{
"UNKNOWN",
"UNKNOWN"} },
64 "A Bioseq \"extension\" is used for special classes of Bioseq. This class of \ 65 Bioseq should not have one but it does. This is probably a software error."} },
68 "This class of Bioseq requires an \"extension\" but it is missing or of the \ 69 wrong type. This is probably a software error."} },
72 "No actual sequence data was found on this Bioseq. This is probably a \ 73 software problem."} },
75{
"SeqDataNotAllowed",
76 "The wrong type of sequence data was found on this Bioseq. This is probably a \ 77 software problem."} },
80 "This Bioseq has an invalid representation class. This is probably a software \ 84 "This protein Bioseq is represented as circular. Circular topology is \ 85 normally used only for certain DNA molecules, for example, plasmids."} },
87{
"BadProteinMoltype",
88 "This protein Bioseq has strandedness indicated. Strandedness is normally a \ 89 property only of DNA sequences. Please unset the strandedness."} },
92 "It is not clear whether this sequence is nucleic acid or protein. Please set \ 93 the appropriate molecule type (Bioseq.mol)."} },
96 "Most sequences are either nucleic acid or protein. However, the molecule \ 97 type (Bioseq.mol) is set to \"other\". It should probably be set to nucleic \ 98 acid or a protein."} },
101 "This sequence is marked as having an uncertain length, but the length is \ 105 "The length indicated for this sequence is invalid. This is probably a \ 106 software error."} },
108{
"InvalidAlphabet",
109 "This Bioseq has an invalid alphabet (e.g. protein codes on a nucleic acid or \ 110 vice versa). This is probably a software error."} },
112{
"SeqDataLenWrong",
113 "The length of this Bioseq does not agree with the length of the actual data. \ 114 This is probably a software error."} },
117 "Something is very wrong with this entry. The validator cannot open a SeqPort \ 118 on the Bioseq. Further testing cannot be done."} },
121 "Invalid residue codes were found in this Bioseq."} },
124 "Stop codon symbols were found in this protein Bioseq."} },
126{
"PartialInconsistent",
127 "This segmented sequence is described as complete or incomplete in several \ 128 places, but these settings are inconsistent."} },
131 "This Bioseq is unusually short (less than 4 amino acids or less than 11 \ 132 nucleic acids). GenBank does not usually accept such short sequences."} },
135 "No SeqIds were found on this Bioseq. This is probably a software error."} },
138 "Delta sequences should only be HTGS-1 or HTGS-2."} },
140{
"LongHtgsSequence",
141 "HTGS-1 or HTGS-2 sequences must be < 350 KB in length."} },
143{
"LongLiteralSequence",
144 "Delta literals must be < 350 KB in length."} },
146{
"ConflictingIdsOnBioseq",
147 "Two SeqIds of the same class was found on this Bioseq. This is probably a software error."} },
150 "The specific type of this nucleic acid (DNA or RNA) is not set."} },
152{
"ConflictingBiomolTech",
153 "HTGS/STS/GSS records should be genomic DNA. There is a conflict between the \ 154 technique and expected molecule type."} },
156{
"SeqIdNameHasSpace",
157 "The Seq-id.name field should be a single word without any whitespace. This should be \ 158 fixed by the database staff."} },
160{
"IdOnMultipleBioseqs",
161 "There are multiple occurrences of the same Seq-id in this record. Sequence \ 162 identifiers must be unique within a record."} },
164{
"DuplicateSegmentReferences",
165 "The segmented sequence refers multiple times to the same Seq-id. This may be due \ 166 to a software error. Please consult with the database staff to fix this record."} },
169 "The protein sequence ends with one or more X (unknown) amino acids."} },
172 "A nucleotide sequence identifier should be 1 letter plus 5 digits or 2 letters \ 173 plus 6 digits, and a protein sequence identifer should be 3 letters plus 5 digits."} },
