LEVEL	NAME	ROLLUP	ASSIGNED	TAXID	READ_COUNT	READ_COUNT_RNR	READ_COUNT_RSNB	TOTAL_BP_MAPPED	TOTAL_BP_MISMATCH	LINEAR_LENGTH	LINEAR_DOC	PATHOGEN	SCORE	REL_ABUNDANCE	ABUNDANCE	LINEAR_COV	NOTE	RPKM	PRI_READ_COUNT	REB_READ_COUNT	REB_READ_COUNT_RNR	TOL_RS_READ_CNT	TOL_NS_READ_CNT	TOL_RS_RNR	TOL_NS_RNR	STR	SPE	GEN	FAM	ORD	CLA	PHY	SK	ROOT	STR_rnb	SPE_rnb	GEN_rnb	FAM_rnb	ORD_rnb	CLA_rnb	PHY_rnb	SK_rnb	ROOT_rnb	STR_rnr	SPE_rnr	GEN_rnr	FAM_rnr	ORD_rnr	CLA_rnr	PHY_rnr	SK_rnr	ROOT_rnr	STR_rni	SPE_rni	GEN_rni	FAM_rni	ORD_rni	CLA_rni	PHY_rni	SK_rni	ROOT_rni	SOURCE	LOCATION	HOST	DISEASE	DIFF_MEAN	DIFF_SD	MC_ERROR	HPD_2.5	HPD_97.5	P<0	P>0	SCORE_UNIQ	SCORE_TTEST
superkingdom	Bacteria	320590		2	6967817	320590.29	316231.00	1047185960	9358178	159588253	6.5618		0.9710	0.9998	320590	0.4536		2.8397	320657	6968081.818222525	320602.56834551174	6960933	6884	320310.18000386783	280.1132294337887	95	2225966	28904	4704799	460	108	343	258	6884	89.80	140661.34	1687.09	173713.24	27.99	5.65	17.61	28.27	275.74	95.00	142183.00	1717.00	176234.21	28.54	5.68	18.26	28.49	280.11	89.80	2200675.67	28417.46	4635948.06	450.48	107.42	324.48	256.06	6762.23												0.971008932251601	
superkingdom	Viruses	71		10239	442	71.33	54.52	64075	1094	5781	11.0837		0.8069	0.0002	71	0.0224		0.8617	68	177.18177747514406	59.05385689632712	177	265	59.0	12.328969106427248	108	69	0	0	0	0	0	0	265	45.63	8.89	0	0	0	0	0	0	12.01	48.00	11.00	0	0	0	0	0	0	12.33	101.22	55.17	0	0	0	0	0	0	260.70												0.8068983605913069	
phylum	Proteobacteria	320590		1224	6967817	320590.29	316202.73	1047185960	9358178	159588253	6.5618		0.9710	1.0000	320590	0.4536		2.8397	320657	6967817.0	320590.2932333016	6960675	7142	320281.6877780381	308.60545526351456	95	2225966	28904	4704799	460	108	343	258	6884	89.80	140661.34	1687.09	173713.24	27.99	5.65	17.61	28.27	275.74	95.00	142183.00	1717.00	176234.21	28.54	5.68	18.26	28.49	280.11	89.80	2200675.67	28417.46	4635948.06	450.48	107.42	324.48	256.06	6762.23												0.971008932251601	
class	Gammaproteobacteria	320590		1236	6967817	320590.29	316185.12	1047185960	9358178	159588253	6.5618		0.9710	1.0000	320590	0.4536		2.8397	320657	6967817.0	320590.2932333016	6960332	7485	320263.4324656981	326.8607676035043	95	2225966	28904	4704799	460	108	343	258	6884	89.80	140661.34	1687.09	173713.24	27.99	5.65	17.61	28.27	275.74	95.00	142183.00	1717.00	176234.21	28.54	5.68	18.26	28.49	280.11	89.80	2200675.67	28417.46	4635948.06	450.48	107.42	324.48	256.06	6762.23												0.971008932251601	
