USEARCH manual

‑uparseout option

Output file, UPARSE tabbed format. Supported by cluster_otus and uparse_ref. There are five or six fields, as shown in the following table.

Field		Description
1		Query label.
2		Classification. For cluster_otus, this field is otu, match or chimera. otu: New OTU. Sequence is <97% to existing OTU and is not chimeric. match: Assigned to existing OTU (>= 97% match). chimera: Sequence is chimeric. For uparse_ref, it is perfect, good, noisy, chimera or other. perfect: 100% match to a reference sequence. good: >=99% match to reference sequence. noisy: >= 97% match to reference sequence chimera: matches chimeric model constructed from reference sequences other: < 97% match and not chimeric.
3		Percent identity between the query sequence and the top hit in the reference database. With cluster_otus, the reference database is the current set of OTUs. If no hit was found, this field is set to *,
4		Percent identity between the query sequence and the maximum parsimony model. If no model is made, e.g. because the database is empty, then this field is set to *.
5		OTU label(s). If the model is chimeric, then the labels and start-end segment coordinates are given. Otherwise, the label of the reference sequence. For cluster_otus, this will be the label of an existing OTU. If no model is constructed, this field is set to *.
6		New label. This field is included only with cluster_otus when the -relabel option is specified. For new OTUs (otu in field 2), this original label is in field 1 and the new label is in field 6.

Example output

Even1.7;size=4383;   otu      *     *       OTU_1
Even1.145;size=21;   otu      *     *       OTU_2
Even1.1733;size=20; match    99.5 *       OTU_2
Even1.942;size=20;   chimera 94.0 100.0   OTU_1(1-141)+OTU_2(142-200)
Even1.1821;size=20; match    98.5 *       OTU_1
Even1.1415;size=19; match    97.0 *       OTU_2