175{
"PartsOutOfOrder",
176 "The parts inside a segmented set should correspond to the seq_ext of the segmented \ 177 bioseq. A difference will affect how the flatfile is displayed."} },
179{
"BadSecondaryAccn",
180 "A secondary accession usually indicates a record replaced or subsumed by the current \ 181 record. In this case, the current accession and secondary are the same."} },
184 "GI numbers are assigned to sequences by NCBI's sequence tracking database. 0 is not \ 185 a legal value for a gi number."} },
188 "The MolInfo biomol field is inconsistent with the Bioseq molecule type field."} },
190{
"HistoryGiCollision",
191 "The Bioseq history gi refers to this Bioseq, not to its predecessor or successor."} },
193{
"GiWithoutAccession",
194 "The Bioseq has a gi identifier but no GenBank/EMBL/DDBJ accession identifier."} },
196{
"MultipleAccessions",
197 "The Bioseq has a gi identifier and more than one GenBank/EMBL/DDBJ accession identifier."} },
199{
"HistAssemblyMissing",
200 "The Bioseq has a TPA identifier but does not have a Seq-hist.assembly alignment. This \ 201 should be annotated or calculated by the database, resulting in a PRIMARY block visible \ 202 in the flatfile."} },
205 "The Bioseq has one or more N bases at the end."} },
207{
"UnexpectedIdentifierChange",
208 "The set of sequence identifiers on a Bioseq are not consistent with the previous version \ 209 of the record in the database."} },
211{
"InternalNsInSeqLit",
212 "There are runs of many Ns inside the SeqLit component of a delta Bioseq."} },
214{
"SeqLitGapLength0",
215 "A SeqLit component of a delta Bioseq can specify a gap, but it should not be a gap \ 218{
"TpaAssemblyProblem",
219 "Third party annotation records should have a TpaAssembly user object and a \ 220 Seq-hist.assembly alignment for the PRIMARY block."} },
223 "A SeqLoc component of a delta Bioseq is suspiciously small."} },
226 "HTGS delta records should have gaps between each sequence segment."} },
228{
"CompleteTitleProblem",
229 "The sequence title has complete genome in it, but it is not marked as complete."} },
231{
"CompleteCircleProblem",
232 "This sequence has a circular topology, but it is not marked as complete."} },
235 "High throughput genomic sequences without gaps should have quality score graphs."} },
238 "Gap symbols found in this protein Bioseq."} },
240{
"BadProteinStart",
241 "A gap symbols was found at the start of this protein Bioseq."} },
244 "The Bioseq has a gap at the end."} },
246{
"OverlappingDeltaRange",
247 "The Bioseq has a gap at the end."} },
250 "The protein sequence starts with one or more X (unknown) amino acids."} },
252{
"InternalNsInSeqRaw",
253 "There are runs of greater than 100 Ns within sequence. Please describe \ 254 what these Ns represent with your sequence submission."} },
256{
"InternalNsAdjacentToGap",
257 "There are Ns directly adjacent to a SeqLit gap in a delta Bioseq."} },
259{
"CaseDifferenceInSeqID",
260 "Multiple Bioseqs have the same Seq-id except for capitalization. Sequence \ 261 identifiers must be unique in a case-insensitive manner within a record."} },
263{
"DeltaComponentIsGi0",
264 "Delta component refers to gi 0. This indicates an error in database processing of this record."} },
266{
"FarFetchFailure",
267 "Fetching of a far feature location or component bioseq was needed, but no fetch \ 268 function is registered in the program."} },
270{
"InternalGapsInSeqRaw",
271 "Raw sequences should not have gap characters."} },
273{
"SelfReferentialSequence",
274 "A delta sequence must refer to other components, not to itself."} },
277 "A delta sequence component should be described as a specific interval, not as \ 278 the whole of a sequence."} },
