view test-data/beta_bracken_3.tabular @ 0:bc508fe30940 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools commit 3dfd5d7d5870695d24d2ede7b321bcaac25e0209
author iuc
date Fri, 13 Jan 2023 13:22:07 +0000
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name	taxonomy_id	taxonomy_lvl	kraken_assigned_reads	added_reads	new_est_reads	fraction_total_reads
Enterococcus faecium	1352	S	19117311	5606915	24724226	0.91976
Enterococcus avium	33945	S	185099	8604	193703	0.00721
Enterococcus faecalis	1351	S	23719	2158	25877	0.00096
Enterococcus durans	53345	S	21563	1616	23179	0.00086
Enterococcus hirae	1354	S	18570	853	19423	0.00072
Enterococcus lactis	357441	S	14452	35311	49763	0.00185
Enterococcus mundtii	53346	S	13586	228	13814	0.00051
Enterococcus casseliflavus	37734	S	11263	3466	14729	0.00055
Enterococcus sp. FDAARGOS_375	2060307	S	5363	6531	11894	0.00044
Enterococcus sp. DA9	2603296	S	3725	15804	19529	0.00073
Enterococcus sp. FDAARGOS_553	2420313	S	339	1348	1687	0.00006
Enterococcus sp. M190262	2582830	S	162	175	337	0.00001
Enterococcus sp. CR-Ec1	2057791	S	58	52	110	0.00000
Enterococcus thailandicus	417368	S	5457	126	5583	0.00021
Enterococcus cecorum	44008	S	2805	68	2873	0.00011
Enterococcus saigonensis	1805431	S	2378	312	2690	0.00010
Enterococcus rotai	118060	S	1300	3	1303	0.00005
Enterococcus raffinosus	71452	S	1102	0	1102	0.00004
Enterococcus gilvus	160453	S	246	8	254	0.00001
Enterococcus gallinarum	1353	S	190	300	490	0.00002
Enterococcus wangshanyuanii	2005703	S	147	0	147	0.00001
Enterococcus innesii	2839759	S	72	0	72	0.00000
Vagococcus carniphilus	218144	S	693	52	745	0.00003
Vagococcus fluvialis	2738	S	281	0	281	0.00001
Vagococcus penaei	633807	S	62	1	63	0.00000
Vagococcus teuberi	519472	S	52	1	53	0.00000
Vagococcus lutrae	81947	S	33	0	33	0.00000
Vagococcus xieshaowenii	2562451	S	25	3	28	0.00000
Vagococcus zengguangii	2571750	S	24	2	26	0.00000
Vagococcus coleopterorum	2714946	S	12	0	12	0.00000
Tetragenococcus koreensis	290335	S	423	44	467	0.00002
Tetragenococcus halophilus	51669	S	82	10	92	0.00000
Tetragenococcus osmophilus	526944	S	52	14	66	0.00000
Melissococcus plutonius	33970	S	13	0	13	0.00000
Streptococcus thermophilus	1308	S	91845	3570	95415	0.00355
Streptococcus pyogenes	1314	S	2298	203	2501	0.00009
Streptococcus suis	1307	S	1790	39	1829	0.00007
Streptococcus agalactiae	1311	S	1315	1759	3074	0.00011
Streptococcus cristatus	45634	S	772	702	1474	0.00005
Streptococcus parauberis	1348	S	174	7	181	0.00001
Streptococcus pneumoniae	1313	S	156	159	315	0.00001
Streptococcus salivarius	1304	S	96	7	103	0.00000
Streptococcus infantis	68892	S	93	113	206	0.00001
Streptococcus sp. HSISS2	1316411	S	16	1	17	0.00000
Streptococcus sp. DAT741	1940319	S	16	2	18	0.00000
Streptococcus sp. HSISS3	1316412	S	11	1	12	0.00000
Streptococcus dysgalactiae	1334	S	47	17	64	0.00000
Streptococcus equi	1336	S	12	0	12	0.00000
