chrY	1	34821	1	F	BX640545.2	1	34821	+
chrY	34822	84821	2	N	50000	contig	no
chrY	84822	122592	3	F	AL954722.18	1	37771	+
chrY	122593	157464	4	F	BX537334.4	1	34872	-
chrY	157465	171384	5	F	BX000483.7	1999	15918	+
chrY	171385	201384	6	N	30000	contig	no
chrY	201385	232395	7	F	AL954664.17	8190	39200	-
chrY	232396	265528	8	F	BX000476.5	208	33340	+
chrY	265529	482251	9	F	AL732314.18	2001	218723	+
chrY	482252	550112	10	F	BX004827.18	51695	119555	+
chrY	550113	723877	11	F	AL683871.15	2001	175765	+
chrY	723878	837875	12	F	AL672311.26	2001	115998	+
chrY	837876	967557	13	F	AL672277.20	2001	131682	+
chrY	967558	1017557	14	N	50000	contig	no
chrY	1017558	1054113	15	F	BX908402.3	1	36556	+
chrY	1054114	1104113	16	N	50000	contig	no
chrY	1104114	1147822	17	F	BX649635.3	1	43709	+
chrY	1147823	1184234	18	F	BX901949.9	1685	38096	+
chrY	1184235	1274234	19	N	90000	contig	no
chrY	1274235	1307891	20	F	BX908382.8	1	33657	+
chrY	1307892	1390773	21	F	BX649553.6	2001	84882	+
chrY	1390774	1425289	22	F	BX901885.7	1	34516	+
chrY	1425290	1458955	23	F	BX119906.16	2001	35666	+
chrY	1458956	1618348	24	F	AL683870.15	1001	160393	+
chrY	1618349	1661433	25	F	AL691415.17	1	43085	+
chrY	1661434	1849259	26	F	AL683807.22	1	187826	+
chrY	1849260	1966556	27	F	AL672040.10	1	117297	+
chrY	1966557	2028238	28	F	CR381640.8	2001	63682	+
chrY	2028239	2128238	29	N	100000	contig	no
chrY	2128239	2165561	30	F	CR856018.10	1	37323	+
chrY	2165562	2202890	31	F	CR381696.5	2000	39328	+
chrY	2202891	2280454	32	F	BX649443.16	2001	79564	+
chrY	2280455	2333896	33	F	BX119919.5	1	53442	-
chrY	2333897	2514591	34	F	AC079176.15	1	180695	-
chrY	2514592	2593088	35	F	AC097314.27	1	78497	-
chrY	2593089	2709520	36	F	AC006209.25	23323	139754	-
chrY	2709521	2838553	37	F	AC006040.3	57272	186304	+
chrY	2838554	2845472	38	F	AC074181.1	1	6919	+
chrY	2845473	2999955	39	F	AC006157.2	1	154483	+
chrY	2999956	3170037	40	F	AC006032.2	1	170082	+
chrY	3170038	3247254	41	F	AC006152.4	1	77217	+
chrY	3247255	3316539	42	F	AC011305.2	1	69285	+
chrY	3316540	3471638	43	F	AC009479.4	1	155099	+
chrY	3471639	3567129	44	F	AC019058.4	1	95491	+
chrY	3567130	3650550	45	F	AC024038.6	1	83421	+
chrY	3650551	3827222	46	F	AC012078.3	1	176672	+
chrY	3827223	3945458	47	F	AC010094.5	1	118236	+
chrY	3945459	4015462	48	F	AC010737.4	1	70004	+
chrY	4015463	4164401	49	F	AC010084.3	1	148939	+
chrY	4164402	4316800	50	F	AC010905.3	1	152399	+
chrY	4316801	4335619	51	F	AC010106.2	1	18819	+
chrY	4335620	4367320	52	F	AC024703.5	1	31701	+
chrY	4367321	4576407	53	F	AC012077.4	1	209087	+
chrY	4576408	4712669	54	F	AC010142.4	1	136262	+
chrY	4712670	4829264	55	F	AC019060.5	1	116595	+
chrY	4829265	4917080	56	F	AC023423.5	1	87816	+
chrY	4917081	5077603	57	F	AC010722.2	1	160523	+
chrY	5077604	5237705	58	F	AC010685.3	1	160102	+
chrY	5237706	5281650	59	F	AC010129.3	1	43945	+
chrY	5281651	5445957	60	F	AC012067.2	1	164307	+
chrY	5445958	5520761	61	F	AC012667.2	1	74804	+
chrY	5520762	5697342	62	F	AC010081.4	1	176581	+
chrY	5697343	5811187	63	F	AC010874.3	1	113845	+
chrY	5811188	5947272	64	F	AC010977.4	1	136085	+
chrY	5947273	6015798	65	F	AC016681.2	1	68526	+
chrY	6015799	6163940	66	F	AC010140.3	1	148142	+
