T-Trees

A novel tree-based approach for Genome-Wide Association Studies

Supplementary data

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6	Best: rs3094703 (2)	Gene	30.47-30.47Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs3094050		30466570	0.1722	0.03375	0.486	1.202e-29	0.00033	187
	rs3094703		30466936	0.172	0.03914	0.4852	1.905e-29	0.00042	166
6	Best: rs6930444 (2)	Gene	30.87-30.90Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs6930444		30871611	0.03002	0.7972	0.6268	2.446e-14	0.00051	144
	rs12215119	LINC00243 NCBI Gene Pubmed Genecard	30903307	0.1383	0.002861	1	5.264e-17	0.00039	171
6	Best: rs3130544 (2)	Gene	31.17-31.20Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs3130544		31166319	0.1876	0.06197	0.2747	3.79e-35	0.00055	135
	rs9263702	PSORS1C1 NCBI Gene Pubmed Genecard	31202174	0.05032	0.0001772	0.01384	8.124e-10	0.00041	168
6	Best: rs3132486 (2)	Gene	31.35-31.35Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs3132486		31351149	0.3991	0.2917	0.2823	3.146e-48	0.00095	103
	rs2524067		31353800	0.2173	0.5411	0.6106	2.545e-36	0.00042	164
6	Best: rs9273363 (185)	Gene	31.44-33.06Mb	MAF	HWE(case)	HWE(cont)	p-value	imp.	rank
	rs2523537		31443686	0.144	0.002837	0.2043	1.062e-28	0.00043	162
	rs2596437		31447065	0.1436	0.5939	0.08891	8.016e-33	0.00045	157
	rs12178292		31448412	0.3877	0.2634	0.7076	2.32e-42	0.00052	143
	rs2523638		31452252	0.3985	0.1318	0.8533	3.324e-43	0.00058	131
	rs3997982		31452273	0.1437	0.8944	0.2315	2.106e-32	0.00047	152
	rs2596571		31456001	0.2186	0.8618	0.07227	2.362e-40	0.00054	137
	rs2523485		31459014	0.1276	0.4506	0.5374	4.505e-32	0.00059	130
	rs3099849		31459394	0.1437	0.8957	0.3127	1.828e-31	0.00044	158
	rs9266774		31460859	0.1306	0.1283	0.6023	4.351e-32	0.0016	67
	rs9266775		31461396	0.1302	0.1091	0.6021	1.117e-31	0.0016	68
	rs2395485		31467627	0.2818	0.006432	0.1348	7.201e-20	0.00036	175
	rs2596517		31468074	0.1441	0.6927	0.2329	2.669e-32	0.00046	154
	rs2516516		31551549	0.1216	0.5206	0.08618	5.43e-31	0.0004	170
	rs2248459		31554689	0.4012	0.004679	0.7733	1.821e-60	0.002	60
	rs2248462		31554775	0.1889	0.01696	0.2056	3.359e-28	0.00094	105
	rs2248617		31556512	0.4025	0.01352	0.9346	9.396e-60	0.0019	62
	rs3099844		31556955	0.1851	0.06537	0.8192	1.042e-44	0.0012	80
	rs2516422		31557248	0.1887	0.017	0.224	5.558e-28	0.00095	104
	rs2523467		31565557	0.283	0.006474	0.22	2.032e-21	0.00053	142
	rs2395034		31568122	0.1915	0.01435	0.3464	2.934e-28	0.00095	102
	rs3131631		31592662	0.2046	0.7221	0.7645	5.108e-31	0.00035	176
	rs9348876		31683255	0.05584	0.4347	1	7.79e-20	0.0016	69
	rs2736177		31694073	0.1027	1	0.2529	1.776e-55	0.0032	42