Streptococcus gallolyticus	315405	S	54	7	61	0.00000
Streptococcus anginosus	1328	S	25	4	29	0.00000
Streptococcus constellatus	76860	S	16	103	119	0.00000
Streptococcus mitis	28037	S	42	1	43	0.00000
Streptococcus lutetiensis	150055	S	39	18	57	0.00000
Streptococcus pluranimalium	82348	S	30	0	30	0.00000
Streptococcus gordonii	1302	S	24	0	24	0.00000
Streptococcus vestibularis	1343	S	22	0	22	0.00000
Streptococcus pasteurianus	197614	S	20	18	38	0.00000
Streptococcus iniae	1346	S	20	0	20	0.00000
Streptococcus oralis	1303	S	17	0	17	0.00000
Streptococcus parasuis	1501662	S	16	0	16	0.00000
Streptococcus mutans	1309	S	11	0	11	0.00000
Streptococcus equinus	1335	S	10	0	10	0.00000
Lactococcus lactis	1358	S	554	571	1125	0.00004
Lactococcus raffinolactis	1366	S	255	9	264	0.00001
Lactococcus cremoris	1359	S	253	85	338	0.00001
Lactococcus garvieae	1363	S	223	40	263	0.00001
Lactococcus piscium	1364	S	22	18	40	0.00000
Lactococcus taiwanensis	1151742	S	16	0	16	0.00000
Lactococcus sp. LG606	2816912	S	10	9	19	0.00000
Jeotgalibaca sp. PTS2502	1903686	S	3404	392	3796	0.00014
Jeotgalibaca arthritidis	1868794	S	59	7	66	0.00000
Jeotgalibaca ciconiae	2496265	S	27	0	27	0.00000
Jeotgalibaca porci	1868793	S	25	1	26	0.00000
Granulicatella adiacens	46124	S	1042	0	1042	0.00004
Granulicatella elegans	137732	S	46	0	46	0.00000
Carnobacterium viridans	174587	S	93	0	93	0.00000
Carnobacterium maltaromaticum	2751	S	63	14	77	0.00000
Carnobacterium divergens	2748	S	56	5	61	0.00000
Carnobacterium inhibens	147709	S	24	6	30	0.00000
Marinilactibacillus sp. 15R	1911586	S	50	1	51	0.00000
Dolosigranulum pigrum	29394	S	17	0	17	0.00000
Limosilactobacillus vaginalis	1633	S	831	20	851	0.00003
Limosilactobacillus reuteri	1598	S	704	22	726	0.00003
Limosilactobacillus fermentum	1613	S	73	10	83	0.00000
Leuconostoc gelidum	1244	S	866	0	866	0.00003
Leuconostoc citreum	33964	S	37	23	60	0.00000
Leuconostoc lactis	1246	S	25	3	28	0.00000
Lactobacillus sp. wkB8	1545702	S	302	8	310	0.00001
Lactobacillus delbrueckii	1584	S	276	4	280	0.00001
Lactobacillus acidophilus	1579	S	43	19	62	0.00000
Lactobacillus jensenii	109790	S	18	1	19	0.00000
Lactobacillus iners	147802	S	17	0	17	0.00000
Lactobacillus johnsonii	33959	S	16	0	16	0.00000
Lactobacillus amylovorus	1604	S	14	0	14	0.00000
Lactobacillus acetotolerans	1600	S	12	0	12	0.00000
Lactobacillus helveticus	1587	S	10	0	10	0.00000
Weissella cibaria	137591	S	121	10	131	0.00000
Weissella jogaejeotgali	1631871	S	84	10	94	0.00000
Weissella hellenica	46256	S	18	1	19	0.00000
Weissella confusa	1583	S	15	1	16	0.00000
Ligilactobacillus salivarius	1624	S	153	4	157	0.00001
Ligilactobacillus murinus	1622	S	64	4	68	0.00000
Ligilactobacillus ruminis	1623	S	15	0	15	0.00000
Ligilactobacillus agilis	1601	S	14	0	14	0.00000
Lactiplantibacillus plantarum	1590	S	137	200	337	0.00001
Lactiplantibacillus paraplantarum	60520	S	11	0	11	0.00000
Pediococcus acidilactici	1254	S	68	2	70	0.00000