chrY	6163941	6386252	67	F	AC006335.2	1	222312	+
chrY	6386253	6441403	68	F	AC010154.3	1	55151	+
chrY	6441404	6607550	69	F	AC010144.4	1	166147	+
chrY	6607551	6623520	70	F	AC010728.4	1	15970	+
chrY	6623521	6823534	71	F	AC013412.3	1	200014	+
chrY	6823535	6877729	72	F	AC011297.3	1	54195	+
chrY	6877730	7044045	73	F	AC012068.5	1	166316	+
chrY	7044046	7154095	74	F	AC010104.3	1	110050	+
chrY	7154096	7233943	75	F	AC010143.3	1	79848	+
chrY	7233944	7405192	76	F	AC007284.4	1	171249	+
chrY	7405193	7521780	77	F	AC007247.5	1	116588	+
chrY	7521781	7638889	78	F	AC007274.3	1	117109	+
chrY	7638890	7808593	79	F	AC007275.4	1	169704	+
chrY	7808594	7883829	80	F	AC010678.4	1	75236	+
chrY	7883830	7997798	81	F	AC010902.4	1	113969	+
chrY	7997799	8184715	82	F	AC016749.4	1	186917	+
chrY	8184716	8278929	83	F	AC051663.9	1	94214	+
chrY	8278930	8370383	84	F	AC025731.12	1	91454	+
chrY	8370384	8544585	85	F	AC016991.5	1	174202	+
chrY	8544586	8634069	86	F	AC064829.6	1	89484	+
chrY	8634070	8774803	87	F	AC009491.3	1	140734	+
chrY	8774804	8962150	88	F	AC007967.3	1	187347	+
chrY	8962151	8972934	89	F	AC068719.3	1	10784	+
chrY	8972935	8974955	90	F	AC079126.3	1	2021	+
chrY	8974956	9024955	91	N	50000	clone	no
chrY	9024956	9030327	92	F	AC079125.4	1	5372	+
chrY	9030328	9178185	93	F	AC009952.4	1	147858	+
chrY	9178186	9190963	94	F	AC025732.9	1	12778	+
chrY	9190964	9301322	95	F	AC006158.6	1	110359	+
chrY	9301323	9901322	96	N	600000	clone	no
chrY	9901323	10013703	97	F	AC006156.5	1	112381	+
chrY	10013704	10088698	98	F	AC025819.7	1	74995	+
chrY	10088699	10250877	99	F	AC017019.3	1	162179	+
chrY	10250878	10283186	100	F	AC010891.2	1	32309	+
chrY	10283187	10456943	101	F	AC006986.3	1	173757	+
chrY	10456944	10622784	102	F	AC006987.2	1	165841	+
chrY	10622785	10714553	103	F	AC010970.3	1	91769	+
chrY	10714554	11214553	104	N	500000	clone	no
chrY	11214554	11253954	105	F	AC069323.5	1	39401	+
chrY	11253955	11653954	106	N	400000	centromere	no
chrY	11653955	11738549	107	F	AC140113.3	71061	155655	-
chrY	11738550	11861114	108	F	AC134878.3	33249	155813	-
chrY	11861115	12003063	109	F	AC134882.2	10706	152654	-
chrY	12003064	12208578	110	F	AC134879.3	1	205515	-
chrY	12208579	12308578	111	N	100000	centromere	no
chrY	12308579	12468100	112	F	AC011293.5	1	159522	+
chrY	12468101	12581699	113	F	AC012502.3	1	113599	+
chrY	12581700	12759636	114	F	AC011302.3	1	177937	+
chrY	12759637	12838587	115	F	AC013735.5	1	78951	+
chrY	12838588	12911566	116	F	AC004772.2	40021	112999	+
chrY	12911567	12936024	117	F	AC005942.2	1	24458	-
chrY	12936025	13059669	118	F	AC002992.1	2001	125645	+
chrY	13059670	13234892	119	F	AC004617.2	1	175223	+
chrY	13234893	13319390	120	F	AC004810.1	1	84498	-
chrY	13319391	13515290	121	F	AC002531.1	2001	197900	+
chrY	13515291	13619376	122	F	AC004474.1	44195	148280	+
chrY	13619377	13664255	123	F	AC006565.4	1	44879	-
chrY	13664256	13879980	124	F	AC005820.1	1	215725	-
chrY	13879981	13952171	125	F	AC010877.3	64839	137029	+
chrY	13952172	14123978	126	F	AC006376.2	1	171807	+
chrY	14123979	14159738	127	F	AC007004.3	1	35760	+
chrY	14159739	14264748	128	F	AC006383.2	1	105010	+
chrY	14264749	14466902	129	F	AC006371.2	1	202154	+
