Table 3.
Attributes of the 43 types of VADR alerts organized by the stage in which they are detected
| code | S/F | error message | description |
|---|---|---|---|
| Fatal alerts detected in the classification stage | |||
| noannotn ∗ | S | NO_ANNOTATION | no significant similarity detected |
| revcompl ∗ | S | REVCOMPLEM | sequence appears to be reverse complemented |
| incsbgrp | S | INCORRECT_SPECIFIED_SUBGROUP | score difference too large between best overall model and best specified subgroup model |
| incgroup | S | INCORRECT_SPECIFIED_GROUP | score difference too large between best overall model and best specified group model |
| Non-fatal alerts detected in the classification stage | |||
| qstsbgrp | S | QUESTIONABLE_SPECIFIED_SUBGROUP | best overall model is not from specified subgroup |
| qstgroup | S | QUESTIONABLE_SPECIFIED_GROUP | best overall model is not from specified group |
| indfclas | S | INDEFINITE_CLASSIFICATION | low score difference between best overall model and second best model (not in best model’s subgroup) |
| lowscore | S | LOW_SCORE | score to homology model below low threshold |
| Fatal alerts detected in the coverage stage | |||
| lowcovrg | S | LOW_COVERAGE | low sequence fraction with significant similarity to homology model |
| dupregin | S | DUPLICATE_REGIONS | similarity to a model region occurs more than once |
| discontn | S | DISCONTINUOUS_SIMILARITY | not all hits are in the same order in the sequence and the homology model |
| indfstrn | S | INDEFINITE_STRAND | significant similarity detected on both strands |
| lowsim5s | S | LOW_SIMILARITY_START | significant similarity not detected at 5’ end of the sequence |
| lowsim3s | S | LOW_SIMILARITY_END | significant similarity not detected at 3’ end of the sequence |
| lowsimis | S | LOW_SIMILARITY | internal region without significant similarity |
| Non-fatal alerts detected in the coverage stage | |||
| biasdseq | S | BIASED_SEQUENCE | high fraction of score attributed to biased sequence composition |
| Fatal alerts detected in the annotation stage | |||
| unexdivg ∗ | S | UNEXPECTED_DIVERGENCE | sequence is too divergent to confidently assign nucleotide-based annotation |
| noftrann ∗ | S | NO_FEATURES_ANNOTATED | sequence similarity to homology model does not overlap with any features |
| mutstart | F | MUTATION_AT_START | expected start codon could not be identified |
| mutendcd | F | MUTATION_AT_END | expected stop codon could not be identified, predicted CDS stop by homology is invalid |
| mutendns | F | MUTATION_AT_END | expected stop codon could not be identified, no in-frame stop codon exists 3’ of predicted valid start codon |
| mutendex | F | MUTATION_AT_END | expected stop codon could not be identified, first in-frame stop codon exists 3’ of predicted stop position |
| unexleng | F | UNEXPECTED_LENGTH | length of complete coding (CDS or mat_peptide) feature is not a multiple of 3 |
| cdsstopn | F | CDS_HAS_STOP_CODON | in-frame stop codon exists 5’ of stop position predicted by homology to reference |
| peptrans | F | PEPTIDE_TRANSLATION_PROBLEM | mat_peptide may not be translated because its parent CDS has a problem |
| pepadjcy | F | PEPTIDE_ADJACENCY_PROBLEM | predictions of two mat_peptides expected to be adjacent are not adjacent |
| indfantn | F | INDEFINITE_ANNOTATION | nucleotide-based search identifies CDS not identified in protein-based search |
| indf5gap | F | INDEFINITE_ANNOTATION_START | alignment to homology model is a gap at 5’ boundary |
| indf5loc | F | INDEFINITE_ANNOTATION_START | alignment to homology model has low confidence at 5’ boundary |
| indf3gap | F | INDEFINITE_ANNOTATION_END | alignment to homology model is a gap at 3’ boundary |
| indf3loc | F | INDEFINITE_ANNOTATION_END | alignment to homology model has low confidence at 3’ boundary similarity |
| lowsim5f | F | LOW_FEATURE_SIMILARITY_START | region within annotated feature at 5’ end of sequence lacks significant |
| lowsim3f | F | LOW_FEATURE_SIMILARITY_END | region within annotated feature at 3’ end of sequence lacks significant similarity |
| lowsimif | F | LOW_FEATURE_SIMILARITY | region within annotated feature lacks significant similarity |
| Fatal alerts detected in the protein validation stage | |||
| cdsstopp | F | CDS_HAS_STOP_CODON | stop codon in protein-based alignment |
| indfantp | F | INDEFINITE_ANNOTATION | protein-based search identifies CDS not identified in nucleotide-based search |
| indf5plg | F | INDEFINITE_ANNOTATION_START | protein-based alignment extends past nucleotide-based alignment at 5’ end |
| indf5pst | F | INDEFINITE_ANNOTATION_START | protein-based alignment does not extend close enough to nucleotide-based alignment 5’ endpoint |
| indf3plg | F | INDEFINITE_ANNOTATION_END | protein-based alignment extends past nucleotide-based alignment at 3’ end |
| indf3pst | F | INDEFINITE_ANNOTATION_END | protein-based alignment does not extend close enough to nucleotide -based alignment 3’ endpoint |
| indfstrp | F | INDEFINITE_STRAND | strand mismatch between protein-based and nucleotide-based predictions |
| insertnp | F | INSERTION_OF_NT | too large of an insertion in protein-based alignment |
| deletinp | F | DELETION_OF_NT | too large of a deletion in protein-based alignment |
The S/F column indicates whether the alert applies to an entire sequence (S) or to one feature (F) in a sequence. The five non-fatal alerts (four detected in the classification stage, and one in the coverage stage) do not cause a sequence to fail and are not reported in the output feature table. Codes marked with ∗ are always fatal; all other codes can be set to fatal or non-fatal with command-line options to v-annotate.pl