131
131
$^ RnaDnaConflict, 35
132
132
The MolInfo biomol field is inconsistent with the Bioseq molecule type field.
134
$^ HistoryGiCollision, 36
135
The Bioseq history gi refers to this Bioseq, not to its predecessor or successor.
137
$^ GiWithoutAccession, 37
138
The Bioseq has a gi identifier but no GenBank/EMBL/DDBJ accession identifier.
140
$^ MultipleAccessions, 38
141
The Bioseq has a gi identifier and more than one GenBank/EMBL/DDBJ accession identifier.
143
$^ HistAssemblyMissing, 39
144
The Bioseq has a TPA identifier but does not have a Seq-hist.assembly alignment. This
145
should be annotated or calculated by the database, resulting in a PRIMARY block visible
149
The Bioseq has one or more N bases at the end.
151
$^ UnexpectedIdentifierChange, 41
152
The set of sequence identifiers on a Bioseq are not consistent with the previous version
153
of the record in the database.
155
$^ InternalNsInSeqLit, 42
156
There are runs of many Ns inside the SeqLit component of a delta Bioseq.
158
$^ SeqLitGapLength0, 43
159
A SeqLit component of a delta Bioseq can specify a gap, but it should not be a gap
162
$^ TpaAssmeblyProblem, 44
163
Third party annotation records should have a TpaAssembly user object and a
164
Seq-hist.assembly alignment for the PRIMARY block.
167
A SeqLoc component of a delta Bioseq is suspiciously small.
170
HTGS delta records should have gaps between each sequence segment.
172
$^ CompleteTitleProblem, 47
173
The sequence title has complete genome in it, but it is not marked as complete.
175
$^ CompleteCircleProblem, 48
176
This sequence has a circular topology, but it is not marked as complete.
179
High throughput genomic sequences without gaps should have quality score graphs.
136
183
$^ BioSourceMissing, 1
214
260
automatically generated title. This may be a curated exception, or it may
215
261
be out of synch with the current annotation.
264
There are two descriptors of the same type which are inconsistent with each
265
other. Please make them consistent.
267
$^ ObsoleteSourceLocation, 21
268
There is a source location that is no longer legal for use in GenBank records.
270
$^ ObsoleteSourceQual, 22
271
There is a source qualifier that is no longer legal for use in GenBank records.
273
$^ StructuredSourceNote, 23
274
The name of a structured source field is present as text in a note. The data
275
should probably be put into the appropriate field instead.
277
$^ UnnecessaryBioSourceFocus, 24
278
Focus should not be set on a BioSource descriptor in records where there is no
281
$^ RefGeneTrackingWithoutStatus, 25
282
The RefGeneTracking user object does not have the required Status field set.
284
$^ UnwantedCompleteFlag, 26
285
The Mol-info.completeness flag should not be set on a genomic sequence unless
286
the title also says it is a complete sequence or complete genome.
288
$^ CollidingPublications, 27
289
Multiple publication descriptors with the same PMID or MUID apply to a Bioseq.
290
The lower-level ones are redundant, and should be removed.
292
$^ TransgenicProblem, 28
293
A BioSource descriptor with /transgenic set must be accompanied by a BioSource
294
feature on the nucleotide record.
219
298
$^ NonAsciiAsn, 1
274
360
Bioseq packaged in the set, perhaps within a nuc-prot set. RefSeq records may
275
361
however be referenced remotely.
363
$^ InconsistentMolInfoBiomols, 12
364
Mol-info.biomol is inconsistent within a segset or parts set.
366
$^ ArchaicFeatureLocation, 13
367
A feature location should refer to the accession or gi number, not a local or general ID.
369
$^ ArchaicFeatureProduct, 14
370
A feature product should refer to the accession or gi number, not a local or general ID.
372
$^ GraphPackagingProblem, 15
373
A graph should be packaged on its bioseq, or on a set containing the Bioseq.