chrY	14466903	14639848	130	F	AC006370.2	1	172946	+
chrY	14639849	14742756	131	F	AC018677.3	1	102908	+
chrY	14742757	14779500	132	F	AC010720.4	1	36744	+
chrY	14779501	14953720	133	F	AC010723.3	1	174220	+
chrY	14953721	14981864	134	F	AC019191.4	1	28144	+
chrY	14981865	15158188	135	F	AC010726.4	1	176324	+
chrY	15158189	15267382	136	F	AC010979.3	1	109194	+
chrY	15267383	15447103	137	F	AC010879.2	1	179721	+
chrY	15447104	15512578	138	F	AC011903.4	1	65475	+
chrY	15512579	15557501	139	F	AC017032.3	1	44923	+
chrY	15557502	15714967	140	F	AC006989.3	1	157466	+
chrY	15714968	15795304	141	F	AC011289.4	1	80337	+
chrY	15795305	15909741	142	F	AC010972.3	1	114437	+
chrY	15909742	15967360	143	F	AC007007.3	1	57619	+
chrY	15967361	16111420	144	F	AC006998.3	1	144060	+
chrY	16111421	16274030	145	F	AC006382.3	1	162610	+
chrY	16274031	16413824	146	F	AC006462.3	1	139794	+
chrY	16413825	16509580	147	F	AC006336.4	1	95756	+
chrY	16509581	16528817	148	F	AC016671.3	1	19237	+
chrY	16528818	16695020	149	F	AC017020.4	1	166203	+
chrY	16695021	16899873	150	F	AC011749.2	1	204853	+
chrY	16899874	16926987	151	F	AC053516.10	1	27114	+
chrY	16926988	17103738	152	F	AC010135.3	1	176751	+
chrY	17103739	17166324	153	F	AC010128.3	1	62586	+
chrY	17166325	17345839	154	F	AC011751.2	1	179515	+
chrY	17345840	17488621	155	F	AC016678.4	1	142782	+
chrY	17488622	17510633	156	F	AC015979.4	1	22012	+
chrY	17510634	17659631	157	F	AC007034.4	1	148998	+
chrY	17659632	17766833	158	F	AC007043.3	1	107202	+
chrY	17766834	17879511	159	F	AC006999.2	1	112678	+
chrY	17879512	17886218	160	F	AC007042.3	1	6707	+
chrY	17886219	17923463	161	F	AC091329.3	1	37245	+
chrY	17923464	18051552	162	F	AC007972.4	1	128089	+
chrY	18051553	18230132	163	F	AC015978.4	1	178580	+
chrY	18230133	18244934	164	F	AC068704.4	1	14802	+
chrY	18244935	18443908	165	F	AC007742.4	1	198974	+
chrY	18443909	18474219	166	F	AC095381.1	1	30311	+
chrY	18474220	18653273	167	F	AC009976.4	1	179054	+
chrY	18653274	18698502	168	F	AC095380.1	1	45229	+
chrY	18698503	18861991	169	F	AC024183.4	1	163489	+
chrY	18861992	19023659	170	F	AC007241.3	1	161668	+
chrY	19023660	19090333	171	F	AC069130.6	1	66674	+
chrY	19090334	19096847	172	F	AC073962.5	1	6514	+
chrY	19096848	19134213	173	F	AC068541.7	1	37366	+
chrY	19134214	19290370	174	F	AC022486.4	1	156157	+
chrY	19290371	19464252	175	F	AC007379.2	1	173882	+
chrY	19464253	19623962	176	F	AC009235.4	1	159710	+
chrY	19623963	19808739	177	F	AC007244.2	1	184777	+
chrY	19808740	19871998	178	F	AC021210.4	1	63259	+
chrY	19871999	20023872	179	F	AC010133.4	1	151874	+
chrY	20023873	20066067	180	F	AC012062.4	1	42195	+
chrY	20066068	20189568	181	F	AC010137.3	1	123501	+
chrY	20189569	20221039	182	F	AC009977.4	1	31471	+
chrY	20221040	20400963	183	F	AC010889.3	1	179924	+
chrY	20400964	20472584	184	F	AC010151.3	1	71621	+
chrY	20472585	20667823	185	F	AC009233.3	1	195239	+
chrY	20667824	20778857	186	F	AC079157.3	1	111034	+
chrY	20778858	20829067	187	F	AC079261.2	1	50210	+
chrY	20829068	20846452	188	F	AC079156.4	1	17385	+
chrY	20846453	20889975	189	F	AC024250.6	1	43523	+
chrY	20889976	20991065	190	F	AC009240.6	1	101090	+
chrY	20991066	21140390	191	F	AC011745.4	1	149325	+