280{
"TSAHistAssemblyMissing",
281 "The Bioseq has a TSA MolInfo tech but does not have a Seq-hist.assembly alignment."} },
283{
"ProteinsHaveGeneralID",
284 "One or more protein Bioseqs have a general Seq-id."} },
287 "This sequence contains too many Ns."} },
289{
"SeqLitDataLength0",
290 "A SeqLit component of a delta Bioseq must not have 0 length."} },
292{
"HighNContentStretch",
293 "This sequence contains long stretches of Ns."} },
295{
"HighNContentPercent",
296 "This sequence contains a high percentage of Ns."} },
298{
"UnknownLengthGapNot100",
299 "Gap of unknown length should have standard length of 100."} },
302 "Inconsistent data in Seq-gap fields."} },
304{
"WGSMasterLacksStrucComm",
305 "WGS Master records require a Genome Assembly Data structured comment user object."} },
307{
"TSAMasterLacksStrucComm",
308 "TSA Master records require an Assembly Data structured comment user object."} },
311 "Sequence has only Ns."} },
313{
"FarLocationExcludesFeatures",
314 "Scaffold points to sequence that has features outside the location."} },
316{
"ProteinShouldNotHaveGaps",
317 "Protein sequences should not have gaps"} },
319{
"MitoMetazoanTooLong",
320 "Mitochondrial Metozoan sequences should be less than 20000 bp"} },
322{
"ESTshouldBemRNA",
323 "EST sequence should be mRNA"} },
325{
"HTGS_STS_GSS_WGSshouldBeGenomic",
326 "HTGS/STS/GSS/WGS sequence should be genomic"} },
328{
"HTGS_STS_GSS_WGSshouldNotBeRNA",
329 "HTGS/STS/GSS/WGS sequence should not be RNA"} },
331{
"mRNAshouldBeSingleStranded",
332 "mRNA should be single stranded not double stranded"} },
334{
"TSAshouldBNotBeDNA",
335 "TSA sequence should not be DNA"} },
337{
"GenomeSeqGapProblem",
338 "Genome submission includes wrong gap type. Gaps for genomes should be Assembly Gaps with linkage evidence."} } ,
340{
"SeqGapBadLinkage",
341 "Problem with linkage in gap"} } ,
343{
"TSAseqGapProblem",
344 "Gaps for TSA should be Assembly Gaps with linkage evidence."} } ,
346{
"WGSseqGapProblem",
347 "Gaps for WGS genomes should be Assembly Gaps with linkage evidence."} } ,
349{
"CompleteGenomeHasGaps",
350 "Title contains 'complete genome' but sequence has gaps"} } ,
352{
"HighNcontent5Prime",
353 "Sequence with a large number or percentage of Ns at the 5' end might need to be trimmed"} } ,
355{
"HighNcontent3Prime",
356 "Sequence with a large number or percentage of Ns at the 3' end might need to be trimmed"} } ,
358{
"HighNpercent5Prime",
359 "Sequence with a large number or percentage of Ns at the 5' end might need to be trimmed"} } ,
361{
"HighNpercent3Prime",
362 "Sequence with a large number or percentage of Ns at the 3' end might need to be trimmed"} } ,
364{
"CircBactGenomeProblem",
365 "Circular bacteria or archaea sequence should be annotated as chromosome or plasmid"} } ,
367{
"ContigsTooShort",
368 "Maximum contig length is shorter than expected"} },
370{
"InstantiatedGapMismatch",
371 "Gap misc_feature does not match gap in delta Bioseq"} } ,
373{
"BadSeqIdCharacter",
374 "An illegal character is present in the sequence identifier."} },
377 "A sequence identifier field is longer than the allowed maximum length."} },
379{
"PrimaryAndThirdPartyMixture",
380 "There is an improper mixture of primary and third party databases within a nuc-prot set."} },
385{
"BioSourceMissing",
386 "The biological source of this sequence has not been described correctly. A \ 387 Bioseq must have a BioSource descriptor that covers the entire molecule. \ 388 Additional BioSource features may also be added to recombinant molecules, \ 389 natural or otherwise, to designate the parts of the molecule. Please add the \ 390 source information."} },