order	Enterobacterales	320590		91347	6967817	320590.29	316179.47	1047185960	9358178	159588253	6.5618		0.9710	0.9998	320590	0.4536		2.8397	320657	6967819.806836992	320590.9818431706	6960224	7593	320257.750228856	332.54300444560954	95	2225966	28904	4704799	460	108	343	258	6884	89.80	140661.34	1687.09	173713.24	27.99	5.65	17.61	28.27	275.74	95.00	142183.00	1717.00	176234.21	28.54	5.68	18.26	28.49	280.11	89.80	2200675.67	28417.46	4635948.06	450.48	107.42	324.48	256.06	6762.23												0.971008932251601	
order	Picornavirales	59		464095	180	59.75	54.52	24705	749	1023	24.1496		0.8069	0.0002	59	0.0186		3.3923	60	177.19316300885538	59.06139013101326	177	3	59.0	0.75	108	69	0	0	0	0	0	0	3	45.63	8.89	0	0	0	0	0	0	0.56	48.00	11.00	0	0	0	0	0	0	0.75	101.22	55.17	0	0	0	0	0	0	2.26												0.8068983605913069	
family	Enterobacteriaceae	320590		543	6967817	320590.29	316151.48	1047185960	9358178	159588253	6.5618		0.9710	0.9998	320590	0.4536		2.8397	320657	6968081.788462862	320602.5534161756	6959764	8053	320229.2083185564	361.0849147451872	95	2225966	28904	4704799	460	108	343	258	6884	89.80	140661.34	1687.09	173713.24	27.99	5.65	17.61	28.27	275.74	95.00	142183.00	1717.00	176234.21	28.54	5.68	18.26	28.49	280.11	89.80	2200675.67	28417.46	4635948.06	450.48	107.42	324.48	256.06	6762.23												0.971008932251601	
family	Picornaviridae	59		12058	180	59.75	54.52	24705	749	1023	24.1496		0.8069	0.0002	59	0.0186		3.3923	60	177.21153713803034	59.06878623244641	177	3	59.0	0.75	108	69	0	0	0	0	0	0	3	45.63	8.89	0	0	0	0	0	0	0.56	48.00	11.00	0	0	0	0	0	0	0.75	101.22	55.17	0	0	0	0	0	0	2.26												0.8068983605913069	
genus	Escherichia	296586		561	6342297	296586.74	142411.85	953242549	8438504	141450940	6.7390		0.9710	0.9249	296586	0.4562		2.9808	299534	6967560.673005957	320465.7357795818	2254916	4087381	143965.99999999965	152620.7361242613	76	2225952	28888	4079701	442	108	316	258	6556	72.30	140656.97	1682.58	150111.91	27.26	5.65	16.77	28.27	262.81	76.00	142178.00	1712.00	152274.46	27.77	5.68	17.38	28.49	266.94	72.30	2200663.34	28402.91	4020305.58	433.10	107.42	298.58	256.06	6441.15												0.971008932251601	
genus	Shigella	24003		620	625520	24003.56	26.39	93943411	919674	18137313	5.1796		0.9365	0.0749	24003	0.4344		1.7916	21123	151.40718012435582	64.55348024955819	49	625471	29.0	23974.55710904066	19	14	16	625098	18	0	27	0	328	17.50	4.37	4.51	23601.33	0.74	0	0.84	0	12.93	19.00	5.00	5.00	23959.75	0.77	0	0.87	0	13.17	17.50	12.33	14.54	615642.48	17.38	0	25.91	0	321.09												0.9364927357945013	
genus	Cardiovirus	59		12103	180	59.75	54.52	24705	749	1023	24.1496		0.8069	0.0002	59	0.0186		3.3923	60	546.9198139185914	131.33294257668737	177	3	59.0	0.75	108	69	0	0	0	0	0	0	3	45.63	8.89	0	0	0	0	0	0	0.56	48.00	11.00	0	0	0	0	0	0	0.75	101.22	55.17	0	0	0	0	0	0	2.26												0.8068983605913069	