chrY	21140391	21249363	192	F	AC007678.3	1	108973	+
chrY	21249364	21437477	193	F	AC009494.2	1	188114	+
chrY	21437478	21456819	194	F	AC026061.8	1	19342	+
chrY	21456820	21557572	195	F	AC009489.3	1	100753	+
chrY	21557573	21722251	196	F	AC007876.2	1	164679	+
chrY	21722252	21858422	197	F	AC009239.3	1	136171	+
chrY	21858423	22029157	198	F	AC010086.4	1	170735	+
chrY	22029158	22150215	199	F	AC010141.2	1	121058	+
chrY	22150216	22310816	200	F	AC021107.3	1	160601	+
chrY	22310817	22360816	201	N	50000	clone	no
chrY	22360817	22384194	202	F	AC078938.3	1	23378	+
chrY	22384195	22403616	203	F	AC024236.5	1	19422	+
chrY	22403617	22587631	204	F	AC007322.4	1	184015	+
chrY	22587632	22688058	205	F	AC007359.3	1	100427	+
chrY	22688059	22757212	206	F	AC023342.3	1	69154	+
chrY	22757213	22817822	207	F	AC025227.6	1	60610	+
chrY	22817823	23005516	208	F	AC007320.3	1	187694	+
chrY	23005517	23210553	209	F	AC008175.2	1	205037	+
chrY	23210554	23230057	210	F	AC016694.2	1	19504	+
chrY	23230058	23386813	211	F	AC010080.2	1	156756	+
chrY	23386814	23417437	212	F	AC016911.6	1	30624	+
chrY	23417438	23583695	213	F	AC006366.4	201	166458	-
chrY	23583696	23691182	214	F	AC010088.4	1	107487	+
chrY	23691183	23794414	215	F	AC053490.2	1	103232	+
chrY	23794415	23811321	216	F	AC007039.6	1	16907	+
chrY	23811322	23991466	217	F	AC006983.4	1	180145	+
chrY	23991467	24140496	218	F	AC009947.2	1	149030	+
chrY	24140497	24157833	219	F	AC016707.2	1	17337	+
chrY	24157834	24324069	220	F	AC016752.2	1	166236	+
chrY	24324070	24353833	221	F	AC025246.6	1	29764	+
chrY	24353834	24474584	222	F	AC073649.3	1	120751	+
chrY	24474585	24538834	223	F	AC073893.4	1	64250	+
chrY	24538835	24614390	224	F	AC068601.8	1	75556	+
chrY	24614391	24751872	225	F	AC023274.2	1	137482	+
chrY	24751873	24941229	226	F	AC012005.4	1	189357	+
chrY	24941230	24948693	227	F	AC013465.4	1	7464	+
chrY	24948694	25102779	228	F	AC016698.3	1	154086	+
chrY	25102780	25206726	229	F	AC010153.3	1	103947	+
chrY	25206727	25291998	230	F	AC025735.4	1	85272	+
chrY	25291999	25395154	231	F	AC010089.4	1	103156	+
chrY	25395155	25397101	232	F	AC006982.3	1	1947	+
chrY	25397102	25572891	233	F	AC006338.6	1	175790	+
chrY	25572892	25724743	234	F	AC016728.4	1	151852	+
chrY	25724744	25888772	235	F	AC006386.4	1	164029	+
chrY	25888773	26066341	236	F	AC006328.5	1	177569	+
chrY	26066342	26203218	237	F	AC007562.4	1	136877	+
chrY	26203219	26348595	238	F	AC010682.3	1	145377	+
chrY	26348596	26443316	239	F	AC017005.7	1	94721	+
chrY	26443317	26625199	240	F	AC007965.3	1	181883	+
chrY	26625200	26798241	241	F	AC006991.3	1	173042	+
chrY	26798242	26906387	242	F	AC024067.4	1	108146	+
chrY	26906388	27086206	243	F	AC013734.4	1	179819	+
chrY	27086207	27194539	244	F	AC019099.6	1	108333	+
chrY	27194540	27228749	245	F	AC073880.5	1	34210	+
chrY	27228750	57228749	246	N	30000000	heterochromatin	no
chrY	57228750	57327044	247	F	AC068123.5	1	98295	+
chrY	57327045	57377044	248	N	50000	clone	no
chrY	57377045	57443437	249	F	AC025226.4	101674	168066	-
chrY	57443438	57614293	250	F	AJ271735.1	69145	240000	+
chrY	57614294	57772954	251	F	AJ271736.1	1	158661	+

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