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Table 3 Attributes of the 43 types of VADR alerts organized by the stage in which they are detected

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

  1. 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