Table 1. Percentages of total reads assigned at different taxonomic levels with different read length cut-offs.

Fragment length	Reads assigned total	Reads assigned genus	Reads assigned species
30 bp_MALTn-Genome	100	100	97
30 bp_MALTn-CDS	86	86	83
30 bp_MALTx	0	0	0
50 bp_MALTn-Genome	100	100	98
50 bp_MALTn-CDS	88	88	86
50 bp_MALTx	0	0	0
70 bp_MALTn-Genome	100	100	98
70 bp_MALTn-CDS	90	90	88
70 bp_MALTx	33	31	25
90 bp_MALTn-Genome	100	100	98
90 bp_MALTn-CDS	91	91	89
90 bp_MALTx	82	75	55
Empirical_MALTn-Genome	99	98	97
Empirical_MALTn-CDS	87	87	86
Empirical_MALTx	16	14	10