From: VADR: validation and annotation of virus sequence submissions to GenBank
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 |