species	Escherichia coli	296289		562	6336188	296289.85	140727.53	952327075	8429295	141181260	6.7454	Pathogen	0.9710	0.9240	296289	0.4622		3.0225	299309	6967595.427233746	320470.1313188907	2226026	4110162	142251.99999999965	154037.8522619117	74	2225952	27176	4075311	438	108	316	258	6555	70.56	140656.97	1548.60	149956.85	27.11	5.65	16.77	28.27	262.78	74.00	142178.00	1575.09	152116.67	27.62	5.68	17.38	28.49	266.91	70.56	2200663.34	26726.03	4015987.34	429.20	107.42	298.58	256.06	6440.15	perirectal swab	USA	Homo sapiens	Gastroenteritis								0.971008932251601	
species	Shigella flexneri	9919		623	261399	9919.44	5.62	39256361	390253	7858733	4.9953		0.9237	0.0309	9919	0.4264		1.6770	8577	37.56072261815673	13.517003542399046	12	261387	6.0	9913.438937965006	4	8	6	261326	4	0	8	0	43	3.82	1.79	1.33	9760.03	0.18	0	0.25	0	1.53	4.00	2.00	1.47	9909.98	0.18	0	0.26	0	1.56	3.82	7.18	5.52	257320.81	3.97	0	7.89	0	42.25												0.9237358670459084	
species	Shigella sonnei	6515		624	170319	6515.94	7.40	25582863	246685	4589767	5.5739	Pathogen	0.9332	0.0203	6515	0.4677		2.0690	5716	31.300602181797274	18.022671389865394	10	170309	8.0	6507.942964716113	6	4	2	170063	5	0	10	0	229	5.77	1.62	0.64	6401.83	0.23	0	0.31	0	9.44	6.00	2.00	0.67	6497.14	0.23	0	0.32	0	9.58	5.77	3.25	1.91	167538.77	4.97	0	9.61	0	224.97	Stool	South Korea	Homo sapiens	Dysentery								0.933247965666763	
species	Shigella boydii	5780		621	150661	5780.04	2.76	22628814	217722	4210775	5.3740	Pathogen	0.9316	0.0180	5780	0.4609		1.9715	5283	12.52024087271891	6.758501771199523	4	150657	3.0	5777.039182849312	2	2	6	150612	5	0	7	0	27	1.81	0.95	1.85	5688.94	0.18	0	0.21	0	0.85	2.00	1.00	2.03	5773.73	0.18	0	0.23	0	0.87	1.81	1.91	5.48	148370.99	4.90	0	6.46	0	26.28	Cases of diarrhea	NA	Homo sapiens	Dysentery								0.9315986421097386	
species	Shigella dysenteriae	1788		622	43141	1788.14	6.10	6475373	65014	1478038	4.3811		0.9365	0.0056	1788	0.3383		1.2753	1547	21.910421527258094	15.769837466132218	7	43134	7.0	1781.1360235102286	7	0	2	43097	4	0	2	0	29	6.10	0	0.70	1750.53	0.15	0	0.06	0	1.11	7.00	0	0.83	1778.90	0.17	0	0.06	0	1.16	6.10	0	1.64	42411.91	3.54	0	1.95	0	27.58												0.9364927357945013	
species	Escherichia fergusonii	296		564	6109	296.88	1.74	915474	9209	269680	3.3947		0.9333	0.0009	296	0.0588		0.2016	225	6.260120436359455	4.5056678474663485	2	6107	2.0	294.8838623496187	2	0	1712	4390	4	0	0	0	1	1.74	0	133.98	155.06	0.15	0	0	0	0.03	2.00	0	136.91	157.78	0.15	0	0	0	0.03	1.74	0	1676.88	4318.24	3.90	0	0	0	1.00												0.9333418574355385	