	rs1046089	PRRC2A NCBI Gene Pubmed Genecard	31710946	0.439	0.9639	0.9684	9.476e-77	0.0032	43
	rs760293	BAG6 NCBI Gene Pubmed Genecard	31719756	0.1345	0.6318	0.5645	2.435e-46	0.0018	64
	rs3130048	BAG6 NCBI Gene Pubmed Genecard	31721718	0.3221	0.04842	0.407	8.842e-36	0.00053	141
	rs805301	BAG6 NCBI Gene Pubmed Genecard	31726100	0.4535	0.9271	0.4354	3.056e-75	0.0029	46
	rs2142234	LY6G5B NCBI Gene Pubmed Genecard	31747108	0.07842	0.001224	0.004225	2.117e-12	0.00043	160
	rs9378164		31751501	0.04756	0.3999	0.0538	4.302e-16	0.0011	85
	rs376510	LY6G6C NCBI Gene Pubmed Genecard	31796179	0.07782	0.8129	0.512	4.619e-17	0.00077	113
	rs805294	LY6G6C NCBI Gene Pubmed Genecard	31796196	0.42	0.002321	0.01321	1.199e-63	0.002	61
	rs707915	MSH5 NCBI Gene Pubmed Genecard MSH5-SAPCD1 NCBI Gene Pubmed Genecard	31818947	0.07734	0.813	0.8672	6.854e-18	0.0009	110
	rs3130484	MSH5 NCBI Gene Pubmed Genecard MSH5-SAPCD1 NCBI Gene Pubmed Genecard	31823861	0.1736	0.06958	1	5.225e-54	0.0023	54
	rs3131379	MSH5 NCBI Gene Pubmed Genecard MSH5-SAPCD1 NCBI Gene Pubmed Genecard	31829012	0.1733	0.03335	0.8673	2.919e-52	0.0023	52
	rs480092	LSM2 NCBI Gene Pubmed Genecard VARS NCBI Gene Pubmed Genecard	31872878	0.1872	0.09503	0.6346	7.362e-16	0.00048	150
	rs2763979	HSPA1B NCBI Gene Pubmed Genecard	31902571	0.4184	0.1151	0.9678	1.151e-65	0.003	45
	rs486416	EHMT2 NCBI Gene Pubmed Genecard	31964049	0.3466	0.01792	0.09253	0.04533	0.00065	122
	rs9267673		31991658	0.1032	0.5295	1	1.015e-06	0.0005	147
	rs644045		31991936	0.3658	6.793e-06	0.004705	0.1364	0.00035	177
	rs541862	CFB NCBI Gene Pubmed Genecard	32024930	0.07517	1	0.3237	5.782e-17	0.00063	128
	rs550513	RDBP NCBI Gene Pubmed Genecard	32028666	0.07667	0.6278	0.4565	1.454e-17	0.00061	129
	rs406936	SKIV2L NCBI Gene Pubmed Genecard	32041140	0.1035	0.2677	0.3697	5.265e-26	0.0011	84
	rs492899	SKIV2L NCBI Gene Pubmed Genecard	32041497	0.1038	0.03308	0.899	1.809e-23	0.0015	74
	rs3130287	TNXB NCBI Gene Pubmed Genecard	32158522	0.09901	0.724	0.1335	6.602e-81	0.0063	21
	rs1150753	TNXB NCBI Gene Pubmed Genecard	32167845	0.1735	0.0303	0.5551	1.904e-56	0.0031	44
	rs1269851	ATF6B NCBI Gene Pubmed Genecard	32200185	0.03877	0.5558	1	3.104e-16	0.00063	127
	rs3130348	AGPAT1 NCBI Gene Pubmed Genecard	32248255	0.2545	0.006254	0.2145	3.329e-11	0.00049	148
	rs3130284	AGPAT1 NCBI Gene Pubmed Genecard	32248465	0.2539	0.004578	0.2549	1.365e-11	0.00055	136
	rs408359	AGPAT1 NCBI Gene Pubmed Genecard	32249861	0.07985	0.7231	0.08281	3.577e-15	0.0015	75
	rs204991	GPSM3 NCBI Gene Pubmed Genecard	32269344	0.2465	0.0003306	0.9124	7.466e-23	0.00033	184
	rs204990	GPSM3 NCBI Gene Pubmed Genecard	32269408	0.2459	0.0003991	1	2.669e-23	0.00034	181
