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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

codeS/Ferror messagedescription
Fatal alerts detected in the classification stage
noannotn SNO_ANNOTATIONno significant similarity detected
revcompl SREVCOMPLEMsequence appears to be reverse complemented
incsbgrpSINCORRECT_SPECIFIED_SUBGROUPscore difference too large between best overall model and best specified subgroup model
incgroupSINCORRECT_SPECIFIED_GROUPscore difference too large between best overall model and best specified group model
Non-fatal alerts detected in the classification stage
qstsbgrpSQUESTIONABLE_SPECIFIED_SUBGROUPbest overall model is not from specified subgroup
qstgroupSQUESTIONABLE_SPECIFIED_GROUPbest overall model is not from specified group
indfclasSINDEFINITE_CLASSIFICATIONlow score difference between best overall model and second best model (not in best model’s subgroup)
lowscoreSLOW_SCOREscore to homology model below low threshold
Fatal alerts detected in the coverage stage
lowcovrgSLOW_COVERAGElow sequence fraction with significant similarity to homology model
dupreginSDUPLICATE_REGIONSsimilarity to a model region occurs more than once
discontnSDISCONTINUOUS_SIMILARITYnot all hits are in the same order in the sequence and the homology model
indfstrnSINDEFINITE_STRANDsignificant similarity detected on both strands
lowsim5sSLOW_SIMILARITY_STARTsignificant similarity not detected at 5’ end of the sequence
lowsim3sSLOW_SIMILARITY_ENDsignificant similarity not detected at 3’ end of the sequence
lowsimisSLOW_SIMILARITYinternal region without significant similarity
Non-fatal alerts detected in the coverage stage
biasdseqSBIASED_SEQUENCEhigh fraction of score attributed to biased sequence composition
Fatal alerts detected in the annotation stage
unexdivg SUNEXPECTED_DIVERGENCEsequence is too divergent to confidently assign nucleotide-based annotation
noftrann SNO_FEATURES_ANNOTATEDsequence similarity to homology model does not overlap with any features
mutstartFMUTATION_AT_STARTexpected start codon could not be identified
mutendcdFMUTATION_AT_ENDexpected stop codon could not be identified, predicted CDS stop by homology is invalid
mutendnsFMUTATION_AT_ENDexpected stop codon could not be identified, no in-frame stop codon exists 3’ of predicted valid start codon
mutendexFMUTATION_AT_ENDexpected stop codon could not be identified, first in-frame stop codon exists 3’ of predicted stop position
unexlengFUNEXPECTED_LENGTHlength of complete coding (CDS or mat_peptide) feature is not a multiple of 3
cdsstopnFCDS_HAS_STOP_CODONin-frame stop codon exists 5’ of stop position predicted by homology to reference
peptransFPEPTIDE_TRANSLATION_PROBLEMmat_peptide may not be translated because its parent CDS has a problem
pepadjcyFPEPTIDE_ADJACENCY_PROBLEMpredictions of two mat_peptides expected to be adjacent are not adjacent
indfantnFINDEFINITE_ANNOTATIONnucleotide-based search identifies CDS not identified in protein-based search
indf5gapFINDEFINITE_ANNOTATION_STARTalignment to homology model is a gap at 5’ boundary
indf5locFINDEFINITE_ANNOTATION_STARTalignment to homology model has low confidence at 5’ boundary
indf3gapFINDEFINITE_ANNOTATION_ENDalignment to homology model is a gap at 3’ boundary
indf3locFINDEFINITE_ANNOTATION_ENDalignment to homology model has low confidence at 3’ boundary similarity
lowsim5fFLOW_FEATURE_SIMILARITY_STARTregion within annotated feature at 5’ end of sequence lacks significant
lowsim3fFLOW_FEATURE_SIMILARITY_ENDregion within annotated feature at 3’ end of sequence lacks significant similarity
lowsimifFLOW_FEATURE_SIMILARITYregion within annotated feature lacks significant similarity
Fatal alerts detected in the protein validation stage
cdsstoppFCDS_HAS_STOP_CODONstop codon in protein-based alignment
indfantpFINDEFINITE_ANNOTATIONprotein-based search identifies CDS not identified in nucleotide-based search
indf5plgFINDEFINITE_ANNOTATION_STARTprotein-based alignment extends past nucleotide-based alignment at 5’ end
indf5pstFINDEFINITE_ANNOTATION_STARTprotein-based alignment does not extend close enough to nucleotide-based alignment 5’ endpoint
indf3plgFINDEFINITE_ANNOTATION_ENDprotein-based alignment extends past nucleotide-based alignment at 3’ end
indf3pstFINDEFINITE_ANNOTATION_ENDprotein-based alignment does not extend close enough to nucleotide -based alignment 3’ endpoint
indfstrpFINDEFINITE_STRANDstrand mismatch between protein-based and nucleotide-based predictions
insertnpFINSERTION_OF_NTtoo large of an insertion in protein-based alignment
deletinpFDELETION_OF_NTtoo 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