species	Cardiovirus A	59		1821749	180	59.75	54.52	24705	749	1023	24.1496		0.8069	0.0002	59	0.0186		3.3923	60	554.0206586178117	132.91720150025728	177	3	59.0	0.75	108	69	0	0	0	0	0	0	3	45.63	8.89	0	0	0	0	0	0	0.56	48.00	11.00	0	0	0	0	0	0	0.75	101.22	55.17	0	0	0	0	0	0	2.26												0.8068983605913069	
strain	Escherichia coli DH1	34661		536056	586764	34661.46	4.00	88255883	708663	9098009	9.7006	Pathogen	0.9709	0.1037	34661	0.9833		11.6741	39074	189357.10299003322	10866.866357104336	4	586760	4.0	34657.459898327485	4	277946	3290	304803	54	12	34	65	556	4.00	21345.25	264.41	12630.11	3.97	0.63	3.25	7.57	24.41	4.00	21552.79	268.57	12795.78	4.05	0.64	3.30	7.62	24.72	4.00	275151.26	3238.08	300679.51	52.77	11.93	33.19	64.65	547.52	perirectal swab	USA	Homo sapiens	Gastroenteritis								0.9708506277713672	
strain	Escherichia coli str. K-12 substr. MG1655	17712		511145.1	296578	17712.21	37.70	44610979	356478	4574265	9.7526	Pathogen	0.9710	0.0530	17712	0.9855		11.8910	20435	1798892.4784053157	103235.23039249121	38	296540	38.0	17674.2066306655	38	140946	1652	153575	29	5	19	32	282	37.70	10964.60	132.49	6366.83	2.11	0.26	1.69	3.76	12.38	38.00	11069.37	134.56	6449.87	2.15	0.26	1.71	3.78	12.52	37.70	139540.32	1626.38	151509.70	28.43	5.00	18.57	31.82	278.25	perirectal swab	USA	Homo sapiens	Gastroenteritis								0.971008932251601	
strain	Escherichia coli str. K-12 substr. MDS42	13812		1110693	253589	13812.07	1.72	38139677	312259	3946967	9.6630	Pathogen	0.9675	0.0413	13812	0.9926		10.8246	15805	94678.55149501661	5433.433178552168	2	253587	2.0	13810.07020780513	2	110375	943	141951	28	0	8	0	282	1.72	7800.93	55.54	5783.97	2.02	0	0.24	0	12.33	2.00	7878.87	56.30	5860.10	2.05	0	0.26	0	12.49	1.72	109240.62	930.01	140027.64	27.43	0	7.40	0	277.90	perirectal swab	USA	Homo sapiens	Gastroenteritis								0.9675090069358935	
strain	Escherichia coli APEC O78	4619		1274814	114759	4619.79	3.60	17242379	161082	2785561	6.1899	Pathogen	0.9396	0.0138	4619	0.5805		3.0001	4256	189357.10299003322	10866.866357104336	4	114755	4.0	4615.7913492599455	4	29737	354	84514	3	0	2	0	145	3.60	1548.85	15.15	2982.33	0.11	0	0.05	0	5.33	4.00	1567.86	15.42	3026.88	0.11	0	0.06	0	5.45	3.60	29371.21	348.58	83251.64	2.91	0	1.65	0	141.58	the lung of a turkey clinically diagnosed with colibacillosis	NA	Turkey; Meleagris gallopavo	Colibacillosis								0.9396041468342802	
strain	Escherichia coli 55989	3684		585055	102027	3684.12	1.86	15328920	143245	2619131	5.8527	Pathogen	0.9371	0.0110	3684	0.5081		2.2271	3369	94678.55149501661	5433.433178552168	2	102025	2.0	3682.118142714667	2	21690	200	79983	12	0	6	0	134	1.86	931.66	7.62	2685.10	0.64	0	0.18	0	4.61	2.00	943.72	7.83	2725.03	0.64	0	0.19	0	4.71	1.86	21415.81	195.03	78805.99	11.91	0	5.72	0	131.07	clinical Enteroaggregative isolate	NA	Homo sapiens	Gastroenteritis								0.9371113259137183	
