- ac: Accession number of the ecoPCR record used as template. (
obiconvert)
- aho_corasick: Total number of occurrences of the provided motifs detected by the Aho–Corasick search. (
obiannotate)
- aho_corasick_Fwd: Number of motif matches on the forward strand when running the Aho–Corasick scanner. (
obiannotate)
- aho_corasick_Rev: Number of motif matches on the reverse complement strand produced by the Aho–Corasick scanner. (
obiannotate)
- ali_dir: Orientation of the alignment window when overlapping reads are aligned ("left" or "right"). (
obikmersim,
obipairing)
- ali_length: Length of the aligned region considered when assembling paired reads. (
obikmersim,
obipairing)
- amplicon_length: Expected size of the in silico amplicon described in an ecoPCR record. (
obiconvert)
- chimera: Flag produced by obiclean identifying sequences detected as chimeric. (
obiclean)
- count: Number of occurrences of the dereplicated sequence in the dataset.
- definition: Text description kept from the original FASTA/FASTQ definition line.
- demultiplex_error: Human‑readable reason explaining why a read could not be assigned to a PCR sample. (
obimultiplex,
obipcr)
- direction: Orientation of the read with respect to the primer set (forward or reverse). (
obimultiplex,
obipcr)
- experiment: Experiment identifier assigned to each multiplexed sample in the NGS filter. (
obimultiplex,
obitagpcr)
- family_name: Scientific name of the family containing the ecoPCR reference sequence. (
obiconvert)
- family_taxid: NCBI taxid of the family containing the ecoPCR reference sequence. (
obiconvert)
- forward_error: Number of mismatches tolerated between the read and the forward primer. (
obimultiplex,
obipcr)
- forward_match: Sequence of the forward primer match extracted from the read. (
obimultiplex,
obipcr)
- forward_mismatch: Mismatch count reported in ecoPCR reference entries for the forward primer. (
obiconvert)
- forward_primer: Forward primer sequence used while demultiplexing or during in silico PCR. (
obiconvert,
obimultiplex,
obipcr)
- forward_tag: Sample tag (index) identified on the forward side of a read. (
obimultiplex,
obipcr)
- forward_tm: Melting temperature of the forward primer reported by ecoPCR. (
obiconvert)
- genus_name: Scientific name of the genus containing the ecoPCR reference sequence. (
obiconvert)
- genus_taxid: NCBI taxid of the genus containing the ecoPCR reference sequence. (
obiconvert)
- landmark_coord: Coordinate of a reference sequence in the landmark space produced by obilandmark. (
obilandmark)
- landmark_id: Identifier of the landmark sequence used as axis when building the landmark space. (
obilandmark)
- merged_sample: Map storing the abundance of each sample contributing to a merged record. (
obimatrix,
obiuniq)
- microsat: Sequence of the detected microsatellite region. (
obimicrosat)
- microsat_from: 1-based start position of the detected microsatellite. (
obimicrosat)
- microsat_left: Left flanking region kept around the detected microsatellite. (
obimicrosat)
- microsat_right: Right flanking region kept around the detected microsatellite. (
obimicrosat)
- microsat_to: End position (1-based, inclusive) of the detected microsatellite. (
obimicrosat)
- microsat_unit: Minimal repeat unit sequence describing the microsatellite. (
obimicrosat)
- microsat_unit_count: Number of times the minimal unit is repeated inside the microsatellite. (
obimicrosat)
- microsat_unit_length: Length (in bases) of the minimal repeat unit in the microsatellite. (
obimicrosat)
- microsat_unit_normalized: Canonical representation of the repeat unit, normalized for strand orientation. (
obimicrosat)
- microsat_unit_orientation: Orientation ("direct" or "reverse") of the repeat unit with respect to the original read. (
obimicrosat)
- mode: Whether a paired-read assembly comes from an actual alignment or from simply joining reads. (
obipairing)
- obiclean_cluster: Identifier of the obiclean cluster containing the sequence. (
obiclean)