393 "This descriptor cannot be used with this Bioseq. A descriptor placed at the \ 394 BioseqSet level applies to all of the Bioseqs in the set. Please make sure \ 395 the descriptor is consistent with every sequence to which it applies."} },
397{
"FileOpenCollision",
398 "FileOpen is unable to find a local file. This is normal, and can be ignored."} },
401 "An unknown or \"other\" modifier was used."} },
404 "No publications were found in this entry which refer to this Bioseq. If a \ 405 publication descriptor is added to a BioseqSet, it will apply to all of the \ 406 Bioseqs in the set. A publication feature should be used if the publication \ 407 applies only to a subregion of a sequence."} },
410 "This entry does not specify the organism that was the source of the sequence. \ 411 Please name the organism."} },
413{
"MultipleBioSources",
414 "There are multiple BioSource or OrgRef descriptors in the same chain with \ 415 the same taxonomic name. Their information should be combined into a single \ 416 BioSource descriptor."} },
419 "This sequence does not have a Mol-info descriptor applying to it. This indicates \ 420 genomic vs. message, sequencing technique, and whether the sequence is incomplete."} },
423 "The country code (up to the first colon) is not on the approved list of countries."} },
426 "The BioSource is missing a taxonID database identifier. This will be inserted by \ 427 the automated taxonomy lookup called by Clean Up Record."} },
429{
"InconsistentBioSources",
430 "This population study has BioSource descriptors with different taxonomic names. \ 431 All members of a population study should be from the same organism."} },
434 "A BioSource should have a taxonomic lineage, which can be obtained from the \ 435 taxonomy network server."} },
437{
"SerialInComment",
438 "Comments that refer to the conclusions of a specific reference should not be \ 439 cited by a serial number inside brackets (e.g., [3]), but should instead be \ 440 attached as a REMARK on the reference itself."} },
442{
"BioSourceNeedsFocus",
443 "Focus must be set on a BioSource descriptor in records where there is a \ 444 BioSource feature with a different organism name."} },
446{
"BadOrganelleLocation",
447 "Only Kinetoplastida have kinetoplasts. Only Chlorarchniophyta \ 448 and Cryptophyta have nucleomorphs. Bacterial or viral source should not have organelle location."} },
450{
"MultipleChromosomes",
451 "There are multiple chromosome qualifiers on this Bioseq. With the exception of \ 452 some pseudoautosomal genes, this is likely to be a biological annotation error."} },
455 "Unassigned SubSource subtype."} },
458 "Unassigned OrgMod subtype."} },
460{
"InconsistentProteinTitle",
461 "An instantiated protein title descriptor should normally be the same as the \ 462 automatically generated title. This may be a curated exception, or it may \ 463 be out of synch with the current annotation."} },
466 "There are two descriptors of the same type which are inconsistent with each \ 467 other. Please make them consistent."} },
469{
"ObsoleteSourceLocation",
470 "There is a source location that is no longer legal for use in GenBank records."} },
472{
"ObsoleteSourceQual",
473 "There is a source qualifier that is no longer legal for use in GenBank records."} },
475{
"StructuredSourceNote",
476 "The name of a structured source field is present as text in a note. The data \ 477 should probably be put into the appropriate field instead."} },
479{
"UnnecessaryBioSourceFocus",
480 "Focus should not be set on a BioSource descriptor in records where there is no \ 481 BioSource feature."} },
483{
"RefGeneTrackingWithoutStatus",
484 "The RefGeneTracking user object does not have the required Status field set."} },
486{
"UnwantedCompleteFlag",