strain	Shigella sonnei Ss046	3220		300269	84145	3220.12	5.77	12638153	121845	2276627	5.5513	Pathogen	0.9332	0.0096	3220	0.4718		2.0796	2800	284035.65448504983	16300.299535656506	6	84139	6.0	3214.118583594017	6	2	1	84014	3	0	6	0	113	5.77	0.81	0.32	3160.51	0.14	0	0.18	0	4.67	6.00	1.00	0.33	3207.72	0.14	0	0.19	0	4.74	5.77	1.62	0.95	82761.32	2.99	0	5.68	0	111.12	epidemic in China in the 1950s	China	Homo sapiens	Dysentery								0.933247965666763	
strain	Shigella boydii CDC 3083-94	2866		344609	74746	2866.09	1.81	11225962	107284	2084023	5.3867	Pathogen	0.9316	0.0086	2866	0.4515		1.9348	2633	94678.55149501661	5433.433178552168	2	74744	2.0	2864.091334599156	2	1	2	74719	2	0	4	0	16	1.81	0.48	0.64	2820.08	0.06	0	0.11	0	0.50	2.00	0.50	0.67	2862.21	0.06	0	0.13	0	0.52	1.81	0.95	1.92	73608.05	1.90	0	3.48	0	15.51	12-year-old boy	USA: Arizona	Homo sapiens	Dysentery								0.9315986421097386	
strain	Shigella flexneri 5 str. 8401	2478		373384	65429	2478.63	1.97	9826133	97201	1966055	4.9979	Pathogen	0.9200	0.0074	2478	0.4298		1.6885	2165	94678.55149501661	5433.433178552168	2	65427	2.0	2476.6275224470032	2	2	3	65397	1	0	2	0	22	1.97	0.45	0.76	2436.95	0.04	0	0.06	0	0.84	2.00	0.50	0.87	2474.31	0.04	0	0.06	0	0.85	1.97	1.79	2.66	64398.90	1.00	0	1.98	0	21.72	NA	NA	Homo sapiens	Dysentery								0.9199955358937933	
strain	Escherichia coli UMN026	2033		585056	44263	2033.44	1.78	6643908	64749	1471150	4.5161	Pathogen	0.9495	0.0061	2033	0.2828		1.2181	1824	94678.55149501661	5433.433178552168	2	44261	2.0	2031.4392005910781	2	14053	759	29434	3	0	2	1	9	1.78	888.89	68.77	1042.37	0.09	0	0.06	0.08	0.28	2.00	901.40	70.04	1059.44	0.10	0	0.06	0.08	0.31	1.78	13849.70	745.74	28959.46	2.90	0	1.74	0.93	8.34	perirectal swab	USA	Homo sapiens	Gastroenteritis								0.9495168928666671	
strain	Shigella dysenteriae Sd197	1788		300267	43141	1788.14	6.10	6475373	65014	1478038	4.3811	Pathogen	0.9365	0.0054	1788	0.3383		1.2753	1547	331374.93023255817	19017.01612493259	7	43134	7.0	1781.1360235102286	7	0	2	43097	4	0	2	0	29	6.10	0	0.70	1750.53	0.15	0	0.06	0	1.11	7.00	0	0.83	1778.90	0.17	0	0.06	0	1.16	6.10	0	1.64	42411.91	3.54	0	1.95	0	27.58	epidemic in China in the 1950s	China	Homo sapiens	Dysentery								0.9364927357945013	
strain	Escherichia coli O44:H18	1716		861906	41114	1716.49	1.91	6169793	61750	1408697	4.3798	Pathogen	NA	0.0051	1716	0.2687		1.0204	1496	94678.55149501661	5433.433178552168	2	41112	2.0	1714.4856612860078	2	10855	415	29797	7	5	4	0	29	1.91	605.61	19.14	1060.57	0.35	0.25	0.12	0	1.01	2.00	615.10	19.41	1078.17	0.38	0.26	0.13	0	1.05	1.91	10686.31	409.42	29309.69	6.60	4.99	3.72	0	27.98	perirectal swab	USA	Homo sapiens	Gastroenteritis								NA	