- obiclean_head: Boolean flag indicating that the sequence is the most abundant variant in its cluster. (
obiclean)
- obiclean_headcount: Abundance of the cluster head sequence. (
obiclean)
- obiclean_internalcount: Cumulated abundance of internal (non-head, non-singleton) variants in the obiclean cluster. (
obiclean)
- obiclean_mutation: Edit description used by obiclean to label the relationship between a sequence and its head. (
obiclean)
- obiclean_samplecount: Total abundance (head + internal + singleton) of the obiclean cluster. (
obiclean)
- obiclean_singletoncount: Number of singleton variants linked to the head in the obiclean graph. (
obiclean)
- obiclean_status: Final obiclean status (head/internal/singleton/bad) attributed to the sequence. (
obiclean)
- obiclean_weight: Relative weight computed for each sequence during obiclean consensus building. (
obiclean)
- obicleandb_dist: Distance distribution between a reference and its neighbors during database cleaning. (
obicleandb)
- obicleandb_level: Taxonomic rank (none/genus/family) reached during the obicleandb validation workflow. (
obicleandb)
- obicleandb_median: Median similarity score within the accepted cluster around a reference sequence. (
obicleandb)
- obicleandb_scores: Raw similarity scores observed for the reference during database validation. (
obicleandb)
- obicleandb_trusted: Probability assigned by obicleandb that the reference sequence is trustworthy. (
obicleandb)
- obicleandb_trusted_on: Number of supporting sequences used to compute the obicleandb trust score. (
obicleandb)
- obiconsensus_consensus: Boolean flag indicating whether a sequence is a consensus sequence produced by obiconsensus. (
obiconsensus)
- obiconsensus_filtered_graph_size: Size of the kmer graph after filtering low-coverage nodes. (
obiconsensus)
- obiconsensus_full_graph_size: Size of the full kmer graph before filtering. (
obiconsensus)
- obiconsensus_kmer_max_occur: Maximum abundance observed for any kmer in the graph used to build the consensus. (
obiconsensus)
- obiconsensus_kmer_size: Kmer size actually used to build the consensus for the sequence. (
obiconsensus)
- obiconsensus_seq_length: Length of the consensus sequence returned by obiconsensus. (
obiconsensus)
- obiconsensus_weight: Cumulated weight (number of supporting reads) of the consensus sequence. (
obiconsensus)
- obikmer_ali_length: Alignment length between the query and the best kmer-matched reference. (
obikmersim)
- obikmer_fast_count: Number of shared kmers discovered during the fast filtering phase. (
obikmersim)
- obikmer_fast_overlap: Estimated overlap length inferred from the kmer matching step. (
obikmersim)
- obikmer_fast_score: Fast alignment score computed before the full alignment stage. (
obikmersim)
- obikmer_identity: Proportion of identical bases in the alignment computed after kmer matching. (
obikmersim)
- obikmer_kmer_size: Size of the kmers that were indexed to perform the similarity search. (
obikmersim)
- obikmer_match_count: Number of references sharing at least the requested number of kmers with the query. (
obikmersim)
- obikmer_match_id: Identifier of the reference sequence selected as best match for a query ("-rev" when aligning the reverse complement). (
obikmersim)
- obikmer_orientation: Orientation (forward/reverse) used when aligning the query to the best kmer match. (
obikmersim)
- obikmer_residual_id: Identity computed after removing the minimal number of shared kmers from the alignment. (
obikmersim)
- obikmer_score: Alignment score resulting from the Smith–Waterman extension after kmer matching. (
obikmersim)
- obikmer_score_norm: Alignment score normalized by alignment length for kmer-based matches. (
obikmersim)
- obikmer_sparse_kmer: Indicates whether sparse kmers were used while building the index. (
obikmersim)
- obimultiplex_amplicon_rank: Rank of the barcode match among all amplicons compatible with the read. (
obimultiplex)
- obimultiplex_direction: Orientation of the read determined during barcode extraction (forward or reverse). (
obimultiplex,
