Table 3.
Description of database fields in ARB files exported from SILVA for SILVA specific fields and entries
| ARB field name | Description |
|---|---|
| align_bp_score_slv | Calculates the number of bases in helices in the aligned sequence taken into account canonical and non canonical basepairing. The cost matrix is taken from ARB Probe_Match (8) |
| align_cutoff_head_slv | Unaligned bases at the beginning of the sequence |
| align_cutoff_tail_slv | Unaligned bases at the end of the sequence |
| align_family_slv | Names and scores of reference sequences in the alignment process |
| align_log_slv | Detailed aligner comments |
| align_quality_slv | Maximal similarity to reference sequence in the seed |
| aligned_slv | Data and time of alignment by Silva |
| ambig_slv | Calculated percent ambiguities in the sequences, a maximum of 2% is allowed |
| homop_slv | Calculated percentages repetitive bases with more than four bases, a maximum of 2% is allowed |
| homop_events_slv | Absolute number of repetitive elements with more than four bases |
| nuc_gene_slv | Aligned bases within gene boundaries |
| pintail_slv | Information about potential sequence anomalies detected by Pintail (22); 100 means no anomalies found. |
| alternative_name_slv | Synonyms or basonyms of the species according to the DSMZ ‘nomenclature up to date’ catalogue |
| seq_quality_slv | Summary sequence quality value calculated based on values from vector, ambiguities and homopolymers, 100 means very good |
| tax_gg | Taxonomy mapped from greengenes |
| tax_gg_name | Organism name in greengenes |
| tax_rdp | Nomenclatural taxonomy mapped from RDP II |
| tax_rdp_name | Organism name in RDP II |
| vector_slv | Percent vector contamination, a maximum of 5% is allowed |