279
377
$^ InvalidForType, 1
516
613
A gene feature on a single Bioseq should have a single interval spanning everything
517
614
considered to be under that gene.
616
$^ FeatContentDup, 59
617
The intervals on this feature are identical to another feature of the same type,
618
and the label and comment are also identical. This is likely to be an error in
619
annotating the record. Note that GenBank format suppresses duplicate features,
620
so use of Graphic view is recommended.
622
$^ BadProductSeqId, 60
623
The feature product refers to a database ID that has a locus name but no accession.
624
This is probably an error in parsing of a submission.
626
$^ RnaProductMismatch, 61
627
The RNA feature product type does not correspond to the RNA feature type. These
628
need to be consistent.
630
$^ MissingCDSproduct, 62
631
The CDS should have a product, but does not. Pseudo or short CDSs (less than 6
632
amino acids), or those marked with a rearrangement required for product exception,
633
are exempt from needing a product.
636
The tRNA codon recognized is an illegal value.
639
The tRNA encoded amino acid is an illegal value.
642
There are gene xrefs but no gene features. Records should normally have single-interval
643
gene features covering other biological features. Gene xrefs are used only to override
644
the inheritance by overlap.
646
$^ UTRdoesNotAbutCDS, 66
647
The 5'UTR and 3'UTR features should exactly abut the CDS feature.
649
$^ BadConflictFlag, 67
650
The coding region conflict flag is set, but the translated product is the
651
same as the instantiated product Bioseq.
653
$^ ConflictFlagSet, 68
654
The coding region conflict flag is appropriately set, but this record should
655
be brought to the attention of the source database for possible correction.
657
$^ LocusTagProblem, 69
658
A gene locus_tag should be a single token, with no spaces.
660
$^ CollidingLocusTags, 70
661
Two gene features should not have the same locus_tag, which is supposed to be
665
An alternative start codon was used. This is rare, and it is expected that
666
confirmatory evidence will be cited.
668
$^ PartialsInconsistent, 72
669
There are several places in an entry where a sequence can be described as
670
either partial or complete. In this entry, these settings are inconsistent.
671
Make sure that the location and product Seq-locs, the Bioseqs, and the
672
SeqFeat partial flag all agree in describing this SeqFeat as partial or
675
$^ GenesInconsistent, 73
676
The gene on the genomic sequence of a genomic product set should be the
677
same as the gene on the cDNA product of the mRNA feature.
679
$^ DuplicateTranslExcept, 74
680
There are multiple /transl_except qualifiers at the same location on this
681
CDS but with different amino acids indicated.
683
$^ TranslExceptAndRnaEditing, 75
684
A CDS has both /exception=RNA editing and /transl_except qualifiers. RNA
685
editing indicates post-transcriptional changes prior to translation. Use
686
/transl_except for individual codon exceptions such as selenocysteine or
687
other nonsense suppressors.
689
$^ NoNameForProtein, 76
690
A protein feature has a description, but no product name.
692
$^ TaxonDbxrefOnFeature, 77
693
A BioSource feature has a taxonID database identifier in the db_xref area
694
common to all features. This db_xref should only exist within the separate
697
$^ UnindexedFeature, 78
698
The location of a feature does not allow it to be mapped to a single Bioseq,
699
or to the segmented parent if on one or more part Bioseqs. It will not show
700
up in flatfile and other formats, and should be corrected or removed.
702
$^ CDSmRNAmismatch, 79
703
There should usually be a one-to-one correspondence between mRNA and CDS
706
$^ UnnecessaryException, 80
707
The feature is marked with an exception qualifier, but the validator does
708
not detect an error that needs to be suppressed.
710
$^ LocusTagProductMismatch, 81
711
In certain records a policy is that the locus_tag of the gene is expected to
712
match the prefix of the general ID of the CDS or mRNA product Bioseq.
715
A fundamental error occurred in software while attempting to transcribe this
716
messenger RNA. It is either a software problem or sever data corruption.
521
720
$^ SeqIdProblem, 1
added
removed
api/valid.msg