487 "The Mol-info.completeness flag should not be set on a genomic sequence, unless \ 488 the title also says it is a complete sequence or complete genome, nor should it \ 489 be set on a plasmid, chromosome, or organelle."} },
491{
"CollidingPublications",
492 "Multiple publication descriptors with the same PMID or MUID apply to a Bioseq. \ 493 The lower-level ones are redundant, and should be removed."} },
495{
"TransgenicProblem",
496 "A BioSource descriptor with /transgenic set must be accompanied by a BioSource \ 497 feature on the nucleotide record."} },
499{
"TaxonomyLookupProblem",
500 "A BioSource descriptor or feature has flags returned by taxonomy lookup that \ 501 are either inconsistent with the data or require a taxonomy consult."} },
504 "There are multiple title descriptors in the same Bioseq or BioseqSet chain."} },
506{
"RefGeneTrackingOnNonRefSeq",
507 "The RefGeneTracking user object should only be in RefSeq records."} },
509{
"BioSourceInconsistency",
510 "There is an internal inconsistency with specific fields in the BioSource."} },
512{
"FastaBracketTitle",
513 "Bracketed [...=...] information remains in the title. This should have been parsed \ 514 out during sequence record generation to obtain qualifier values."} },
517 "Comments, regions, and other text descriptors need a descriptive text string. \ 518 The string provided with this descriptor is empty. If no text is desired, then \ 519 the descriptor should be removed."} },
521{
"BadCollectionDate",
522 "The collection date is not in the required format."} },
524{
"BadPCRPrimerSequence",
525 "The PCR primer sequence has illegal characters or non-IUPAC nucleotides."} },
528 "The title ends with incorrect punctuation marks."} },
530{
"BadPCRPrimerName",
531 "The PCR primer name appears to be a sequence instead of an identifying label."} },
533{
"BioSourceOnProtein",
534 "A BioSource descriptor should not be placed on a protein that is in a nuc-prot set."} },
536{
"BioSourceDbTagConflict",
537 "Multiple db_xrefs with the same database should not appear on a single BioSource."} },
539{
"DuplicatePCRPrimerSequence",
540 "The PCR primer sequence has duplicate subsequences."} },
543 "There are multiple name descriptors in the same Bioseq or BioseqSet chain."} },
545{
"MultipleComments",
546 "There are multiple identical comment descriptors in the same Bioseq or BioseqSet chain."} },
549 "The format of lat_lon should be dd.dd N|S ddd.dd E|W."} },
552 "Latitude or longitude is out of range."} },
555 "Latitude or longitude values appear to be in the wrong hemisphere or swapped."} },
558 "The lat_lon coordinate does not map to the indicated country."} },
561 "The lat_lon coordinate does not map to the indicated state or province."} },
563{
"BadSpecificHost",
564 "A BioSource descriptor or feature has a specific host value that may \ 565 require a taxonomy consult."} },
567{
"RefGeneTrackingIllegalStatus",
568 "The RefGeneTracking user object has an illegal Status value."} },
570{
"ReplacedCountryCode",
571 "The country code (up to the first colon) is no longer on the approved list of countries."} },
573{
"BadInstitutionCode",
574 "The institution (or institution: collection) code is not on the approved list."} },
576{
"BadCollectionCode",
577 "The institution code is recognized, but the collection is not on the approved list."} },
579{
"IncorrectlyFormattedVoucherID",
580 "The voucher is missing a specific identifier."} },
582{
"UnstructuredVoucher",
583 "The voucher needs to be structured as \"<institution-code>:[<collection-code>:]<culture_id>\"."} },
585{
"ChromosomeLocation",
586 "BioSource location is not usually chromosome."} },
588{
"MultipleSourceQualifiers",
589 "BioSource has unexpected multiple qualifiers of the same type."} },
591{
"UnbalancedParentheses",
