Consistency of metagenomic assignment programs in simulated and real data

Garcia-Etxebarria, Koldo; Garcia-Garcerà, Marc; Calafell, Francesc

doi:10.1186/1471-2105-15-90

BMC Bioinformatics

Table 1 Percentage sensitivity and precision in simulated datasets

From: Consistency of metagenomic assignment programs in simulated and real data

	Sensitivity				Precision
	Phymm	Bayesian	BLAST + LCA	Combined	Phymm	Bayesian	BLAST + LCA	Combined
Domain
All genomes	79.45	98.41	98.97	99.16	79.46	98.41	98.97	99.90
All genomes (dominant)	87.36	100	100	100	87.36	100	100	100
Bact genomes	73.05	87.98	96.31	91.28	73.05	87.98	96.32	92.80
Bact genomes (dominant)	74.08	100	100	100	74.08	100	100	100
Synthetic	89.46	99.99	97.99	99.99	89.46	100	100	100
Phylum
All genomes	22.37	39.65	47.60	41.18	39.65	78.99	93.76	95.46
All genomes (dominant)	19.20	31.16	31.16	31.16	85.31	100	100	100
Bact genomes	44.67	64.59	92.83	75.11	53.75	68.03	92.84	94.66
Bact genomes (dominant)	25.22	49.81	100	53.40	34.04	49.81	100	84.10
Synthetic	23.13	40.12	49.73	40.31	23.13	40.12	66.87	40.31
Class
All genomes	21.45	39.30	47.51	40.46	30.40	78.31	93.58	94.91
All genomes (dominant)	15.12	31.16	31.16	31.16	68.66	100	100	100
Bact genomes	34.24	60.43	95.22	71.72	42.65	63.65	95.23	94.79
Bact genomes (dominant)	25.22	25.82	100	43.78	34.04	25.82	100	91.41
Synthetic	5.03	30.56	45.69	30.56	5.03	30.56	61.43	30.56
Order
All genomes	26.55	38.23	47.60	40.45	39.40	78.32	93.58	94.91
All genomes (dominant)	15.12	31.16	31.16	31.16	67.41	31.16	31.16	31.16
Bact genomes	22.24	56.07	95.22	71.72	42.64	63.64	95.22	94.79
Bact genomes (dominant)	0	41.40	100	41.40	0	41.40	100	78.45
Synthetic	4.7	30.56	45.69	30.56	4.7	30.56	61.43	30.56
Family
All genomes	25.31	38.15	47.60	39.37	32.86	39.15	48.84	45.67
All genomes (dominant)	15.12	31.16	31.16	31.16	51.82	31.16	31.16	31.16
Bact genomes	20.18	50.89	95.22	66.06	26.69	56.87	95.22	92.83
Bact genomes (dominant)	0	41.40	100	41.40	0	41.40	100	78.45
Synthetic	0	30.56	45.69	30.56	0	30.56	61.43	30.56
Genus
All genomes	25.30	37.97	47.60	39.17	32.37	38.95	48.84	45.56
All genomes (dominant)	15.12	31.16	31.16	31.16	50.41	31.16	31.16	31.16
Bact genomes	15.56	45.56	95.22	54.23	17.44	46.18	95.23	91.36
Bact genomes (dominant)	0	8.22	100	8.22	0	8.22	100	41.97
Synthetic	NA	NA	NA	NA	NA	NA	NA	NA
Species
All genomes	17.94	36.44	24.46	23.03	17.94	36.44	24.46	32.89
All genomes (dominant)	0	31.16	10.86	10.86	0	31.16	10.86	13.62
Bact genomes	13.12	39.75	73.71	32.96	13.12	39.75	73.72	92.45
Bact genomes (dominant)	0	8.22	100	8.22	0	8.22	100	90.18
Synthetic	NA	NA	NA	NA	NA	NA	NA	NA

NA, not applicable. In the case of the Synthetic set, genus and species levels are not applicable since the “evolved” genomes were based on these or higher levels. The features of each dataset is explained in Methods and their descriptive and diversity parameters in Additional file 1: Table S1.

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