obitagpcr)
- obimultiplex_error: Explanation of the failure encountered during barcode extraction. (
obimultiplex,
obitagpcr)
- obimultiplex_forward_error: Mismatch count observed between the read and the forward primer in the NGS filter. (
obimultiplex,
obitagpcr)
- obimultiplex_forward_match: Portion of the read matching the forward primer. (
obimultiplex,
obitagpcr)
- obimultiplex_forward_matching: Matching model (strict/hamming/indel) used to interpret the forward primer. (
obimultiplex)
- obimultiplex_forward_mismatches: Forward primer mismatch count propagated to paired reads during PCR tagging. (
obitagpcr)
- obimultiplex_forward_primer: Forward primer sequence fetched from the NGS filter entry assigned to the read. (
obimultiplex)
- obimultiplex_forward_proposed_tag: Forward tag proposed by the error-tolerant search before validation. (
obimultiplex)
- obimultiplex_forward_tag: Forward sample tag assigned to the read. (
obimultiplex,
obitagpcr)
- obimultiplex_forward_tag_dist: Edit distance between the observed tag and the expected forward tag. (
obimultiplex)
- obimultiplex_reverse_error: Mismatch count observed between the read and the reverse primer in the NGS filter. (
obimultiplex,
obitagpcr)
- obimultiplex_reverse_match: Portion of the read matching the reverse primer. (
obimultiplex,
obitagpcr)
- obimultiplex_reverse_matching: Matching model (strict/hamming/indel) used to interpret the reverse primer. (
obimultiplex)
- obimultiplex_reverse_mismatches: Reverse primer mismatch count propagated to paired reads during PCR tagging. (
obitagpcr)
- obimultiplex_reverse_primer: Reverse primer sequence fetched from the NGS filter entry assigned to the read. (
obimultiplex)
- obimultiplex_reverse_proposed_tag: Reverse tag proposed by the error-tolerant search before validation. (
obimultiplex)
- obimultiplex_reverse_tag: Reverse sample tag assigned to the read. (
obimultiplex,
obitagpcr)
- obimultiplex_reverse_tag_dist: Edit distance between the observed tag and the expected reverse tag. (
obimultiplex)
- obisplit_frg: Index of the fragment produced by obisplit from the original read. (
obisplit)
- obisplit_group: Name of the splitting group (pool or pattern pair) to which the fragment belongs. (
obisplit)
- obisplit_left_error: Mismatch count tolerated on the left delimiting pattern. (
obisplit)
- obisplit_left_match: Sequence matched by the left delimiting pattern. (
obisplit)
- obisplit_left_pattern: Name of the pattern that delimited the left boundary. (
obisplit)
- obisplit_location: Coordinates of the fragment extracted by obisplit (start..end, 1-based). (
obisplit)
- obisplit_nfrg: Total number of fragments produced from the source read. (
obisplit)
- obisplit_right_error: Mismatch count tolerated on the right delimiting pattern. (
obisplit)
- obisplit_right_match: Sequence matched by the right delimiting pattern. (
obisplit)
- obisplit_right_pattern: Name of the pattern that delimited the right boundary. (
obisplit)
- obisplit_set: Label of the pattern set (pool) used to extract a fragment. (
obisplit)
- obitag_bestid: Best identity score obtained when tagging a sequence with reference databases. (
obitag)
- obitag_bestmatch: Identifier of the best matching reference sequence used for taxonomic assignment. (
obitag)
- obitag_coord: Geographic coordinates of the query when using geometric tagging. (
obitag)
- obitag_geomref_index: Distance index (difference → taxon) stored for landmark-based geometric tagging. (
obirefidx,
obitag)
- obitag_match_count: Number of reference sequences sharing the best score with the query. (
obitag)
- obitag_min_dist: Minimal geometric distance observed between the query and landmark references. (
obitag)
- obitag_rank: Taxonomic rank associated with the assigned reference taxon. (
obitag)
- obitag_ref_index: Precomputed index linking mismatch counts to reference taxa for LCS-based tagging. (
obirefidx,
obitag)
- obitag_similarity_method: Identification method used by obitag ("lcs" or "geometric"). (
obitag)
- pair:
- pairing_fast_count: Number of kmers supporting the initial overlap detection between paired reads. (
obipairing)
- pairing_fast_overlap: Expected overlap length estimated from the fast pre-alignment step. (
obipairing)
- pairing_fast_score: Score computed during the fast overlap detection stage prior to full alignment. (
obipairing)
- pairing_mismatches: Map describing positions and base substitutions observed when merging paired reads. (
obipairing)
- pattern: Pattern sequence tested with
obiannotate --pattern; the tag name is prefixed when --pattern-name is provided. (
obiannotate) - pattern_error: Number of mismatches or indels between the queried pattern and the matched subsequence (prefix follows pattern name). (
obiannotate)
- pattern_location: Genomic coordinates (forward or complement) of the matched pattern (prefix follows pattern name). (
obiannotate)
- pattern_match: Sequence fragment that matched the requested pattern (prefix follows pattern name). (
obiannotate)
- rank: Taxonomic rank assigned to the ecoPCR reference sequence. (
obiconvert)
- reffamidx_cluster_n: Number of clusters created when indexing a family-level reference database. (
obirefidx)
- reffamidx_clusterhead: Boolean flag telling whether the reference sequence is the head of its similarity cluster. (
obirefidx)
- reffamidx_clusterid: Identifier of the cluster head that represents a reference sequence. (
obirefidx)
- reffamidx_clusteridentity: Pairwise identity between a reference sequence and the head of its family cluster. (
obirefidx)
- reffamidx_id: Unique identifier assigned to each reference sequence while building the family index. (
obirefidx)
- reffamidx_in: Index structure created for a given reference sequence to accelerate taxonomic assignment. (
obirefidx)
- reverse_error: Number of mismatches tolerated between the read and the reverse primer. (
obimultiplex,
obipcr)
- reverse_match: Sequence of the reverse primer match extracted from the read. (
obimultiplex,
obipcr)
- reverse_mismatch: Mismatch count reported in ecoPCR reference entries for the reverse primer. (
obiconvert)
- reverse_primer: Reverse primer sequence used while demultiplexing or during in silico PCR. (
obiconvert,
obimultiplex,
obipcr)
- reverse_tag: Sample tag identified on the reverse side of a read. (
obimultiplex,
obipcr)
- reverse_tm: Melting temperature of the reverse primer reported by ecoPCR. (
obiconvert)
- sample: Sample identifier assigned by the NGS filter and propagated to annotated reads. (
obimultiplex,
obitagpcr)
- scientific_name: Scientific name for the current taxonomic annotation. (
obiannotate,
obiconvert,
obitag)
- score: Alignment score computed while merging paired reads. (
obipairing)
- score_norm: Alignment score normalized by the overlap length when assembling paired reads. (
obikmersim,
obipairing)
- seq_a_single: Number of nucleotides trimmed from sequence A because they are single-stranded in the overlap. (
obikmersim,
obipairing)
- seq_ab_match: Number of matching positions observed in the aligned overlap between two sequences. (
obikmersim,
obipairing)
- seq_b_single: Number of nucleotides trimmed from sequence B because they are single-stranded in the overlap. (
obikmersim,
obipairing)
- seq_length: Length of the sequence in nucleotides. (
obiannotate,
obikmersim,
obimicrosat)
- seq_number: Ordinal number assigned to sequences when numbering is requested or needed for taxonomy extraction. (
obiannotate,
obiconvert)
- species_name: Scientific name of the species associated with the ecoPCR reference sequence. (
obiconvert)
- species_taxid: NCBI taxid of the species associated with the ecoPCR reference sequence. (
obiconvert)
- strand: Strand orientation stored in the ecoPCR record. (
obiconvert)
- taxid: Taxonomic identifier of the sequence within the current taxonomy. (
obiconvert,
obipcr,
obitag)
- taxonomic_path: Ordered list of taxids describing the lineage of the annotated sequence. (
obiannotate)
- taxonomic_rank: Rank name corresponding to the assigned taxon. (
obiannotate)