	rs2071278	NOTCH4 NCBI Gene Pubmed Genecard	32273422	0.2062	0.01604	0.537	1.635e-45	0.0016	65
	rs3131294	NOTCH4 NCBI Gene Pubmed Genecard	32288124	0.09146	0.07754	0.1412	2.508e-99	0.0092	16
	rs206015	NOTCH4 NCBI Gene Pubmed Genecard	32290737	0.1126	0.002506	0.8715	4.51e-12	0.00043	163
	rs438475	NOTCH4 NCBI Gene Pubmed Genecard	32294223	0.1385	0.04008	0.4033	1.449e-10	0.00056	134
	rs379464	NOTCH4 NCBI Gene Pubmed Genecard	32294326	0.05936	0.882	0.5111	2.653e-15	0.0018	63
	SNP_A-2064274		32300414	0.0692	1.2e-07	0.004361	1.238e-15	0.0015	72
	rs377763		32307122	0.281	0.000153	0.4077	6.25e-81	0.0067	19
	rs3134926		32308125	0.2676	0.9	0.8242	1.617e-10	0.00042	165
	rs424232		32316302	0.3224	0.02682	0.3574	3.057e-35	0.00066	121
	rs3115576		32324828	0.4383	0.5588	0.14	1.89e-11	0.0003	200
	rs6936204		32325070	0.3393	0.001425	0.0167	4.05e-06	0.0021	55
	rs3130311		32325345	0.4383	0.5894	0.1398	2.485e-11	0.00032	191
	rs1559873		32351107	0.2519	0.001221	0.1678	1.052e-16	0.00033	186
	rs1265777	C6orf10 NCBI Gene Pubmed Genecard	32381136	0.4203	3.477e-06	0.6425	1.351e-17	0.0011	82
	rs9268207	C6orf10 NCBI Gene Pubmed Genecard	32388440	0.252	4.995e-05	0.3943	9.933e-17	0.00033	190
	rs1018433	C6orf10 NCBI Gene Pubmed Genecard	32389488	0.2542	0.001778	0.08234	4.363e-16	0.00033	188
	rs9268230	C6orf10 NCBI Gene Pubmed Genecard	32395545	0.2522	0.07907	0.03595	6.083e-99	0.0056	24
	rs574710	C6orf10 NCBI Gene Pubmed Genecard	32396168	0.4228	1.26e-05	0.7283	1.038e-17	0.0011	89
	rs539703	C6orf10 NCBI Gene Pubmed Genecard	32396440	0.4207	6.697e-06	0.536	6.81e-18	0.0011	83
	rs3132959	C6orf10 NCBI Gene Pubmed Genecard	32406920	0.1644	0.4035	0.03745	1.15e-139	0.016	9
	rs926591	C6orf10 NCBI Gene Pubmed Genecard	32413668	0.4208	4.271e-06	0.6427	1.377e-17	0.0011	86
	rs3129900	C6orf10 NCBI Gene Pubmed Genecard	32413957	0.1079	1	0.06866	1.227e-119	0.013	14
	rs9368716	C6orf10 NCBI Gene Pubmed Genecard	32414068	0.4798	0.005963	0.3552	2.446e-05	0.00046	155
	rs4959093	C6orf10 NCBI Gene Pubmed Genecard	32421075	0.4208	5.29e-06	0.6426	1.648e-17	0.0011	88
	rs910050	C6orf10 NCBI Gene Pubmed Genecard	32423632	0.4121	0.0009852	0.8143	3.119e-20	0.00032	193
	rs910049	C6orf10 NCBI Gene Pubmed Genecard	32423705	0.168	0.06377	0.0001615	2.345e-139	0.014	12
	rs2894249	C6orf10 NCBI Gene Pubmed Genecard	32433813	0.1611	0.5246	0.3487	1.366e-130	0.013	13
	rs3129932	C6orf10 NCBI Gene Pubmed Genecard	32444105	0.1643	0.404	0.04217	2.937e-139	0.014	11
	rs3129933	C6orf10 NCBI Gene Pubmed Genecard	32444139	0.2178	0.0004232	0.1172	1.761e-19	0.00093	106
	rs3129934	C6orf10 NCBI Gene Pubmed Genecard	32444165	0.1082	1	0.05096	7.535e-121	0.012	15