Pediococcus pentosaceus	1255	S	24	1	25	0.00000
Pediococcus damnosus	51663	S	11	1	12	0.00000
Latilactobacillus curvatus	28038	S	51	2	53	0.00000
Latilactobacillus sakei	1599	S	47	3	50	0.00000
Lacticaseibacillus paracasei	1597	S	34	17	51	0.00000
Levilactobacillus brevis	1580	S	35	3	38	0.00000
Periweissella cryptocerci	2506420	S	29	0	29	0.00000
Fructilactobacillus sanfranciscensis	1625	S	15	0	15	0.00000
Loigolactobacillus coryniformis	1610	S	10	2	12	0.00000
Acetilactobacillus jinshanensis	1720083	S	12	0	12	0.00000
Ignavigranum ruoffiae	89093	S	1065	0	1065	0.00004
Aerococcus urinaeequi	51665	S	137	19	156	0.00001
Aerococcus viridans	1377	S	89	22	111	0.00000
Suicoccus acidiformans	2036206	S	10	0	10	0.00000
Staphylococcus aureus	1280	S	12774	12776	25550	0.00095
Staphylococcus pseudintermedius	283734	S	1516	42	1558	0.00006
Staphylococcus warneri	1292	S	176	16	192	0.00001
Staphylococcus haemolyticus	1283	S	102	3	105	0.00000
Staphylococcus epidermidis	1282	S	51	1	52	0.00000
Staphylococcus argenteus	985002	S	13	5	18	0.00000
Staphylococcus hominis	1290	S	13	0	13	0.00000
Staphylococcus xylosus	1288	S	11	0	11	0.00000
Nosocomiicoccus ampullae	489910	S	143	0	143	0.00001
Mammaliicoccus sciuri	1296	S	65	3	68	0.00000
Mammaliicoccus vitulinus	71237	S	11	0	11	0.00000
Abyssicoccus albus	1817405	S	33	0	33	0.00000
Bacillus subtilis	1423	S	5091	4934	10025	0.00037
Bacillus velezensis	492670	S	210	43	253	0.00001
Bacillus amyloliquefaciens	1390	S	63	90	153	0.00001
Bacillus licheniformis	1402	S	62	8	70	0.00000
Bacillus sp. NSP9.1	1071078	S	1635	4	1639	0.00006
Bacillus sp. LJBS17	2859227	S	39	0	39	0.00000
Bacillus sp. ZY-1-1	2093834	S	12	6	18	0.00000
Bacillus sp. COPE52	2233998	S	12	4	16	0.00000
Bacillus sp. OxB-1	98228	S	11	0	11	0.00000
Bacillus sp. 7D3	2851015	S	10	0	10	0.00000
Bacillus thuringiensis	1428	S	255	177	432	0.00002
Bacillus cereus	1396	S	235	464	699	0.00003
Bacillus anthracis	1392	S	166	254	420	0.00002
Bacillus mycoides	1405	S	86	1	87	0.00000
Bacillus wiedmannii	1890302	S	65	0	65	0.00000
Bacillus cytotoxicus	580165	S	13	0	13	0.00000
Bacillus pseudomycoides	64104	S	12	0	12	0.00000
Bacillus altitudinis	293387	S	32	1	33	0.00000
Bacillus aquiflavi	2672567	S	21	0	21	0.00000
Bacillus safensis	561879	S	11	0	11	0.00000
Bacillus methanolicus	1471	S	10	0	10	0.00000
Anoxybacillus sediminis	2613334	S	5062	0	5062	0.00019
Lysinibacillus sphaericus	1421	S	59	20	79	0.00000
Lysinibacillus timonensis	2086577	S	31	0	31	0.00000
Lysinibacillus sp. SGAir0095	2070463	S	14	0	14	0.00000
Lysinibacillus agricola	2590012	S	11	0	11	0.00000
Metabacillus sp. B2-18	2897333	S	85	0	85	0.00000
Metabacillus endolithicus	1535204	S	24	0	24	0.00000
Metabacillus litoralis	152268	S	11	3	14	0.00000
Priestia megaterium	1404	S	28	14	42	0.00000
Priestia flexa	86664	S	19	0	19	0.00000
Virgibacillus sp. 6R	1911587	S	21	6	27	0.00000
Virgibacillus sp. Bac330	2419841	S	11	0	11	0.00000