592 "Qualifier should have matching ( and ) parentheses or [ and ] brackets."} },
594{
"IdenticalInstitutionCode",
595 "BioSource has unexpected multiple bio_material/culture_collection/specimen_voucher \ 596 from the same institution."} },
598{
"BadCountryCapitalization",
599 "The country code does not use the correct capitalization."} },
601{
"WrongVoucherType",
602 "The institution (or institution: collection) code normally uses a different \ 603 bio_material/culture_collection/specimen_voucher type."} },
606 "The title has (PMID #####) embedded in it."} },
609 "The keyword is not appropriate in this record."} },
611{
"NoOrganismInTitle",
612 "A RefSeq record should have the organism name at the beginning of a nucleotide title and bracketed at the end of a protein title."} },
614{
"MissingChromosome",
615 "An NC or AC RefSeq record should have a chromosome annotated."} },
618 "The lat_lon coordinate may be in an adjacent country or in surrounding waters."} },
620{
"BadStrucCommInvalidFieldName",
621 "Structured comment is missing required fields or field values do not conform to correct format."} },
623{
"BadStrucCommInvalidFieldValue",
624 "Structured comment is missing required fields or field values do not conform to correct format."} },
626{
"BadStrucCommMissingField",
627 "Structured comment is missing required fields or field values do not conform to correct format."} },
629{
"BadStrucCommFieldOutOfOrder",
630 "Structured comment is missing required fields or field values do not conform to correct format."} },
632{
"BadStrucCommMultipleFields",
633 "Structured comment is missing required fields or field values do not conform to correct format."} },
635{
"BioSourceNeedsChromosome",
636 "Chromosome should be set on a BioSource descriptor in non-viral complete genomes."} },
638{
"MolInfoConflictsWithBioSource",
639 "Viral lineage information conflicts with MolInfo."} },
641{
"FakeStructuredComment",
642 "Comment descriptor may have been formatted to look like structured comment."} },
644{
"StructuredCommentPrefixOrSuffixMissing",
645 "Structured comments should have a prefix or suffix."} },
648 "The lat_lon coordinate map in a body of water."} },
651 "The lat_lon coordinate is probably in a minor or unnamed body of water."} },
653{
"MissingPersonalCollectionName",
654 "The personal collection does not indicate the name of the collector."} },
656{
"LatLonPrecision",
657 "The precision of lat_lon should be dd.dd N|S ddd.dd E|W."} },
660 "Only one DBLink user object with approved databases should apply to each Bioseq."} },
662{
"FinishedStatusForWGS",
663 "WGS projects should not have the Genome-Assembly-Data structured comment current \ 664 finishing status set to Finished."} },
666{
"BadTentativeName",
667 "A structured comment descriptor or feature has a tentative name value that may \ 668 require a taxonomy consult."} },
670{
"OrganismNotFound",
671 "The indicated organism is not in the taxonomy database."} },
673{
"TaxonomyIsSpeciesProblem",
674 "Taxonomy lookup of the indicated organism reports an is_species_level problem."} },
676{
"TaxonomyConsultRequired",
677 "A taxonomy consult is required for the indicated organism."} },
679{
"TaxonomyNucleomorphProblem",
680 "Taxonomy lookup indicates that the nucleomorph flag should be set for this organism."} },
682{
"InconsistentMolTypeBiomol",
683 "The Bioseq instance molecule field is inconsistent with the Mol-info biomol field."} },
685{
"BadInstitutionCountry",
686 "The institution (or institution: collection) code should not have a <country> modifier."} },
688{
"AmbiguousSpecificHost",
689 "A BioSource descriptor or feature has an ambiguous specific host value that may \ 690 require a taxonomy consult."} },