	rs9268402	C6orf10 NCBI Gene Pubmed Genecard	32449331	0.4883	0.0001066	0.8547	0.002597	0.0011	87
	rs9391858	C6orf10 NCBI Gene Pubmed Genecard	32449376	0.1292	0.8962	0.2866	2.035e-17	0.0023	53
	rs12528797		32453064	0.1031	0.891	0.4619	0.0003095	0.00032	194
	rs7757831		32453161	0.01955	1	0.07818	5.642e-15	0.00064	125
	rs2894254		32453667	0.1745	0.0001712	0.9318	9.976e-62	0.0042	26
	rs6930777		32459544	0.1022	0.782	0.2634	0.000554	0.00034	180
	rs17423649	HCG23 NCBI Gene Pubmed Genecard	32465111	0.1194	0.5151	0.8151	5.496e-10	0.00054	139
	rs17495612	HCG23 NCBI Gene Pubmed Genecard	32467409	0.1228	0.44	0.8792	5.027e-11	0.00057	133
	rs3129953	HCG23 NCBI Gene Pubmed Genecard	32469799	0.2134	0.0001861	0.3606	3.465e-39	0.0014	77
	rs2076533	BTNL2 NCBI Gene Pubmed Genecard	32471505	0.4773	9.078e-05	0.7952	2.357e-13	0.0026	50
	rs2076530	BTNL2 NCBI Gene Pubmed Genecard	32471794	0.4825	6.126e-05	0.9411	2.652e-12	0.0026	49
	rs10947260	BTNL2 NCBI Gene Pubmed Genecard	32481163	0.05214	0.5142	0.01913	3.847e-10	0.00033	189
	rs10947261	BTNL2 NCBI Gene Pubmed Genecard	32481210	0.05487	0.5156	0.03931	5.922e-12	0.00039	172
	rs3763308	BTNL2 NCBI Gene Pubmed Genecard	32482618	0.02628	1	0.6102	3.463e-20	0.00099	96
	rs6930933		32491388	0.2195	9.67e-06	0.6143	1.023e-35	0.00097	99
	rs2001099		32491611	0.221	5.659e-06	0.5747	2.574e-34	0.00084	111
	rs2001097		32491836	0.2196	7.241e-06	0.6149	1.508e-35	0.00099	95
	rs9268541		32492505	0.06823	0.7808	0.07867	3.271e-10	0.00057	132
	rs3135378		32493077	0.2196	7.22e-06	0.5715	2.75e-35	0.00098	98
	rs3135377		32493377	0.1477	0.5474	1	1.003e-157	0.022	6
	rs3135376		32493448	0.2197	7.241e-06	0.4894	2.863e-35	0.0009	109
	rs2395161		32495730	0.2194	7.22e-06	0.6144	1.4e-35	0.00099	97
	rs2395164		32495838	0.2196	5.229e-06	0.5312	7.305e-34	0.001	94
	rs2395167		32496286	0.2203	2.066e-05	0.3454	7.914e-36	0.001	92
	rs2213580		32496552	0.2191	1.454e-05	0.5294	5.291e-35	0.00096	101
	rs3135366		32496687	0.2189	1.466e-05	0.5704	5.079e-35	0.00097	100
	rs9268557		32497283	0.4598	3.295e-08	0.6597	1.074e-45	0.0077	18
	rs9268560		32497490	0.4325	3.412e-07	0.9414	1.497e-34	0.0065	20
	rs3135363		32497626	0.2894	0.003584	0.2042	1.02e-10	0.00064	124
	rs3135342		32504593	0.3258	1.931e-07	0.3506	8.64e-20	0.0007	117
	rs5000563		32512113	0.3256	1.889e-07	0.3981	1.582e-19	0.00063	126
	rs3129872	HLA-DRA NCBI Gene Pubmed Genecard	32515131	0.3255	1.889e-07	0.3983	1.309e-19	0.00066	120
	rs3129877	HLA-DRA NCBI Gene Pubmed Genecard	32516575	0.3271	5.598e-08	0.4774	2.264e-20	0.00069	118
	rs3135393	HLA-DRA NCBI Gene Pubmed Genecard	32516820	0.226	0.000447	0.06781	1.649e-32	0.00092	107
	rs3177928	HLA-DRA NCBI Gene Pubmed Genecard	32520413	0.1273	0.4328	0.5617	3.395e-15	0.0021	56