Cytobacillus oceanisediminis	665099	S	38	0	38	0.00000
Weizmannia coagulans	1398	S	28	4	32	0.00000
Niallia circulans	1397	S	22	0	22	0.00000
Gracilibacillus sp. SSPM10-3	2932255	S	15	0	15	0.00000
Heyndrickxia oleronia	38875	S	12	0	12	0.00000
Halalkalibacterium halodurans	86665	S	14	3	17	0.00000
Neobacillus mesonae	1193713	S	10	0	10	0.00000
Anaerobacillus isosaccharinicus	1532552	S	11	0	11	0.00000
Listeria monocytogenes	1639	S	3960	262	4222	0.00016
Listeria innocua	1642	S	61	12	73	0.00000
Listeria grayi	1641	S	28	0	28	0.00000
Listeria ivanovii	1638	S	11	0	11	0.00000
Brochothrix thermosphacta	2756	S	1155	17	1172	0.00004
Brevibacillus laterosporus	1465	S	287	67	354	0.00001
Paenibacillus physcomitrellae	1619311	S	31	19	50	0.00000
Paenibacillus larvae	1464	S	24	81	105	0.00000
Paenibacillus bovis	1616788	S	22	2	24	0.00000
Paenibacillus sonchi	373687	S	20	17	37	0.00000
Paenibacillus jilunlii	682956	S	17	21	38	0.00000
Paenibacillus uliginis	683737	S	11	1	12	0.00000
Sporosarcina sp. PTS2304	2283194	S	64	5	69	0.00000
Solibacillus silvestris	76853	S	38	2	40	0.00000
Solibacillus sp. R5-41	2048654	S	17	0	17	0.00000
Planococcus sp. 107-1	2908840	S	14	0	14	0.00000
Planococcus antarcticus	161360	S	11	7	18	0.00000
Exiguobacterium sp. S3-2	1389960	S	20	24	44	0.00000
Thermoactinomyces vulgaris	2026	S	41	0	41	0.00000
[Ruminococcus] gnavus	33038	S	351	64	415	0.00002
[Ruminococcus] torques	33039	S	22	5	27	0.00000
Blautia obeum	40520	S	86	13	99	0.00000
Blautia sp. SC05B48	2479767	S	42	5	47	0.00000
Blautia sp. NBRC 113351	2877527	S	19	0	19	0.00000
Blautia producta	33035	S	55	1	56	0.00000
Blautia massiliensis	1737424	S	40	0	40	0.00000
Blautia argi	1912897	S	31	1	32	0.00000
Blautia hansenii	1322	S	24	8	32	0.00000
Blautia pseudococcoides	1796616	S	20	554	574	0.00002
Anaerostipes hadrus	649756	S	333	27	360	0.00001
Anaerobutyricum hallii	39488	S	149	40	189	0.00001
Coprococcus comes	410072	S	102	20	122	0.00000
Coprococcus catus	116085	S	27	3	30	0.00000
Enterocloster bolteae	208479	S	88	8	96	0.00000
Enterocloster clostridioformis	1531	S	25	55	80	0.00000
Sellimonas intestinalis	1653434	S	83	0	83	0.00000
[Clostridium] scindens	29347	S	56	3	59	0.00000
Faecalicatena sp. Marseille-Q4148	2823316	S	50	0	50	0.00000
Roseburia intestinalis	166486	S	21	6	27	0.00000
Roseburia hominis	301301	S	14	3	17	0.00000
Dorea longicatena	88431	S	31	0	31	0.00000
Anaerocolumna cellulosilytica	433286	S	12	0	12	0.00000
Lachnospira eligens	39485	S	14	0	14	0.00000
Ruthenibacterium lactatiformans	1550024	S	1403	14	1417	0.00005
Pseudoclostridium thermosuccinogenes	84032	S	34	0	34	0.00000
Caproiciproducens sp. NJN-50	2507162	S	33	0	33	0.00000
Faecalibacterium prausnitzii	853	S	25	0	25	0.00000
Solibaculum mannosilyticum	2780922	S	20	0	20	0.00000
Flavonifractor plautii	292800	S	20	0	20	0.00000
Clostridioides difficile	1496	S	1266	173	1439	0.00005
Clostridium perfringens	1502	S	77	1	78	0.00000