693 "The altitude must be reported as a number followed by a space and the letter m (for meters)."} },
695{
"RefGeneTrackingOnNucProtSet",
696 "The RefGeneTracking user object should not be on a nuc-prot set."} },
698{
"InconsistentDates",
699 "There are two date descriptors that are inconsistent with each \ 700 other. Please make them consistent."} },
702{
"MultipleTaxonIDs",
703 "There are multiple BioSources with multiple taxonIDs in this RefSeq record."} },
705{
"ScaffoldLacksBioProject",
706 "There is no BioProject database link for this scaffold record."} },
708{
"CompleteGenomeLacksBioProject",
709 "There is no BioProject database link for this complete genome record."} },
711{
"TaxonomyPlastidsProblem",
712 "Taxonomy lookup indicates that the plastids flag should be set for this organism."} },
714{
"OrganismIsUndefinedSpecies",
715 "Organism is an undefined species and does not have a specific identifier."} },
717{
"SuspectedContaminatedCellLine",
718 "Suspected contaminated cell line."} },
720{
"WrongOrganismFor16SrRNA",
721 "16S ribosomal RNA is not present in eukaryotic ribosomes."} },
723{
"InconsistentWGSFlags",
724 "WGS indicators are used inconsistently in this record."} },
726{
"TitleNotAppropriateForSet",
727 "Only population study, phylogenetic study, ecological sample study, and mutation sets should have title descriptors."} },
729{
"StrainContainsTaxInfo",
730 "Strain contains taxonomic name information"} },
732{
"InconsistentBioSources_ConLocation",
733 "The source location for a contig and scaffold should be the same"} },
735{
"InconsistentRefSeqMoltype",
736 "Genomic RefSeq accession should use genomic or cRNA moltype"} },
738{
"InconsistentMolInfo",
739 "MolInfo descriptors that apply to the same sequence should be consistent"} },
741{
"InconsistentMolInfoTechnique",
742 "MolInfo descriptors that apply to the same sequence should be consistent"} },
744{
"InconsistentTaxName",
745 "Source descriptors that apply to the same sequence should have the same organism name"} },
747{
"InconsistentMolType",
748 "RNA biomol values should be accompanied by RNA molecule type values"} },
750{
"InconsistentGenBankblocks",
751 "Only one GenBankBlock descriptor should apply to a sequence"} },
753{
"InconsistentTaxNameSet",
754 "Organism names in a population set should be consistent"} },
756{
"InconsistentTPA",
757 "TPA:experimental and TPA:inferential should not both be in the same set of keywords"} },
759{
"BacteriaMissingSourceQualifier",
760 "Bacteria should have strain or isolate or environmental sample"} },
762{
"BadBioSourceFrequencyValue",
763 "Frequency should be a number less than 1"}},
765{
"BadPlasmidChromosomeLinkageName",
766 "Problematic plasmid/chromosome/linkage group name"}},
769 "Plastid name should only appear for plastid location"}},
771{
"EnvironSampleMissingQualifier",
772 "Environmental sample should also have isolation source or specific host annotated"}},
774{
"InconsistentVirusMoltype",
775 "Molecule type is unexpected for specified virus type"}},
777{
"InvalidMatingType",
778 "Unexpected use of /mating_type qualifier"}},
780{
"InvalidSexQualifier",
781 "Sex qualifier should only be used for some types of organisms"}},
783{
"InvalidTissueType",
784 "Tissue-type is inappropriate for bacteria"}},
786{
"MissingEnvironmentalSample",
787 "Environmental-sample qualifier is expected for this sequence"}},
789{
"MissingMetagenomicQualifier",
790 "Metagenomic qualifier is expected for this sequence"}},
792{
"MissingPlasmidLocation",
793 "Plasmid-name is specified, but location is not plasmid"}},
795{
"MissingPlasmidName",
796 "Location is plasmid, but no plasmid-name is provided"}},
798{
"OrgModValueInvalid",
799 "Invalid qualifier value"}},
801{
"StrainWithEnvironSample",
802 "Strain should not be present in an environmental sample"}},