	rs7194	HLA-DRA NCBI Gene Pubmed Genecard	32520458	0.371	5.737e-08	0.8483	2.69e-11	0.0029	47
	rs1051336	HLA-DRA NCBI Gene Pubmed Genecard	32520570	0.2256	7.29e-05	0.7618	4.847e-31	0.0005	146
	rs9268831		32535726	0.4677	2.188e-07	0.1425	5.506e-26	0.0039	30
	rs9268856		32537697	0.2814	5.339e-08	0.8082	1.263e-14	0.00042	167
	rs9268861		32537872	0.2416	4.255e-08	0.5398	1.714e-22	0.00048	151
	rs9268862		32538145	0.2808	6.824e-08	0.9609	6.021e-16	0.00038	173
	rs4428528		32538340	0.2539	0.01033	6.914e-05	1.52e-19	0.00043	161
	rs7766843		32538707	0.2815	5.279e-08	0.9227	1.295e-14	0.00046	153
	rs7746922		32538953	0.2881	2.854e-07	1.338e-05	7.869e-11	0.00065	123
	rs7747521		32539083	0.2807	2.029e-07	0.9612	1.102e-14	0.00033	185
	rs9268877		32539125	0.3102	0.02309	0.2936	2.797e-78	0.0083	17
	rs9268878		32539270	0.2815	7.27e-08	0.8462	1.078e-14	0.00041	169
	rs9269186	HLA-DRB3 NCBI Gene Pubmed Genecard	32556394	0.2798	2.032e-08	0.4067	4.481e-15	0.00034	179
	rs9270986		32682038	0.09403	1	0.0861	3.755e-163	0.026	3
	rs9271208		32686981	0.3067	4.825e-07	0.4763	2.12e-33	0.0014	79
	rs4530903		32689867	0.1024	0.2396	1	0.0623	0.0008	112
	rs9271850		32703038	0.3567	7.25e-07	6.921e-05	5.868e-18	0.0011	81
	rs3129768		32703061	0.1199	0.1691	0.1654	2.179e-118	0.016	10
	rs9272346	HLA-DQA1 NCBI Gene Pubmed Genecard	32712350	0.2922	0.01043	0.7869	3.433e-151	0.023	4
	rs9272723	HLA-DQA1 NCBI Gene Pubmed Genecard	32717405	0.2586	0.916	0.0004404	1.352e-154	0.022	5
	rs9273363		32734250	0.4671	0.005053	0.6336	0	0.069	1
	rs7775228		32766057	0.1039	0.2854	0.1001	5.741e-23	0.0016	66
	rs9469220		32766288	0.3915	7.422e-06	0.8543	6.446e-114	0.03	2
	rs2647015		32772071	0.08113	0.4315	0.01512	7.14e-30	0.0024	51
	rs2647046		32776314	0.3956	6.873e-09	0.285	0.08167	0.0039	34
	rs2858308		32777978	0.08123	0.7955	0.02477	7.311e-29	0.002	59
	SNP_A-4226034		32778473	0.129	0.1343	0.9368	0.0451	0.00071	115
	rs6936863		32792007	0.3286	1.943e-08	0.1586	1.696e-84	0.016	8
	rs9461799		32797507	0.3242	0.5447	0.6669	6.273e-43	0.0033	40
	rs9469240		32797979	0.3306	0.9522	0.876	3.693e-42	0.0034	39
	rs2859090		32808811	0.2444	8.891e-06	0.7142	4.815e-07	0.00044	159
	rs2227127	HLA-DQA2 NCBI Gene Pubmed Genecard	32819760	0.3197	0.7114	0.2397	1.802e-45	0.0038	36
	rs9276429	HLA-DQA2 NCBI Gene Pubmed Genecard	32820082	0.4821	0.3977	0.7679	1.348e-46	0.0041	27
	rs9276431	HLA-DQA2 NCBI Gene Pubmed Genecard	32820225	0.4821	0.3974	0.7961	6.611e-47	0.0039	31
	rs9276432	HLA-DQA2 NCBI Gene Pubmed Genecard	32820362	0.4817	0.372	0.7962	2.248e-46	0.0038	35
	rs2239800	HLA-DQA2 NCBI Gene Pubmed Genecard	32821245	0.05111	0.6374	1.421e-05	9.219e-23	0.0015	73