Clostridium tetani	1513	S	35	0	35	0.00000
Clostridium botulinum	1491	S	12	15	27	0.00000
Clostridium intestinale	36845	S	12	0	12	0.00000
Clostridium tyrobutyricum	1519	S	11	0	11	0.00000
Clostridium beijerinckii	1520	S	11	2	13	0.00000
Eubacterium sp. NSJ-61	2764325	S	56	2	58	0.00000
Mogibacterium pumilum	86332	S	25	2	27	0.00000
Christensenella minuta	626937	S	20	0	20	0.00000
Veillonella parvula	29466	S	857	2	859	0.00003
Phascolarctobacterium faecium	33025	S	21	1	22	0.00000
Parvimonas micra	33033	S	625	22	647	0.00002
Amedibacterium intestinale	2583452	S	145	6	151	0.00001
[Clostridium] innocuum	1522	S	73	1	74	0.00000
Erysipelatoclostridium ramosum	1547	S	68	0	68	0.00000
Faecalibacillus intestinalis	1982626	S	98	17	115	0.00000
Erysipelothrix larvae	1514105	S	17	0	17	0.00000
Erysipelothrix rhusiopathiae	1648	S	14	0	14	0.00000
Longicatena caecimuris	1796635	S	25	0	25	0.00000
Turicibacter sp. TJ11	2806443	S	10	0	10	0.00000
Actinomyces sp. oral taxon 414	712122	S	136	13	149	0.00001
Arcanobacterium haemolyticum	28264	S	21	2	23	0.00000
Schaalia odontolytica	1660	S	10	0	10	0.00000
Mycobacterium tuberculosis	1773	S	17	8	25	0.00000
Bifidobacterium longum	216816	S	53	3	56	0.00000
Cutibacterium acnes	1747	S	14	1	15	0.00000
Eggerthella lenta	84112	S	135	12	147	0.00001
Mycoplasma mycoides	2102	S	250	2	252	0.00001
Mycoplasma capricolum	2095	S	24	6	30	0.00000
Mycoplasmopsis bovirhinis	29553	S	32	0	32	0.00000
Mycoplasmopsis gallinacea	29556	S	19	0	19	0.00000
Klebsiella pneumoniae	573	S	460831	1030977	1491808	0.05550
Klebsiella quasipneumoniae	1463165	S	4116	19763	23879	0.00089
Klebsiella variicola	244366	S	4115	7438	11553	0.00043
Klebsiella quasivariicola	2026240	S	1304	483	1787	0.00007
Klebsiella africana	2489010	S	959	238	1197	0.00004
Klebsiella sp. WP4-W18-ESBL-05	2675713	S	547	1351	1898	0.00007
Klebsiella sp. PL-2018	2851540	S	46	0	46	0.00000
Klebsiella sp. CTHL.F3a	2873296	S	45	0	45	0.00000
Klebsiella sp. A52	2834819	S	43	0	43	0.00000
Klebsiella sp. KPN54798	2897413	S	30	0	30	0.00000
Klebsiella sp. P1CD1	2267618	S	21	129	150	0.00001
Klebsiella aerogenes	548	S	815	92	907	0.00003
Klebsiella michiganensis	1134687	S	547	11082	11629	0.00043
Klebsiella oxytoca	571	S	519	180	699	0.00003
Klebsiella grimontii	2058152	S	241	1042	1283	0.00005
Klebsiella huaxiensis	2153354	S	124	13	137	0.00001
Raoultella ornithinolytica	54291	S	316	170	486	0.00002
Raoultella planticola	575	S	56	5	61	0.00000
Raoultella sp. XY-1	2799495	S	10	38	48	0.00000
Escherichia coli	562	S	2179	23338	25517	0.00095
Escherichia fergusonii	564	S	17	4	21	0.00000
Escherichia marmotae	1499973	S	17	1	18	0.00000
Escherichia albertii	208962	S	13	1	14	0.00000
Enterobacter cloacae complex sp. ECL411	2912629	S	232	0	232	0.00001
Enterobacter cloacae complex sp.	2027919	S	51	23	74	0.00000
Enterobacter hormaechei	158836	S	267	223	490	0.00002
Enterobacter cloacae	550	S	224	59	283	0.00001
Enterobacter roggenkampii	1812935	S	201	75	276	0.00001