strain	Escherichia coli 042	1716		216592	41114	1716.49	1.91	6169793	61750	1408697	4.3798	Pathogen	0.9367	0.0051	1716	0.2687		1.0204	1496	94678.55149501661	5433.433178552168	2	41112	2.0	1714.4856612860078	2	10855	415	29797	7	5	4	0	29	1.91	605.61	19.14	1060.57	0.35	0.25	0.12	0	1.01	2.00	615.10	19.41	1078.17	0.38	0.26	0.13	0	1.05	1.91	10686.31	409.42	29309.69	6.60	4.99	3.72	0	27.98	NA	NA	Homo sapiens	diarrhea								0.9367183790533192	
strain	Escherichia coli SMS-3-5	1300		439855	33117	1300.70	2.77	4971094	50086	1247669	3.9843	Pathogen	0.9317	0.0039	1300	0.2462		0.7997	1080	142017.82724252492	8150.149767828253	3	33114	3.0	1297.6956437300291	3	7643	269	25145	1	0	1	2	53	2.77	394.72	11.45	868.43	0.04	0	0.03	0.16	1.99	3.00	401.43	11.68	882.32	0.04	0	0.03	0.16	2.03	2.77	7515.93	264.21	24750.77	1.00	0	0.99	1.99	51.80	perirectal swab	USA	Homo sapiens	Gastroenteritis								0.9316753610032443	
strain	Escherichia coli ED1a	915		585397	24212	915.57	2.80	3631934	36725	960926	3.7796	Pathogen	0.9295	0.0027	915	0.1845		0.5477	864	142017.82724252492	8150.149767828253	3	24209	3.0	912.571091515653	3	6162	188	17850	0	0	1	0	8	2.80	281.57	6.74	609.01	0	0	0.11	0	0.25	3.00	286.15	6.85	619.20	0	0	0.11	0	0.26	2.80	6059.31	184.77	17553.70	0	0	1.00	0	7.74	NA	NA	Homo sapiens	Gastroenteritis								0.9294978539888312	
strain	Escherichia coli CFT073	773		199310	21871	773.15	1.94	3281685	33172	942060	3.4835	Pathogen	0.9286	0.0023	773	0.1801		0.4605	640	94678.55149501661	5433.433178552168	2	21869	2.0	771.14797087838	2	5302	257	16284	9	0	0	0	17	1.94	213.31	9.11	534.78	0.72	0	0	0	0.53	2.00	217.25	9.23	543.41	0.72	0	0	0	0.55	1.94	5206.49	253.62	16025.79	8.98	0	0	0	16.50	NA	USA: Maryland	Homo sapiens	Urinary tract infection								0.9285992232017007	
strain	Escherichia fergusonii ATCC 35469	296		585054	6109	296.88	1.74	915474	9209	269680	3.3947		0.9333	0.0009	296	0.0588		0.2016	225	94678.55149501661	5433.433178552168	2	6107	2.0	294.8838623496187	2	0	1712	4390	4	0	0	0	1	1.74	0	133.98	155.06	0.15	0	0	0	0.03	2.00	0	136.91	157.78	0.15	0	0	0	0.03	1.74	0	1676.88	4318.24	3.90	0	0	0	1.00												0.9333418574355385	
strain	Encephalomyocarditis virus	57		12104.3	168	57.63	45.63	23108	658	864	26.7454	Pathogen	0.8069	0.0002	57	0.0184		3.8202	57	5112641.780730897	130402.39628525205	108	60	48.0	9.633333333333333	108	58	0	0	0	0	0	0	2	45.63	7.31	0	0	0	0	0	0	0.38	48.00	9.13	0	0	0	0	0	0	0.50	101.22	45.95	0	0	0	0	0	0	1.51			glis glis; Homo sapiens; mus musculus; pan paniscus; pan troglodytes; rattus norvegicus; sus scrofa; sus scrofa domesticus; tamiasciurus hudsonicus	Encephalitis								0.8068983605913069	