	rs9276435	HLA-DQA2 NCBI Gene Pubmed Genecard	32821845	0.218	9.805e-06	0.2436	6.346e-11	0.00031	196
	rs9276440	HLA-DQA2 NCBI Gene Pubmed Genecard	32822761	0.4789	0.2792	1	1.007e-45	0.0039	32
	rs9276448		32823607	0.0806	0.782	0.1818	0.007424	0.00054	140
	rs9276490	MIR3135B NCBI Gene Pubmed Genecard	32826659	0.4774	0.4212	0.9705	1.292e-46	0.0044	25
	rs5014418	MIR3135B NCBI Gene Pubmed Genecard	32827359	0.08271	0.3453	0.4371	0.008196	0.00049	149
	rs7768538	HLA-DQB2 NCBI Gene Pubmed Genecard	32837799	0.4812	0.3978	0.74	2.283e-45	0.0036	38
	rs7453920	HLA-DQB2 NCBI Gene Pubmed Genecard	32837990	0.4823	0.3725	0.7961	9.737e-46	0.004	29
	rs6902723	HLA-DQB2 NCBI Gene Pubmed Genecard	32839938	0.4157	0.2551	0.8827	2.565e-29	0.0014	78
	rs6903130	HLA-DQB2 NCBI Gene Pubmed Genecard	32840188	0.4165	0.2551	0.6315	6.225e-30	0.0015	70
	rs6919798	HLA-DQB2 NCBI Gene Pubmed Genecard	32840868	0.07888	0.1516	1	0.03015	0.00034	178
	rs9296043		32844081	0.336	1	0.7857	6.67e-40	0.0029	48
	rs9296044		32844122	0.3401	0.6855	0.3362	1.552e-40	0.0033	41
	rs1015575		32846093	0.3219	1.873e-05	0.61	1.021e-46	0.0057	23
	rs2857212		32848389	0.3144	0.1107	0.6948	9.917e-53	0.006	22
	rs2621419		32848984	0.3429	0.8791	6.345e-05	0.1176	0.0003	198
	rs2857210		32849720	0.3253	0.2022	0.4771	0.8099	0.0003	197
	rs2621416		32849846	0.2547	0.3271	0.8821	0.02649	0.00033	183
	rs12661352		32853505	0.04208	0.6237	0.0001287	3.296e-16	0.0007	116
	rs17429127		32859592	0.05009	1	0.05534	1.431e-22	0.0014	76
	rs9276712		32867230	0.04957	1	0.2332	3.381e-22	0.0015	71
	rs2621383		32867313	0.3627	0.02874	0.7861	1.379e-08	0.00032	195
	rs2621330	HLA-DOB NCBI Gene Pubmed Genecard	32889502	0.0496	0.4627	0.01384	6.978e-09	0.00045	156
	rs17501267	HLA-DOB NCBI Gene Pubmed Genecard	32890127	0.03466	1	0.8341	4.315e-16	0.00037	174
	rs2071474	HLA-DOB NCBI Gene Pubmed Genecard	32890560	0.2279	0.6239	0.9629	1.276e-35	0.002	57
	rs9784858		32895153	0.1033	0.1524	1	6.555e-18	0.00067	119
	rs17429458		32895315	0.03445	1	0.8332	8.933e-16	0.00032	192
	rs10484565	TAP2 NCBI Gene Pubmed Genecard	32903010	0.0941	0.1811	0.8931	4.736e-17	0.00054	138
	rs4148873	TAP2 NCBI Gene Pubmed Genecard	32908390	0.1234	0.1037	0.05321	6.614e-25	0.002	58
	rs241428	TAP2 NCBI Gene Pubmed Genecard	32912048	0.05349	0.07915	0.6245	9.022e-16	0.001	93
	rs241427	TAP2 NCBI Gene Pubmed Genecard	32912392	0.2774	0.6015	0.4617	4.745e-66	0.004	28
	rs241403	LOC100294145 NCBI Gene Pubmed Genecard	32974970	0.425	0.8017	0.359	2.938e-48	0.0011	90
	rs3101942	LOC100294145 NCBI Gene Pubmed Genecard	32978035	0.3286	0.653	0.06624	2.238e-73	0.0037	37
	rs188245		33063954	0.4938	0.6732	0.6818	2.714e-44	0.0009	108