Enterobacter asburiae	61645	S	38	12	50	0.00000
Enterobacter kobei	208224	S	25	14	39	0.00000
Enterobacter ludwigii	299767	S	11	2	13	0.00000
Enterobacter cancerogenus	69218	S	10	0	10	0.00000
Enterobacter sp. JBIWA005	2831891	S	609	0	609	0.00002
Enterobacter sp. DNB-S2	2720029	S	14	0	14	0.00000
Enterobacter mori	539813	S	277	81	358	0.00001
Salmonella enterica	28901	S	368	1315	1683	0.00006
Salmonella sp.	599	S	43	1737	1780	0.00007
Citrobacter freundii	546	S	137	88	225	0.00001
Citrobacter portucalensis	1639133	S	33	40	73	0.00000
Citrobacter arsenatis	2546350	S	66	9	75	0.00000
Citrobacter amalonaticus	35703	S	14	10	24	0.00000
Leclercia adecarboxylata	83655	S	176	35	211	0.00001
Leclercia sp. J807	2681307	S	62	2	64	0.00000
Shigella boydii	621	S	84	252	336	0.00001
Shigella flexneri	623	S	64	214	278	0.00001
Shigella dysenteriae	622	S	12	136	148	0.00001
Cronobacter sakazakii	28141	S	35	47	82	0.00000
Cronobacter universalis	535744	S	13	0	13	0.00000
Kosakonia radicincitans	283686	S	16	19	35	0.00000
Yokenella regensburgei	158877	S	38	1	39	0.00000
Jejubacter calystegiae	2579935	S	29	0	29	0.00000
Pluralibacter gergoviae	61647	S	10	0	10	0.00000
Lelliottia amnigena	61646	S	14	0	14	0.00000
Pectobacterium aquaticum	2204145	S	1547	0	1547	0.00006
Serratia fonticola	47917	S	723	13	736	0.00003
Serratia marcescens	615	S	42	6	48	0.00000
Serratia symbiotica	138074	S	11	0	11	0.00000
Yersinia ruckeri	29486	S	246	3	249	0.00001
Pantoea stewartii	66269	S	333	15	348	0.00001
Pantoea agglomerans	549	S	14	0	14	0.00000
Pantoea dispersa	59814	S	11	0	11	0.00000
Proteus mirabilis	584	S	19	2	21	0.00000
Arsenophonus endosymbiont of Aphis craccivora	1231049	S	14	0	14	0.00000
Morganella morganii	582	S	11	8	19	0.00000
Edwardsiella tarda	636	S	10	5	15	0.00000
Vibrio cholerae	666	S	13	1	14	0.00000
Photobacterium damselae	38293	S	11	1	12	0.00000
Gallibacterium anatis	750	S	12	0	12	0.00000
Acinetobacter baumannii	470	S	17	6	23	0.00000
Campylobacter coli	195	S	398	5	403	0.00001
Campylobacter jejuni	197	S	58	5	63	0.00000
Campylobacter sp. RM10537	1032242	S	10	0	10	0.00000
Helicobacter pylori	210	S	12	0	12	0.00000
Neisseria meningitidis	487	S	12	3	15	0.00000
Prevotella nigrescens	28133	S	48	0	48	0.00000
Prevotella enoeca	76123	S	42	11	53	0.00000
Prevotella intermedia	28131	S	11	4	15	0.00000
Phocaeicola vulgatus	821	S	34	22	56	0.00000
Tannerella forsythia	28112	S	14	1	15	0.00000
Porphyromonas endodontalis	28124	S	20	0	20	0.00000
Butyricimonas faecalis	2093856	S	12	11	23	0.00000
Polaribacter sp. HaHaR_3_91	2745561	S	13	0	13	0.00000
Treponema sp. Marseille-Q4132	2766701	S	15	2	17	0.00000
Treponema socranskii	53419	S	15	2	17	0.00000
Fusobacterium necrophorum	859	S	24	1	25	0.00000
Fusobacterium nucleatum	851	S	18	0	18	0.00000
Homo sapiens	9606	S	363	0	363	0.00001
Malassezia restricta	76775	S	20	0	20	0.00000
Sporisorium graminicola	280036	S	10	0	10	0.00000