804{
"UnculturedNeedsEnvSample",
805 "Uncultured should also have /environmental_sample"} },
807{
"BadTextInSourceQualifier",
808 "Qualifier value incorrectly formatted"} },
810{
"OrgModMissingValue",
811 "Qualifier value is missing"} },
813{
"BadAssemblyName",
814 "Assembly Name should not start with 'NCBI' or 'GenBank' in structured comment"} },
816{
"BadKeywordForStrucComm",
817 "Structured Comment is non-compliant, keyword should be removed"} },
819{
"BadKeywordNoTechnique",
820 "Sequences with BARCODE keywords should have Molinfo.tech barcode"} },
822{
"BadKeywordUnverified",
823 "Sequence should not have both BARCODE and UNVERIFIED keywords"} },
825{
"BadStrucCommInvalidPrefix",
826 "Unrecognized structured comment prefix"} },
828{
"BadStrucCommInvalidSuffix",
829 "Unrecognized structured comment suffix"} },
831{
"BINDoesNotMatch",
832 "The organism name should end with sp. plus Barcode Index Number"} },
834{
"CollidingPubMedID",
835 "Multiple different publications should not have the same identifier"} },
837{
"CommentMissingText",
838 "Comment descriptors should not be blank"} },
840{
"DBLinkBadAssembly",
841 "Assembly entries should not appear in DBLink user objects"} },
843{
"DBLinkBadBioProject",
844 "Bad BioProject format"} },
846{
"DBLinkBadBioSample",
847 "Bad BioSample format"} },
849{
"DBLinkBadCapitalization",
850 "Bad DBLink capitalization"} },
852{
"DBLinkBadFormat",
853 "Unrecognized entries appear in DBLink user objects"} },
855{
"DBLinkBadSRAaccession",
856 "Bad Sequence Read Archive format"} },
858{
"DBLinkMissingUserObject",
859 "A DBLink user object descriptor should not be empty"} },
862 "A DBLink object should be placed on a nucleotide sequence, not a set"} },
864{
"InvalidForTypeGIBB",
865 "GIBB descriptors are obsolete"} },
868 "Nucleic acid should not have Molinfo-biomol = peptide"} },
871 "Molinfo-biomol should not be 'other'"} },
873{
"MoltypeOtherGenetic",
874 "Molinfo-biomol should not be 'other genetic'"} },
877 "Molinfo-biomol unknown should not be used"} },
879{
"MultipleDBLinkObjects",
880 "Sequence should not have multiple DBLink objects"} },
882{
"MultipleStrucComms",
883 "Multiple structured comments with prefix "} },
885{
"NoKeywordHasTechnique",
886 "Molinfo.tech barcode without BARCODE keyword"} },
888{
"NoSourceDescriptor",
889 "No source information included on this record."} },
891{
"NucleotideTechniqueOnProtein",
892 "Protein should not have nucleic acid sequence method"} },
894{
"ProteinTechniqueOnNucleotide",
895 "Nucleic acid should not have protein sequence method"} },
897{
"RegionMissingText",
898 "Region descriptor needs text"} },
900{
"StrucCommMissingPrefixOrSuffix",
901 "Structured Comment lacks prefix and/or suffix"} },
903{
"StrucCommMissingUserObject",
904 "Structured Comment user object descriptor is empty"} },
906{
"SyntheticConstructNeedsArtificial",
907 "Synthetic construct should have artificial origin"} },
909{
"SyntheticConstructWrongMolType",
910 "Synthetic construct should have other-genetic"} },
912{
"TaxonomyAmbiguousName",
913 "Taxonomy lookup failed with message 'ambiguous name'"} },
915{
"TaxonomyServiceProblem",
916 "Taxonomy service connection failure"} },
918{
"TitleMissingText",
919 "Title descriptor needs text"} },
921{
"TPAassemblyWithoutTPAKeyword",
922 "Non-TPA record should not have TpaAssembly object"} },
924{
"UserObjectNoData",
925 "User object with no data"} },
927{
"UserObjectNoType",
928 "User object with no type"} },
930{
"WGSmasterLacksBioProject",
931 "WGS master lacks BioProject"} },
933{
"WGSmasterLacksBioSample",
934 "WGS master lacks BioSample"} },
936{
"WGSMasterLacksBothBioSampleBioProject",
937 "WGS master lacks both BioSample and BioProject"} },
939{
"WrongBiomolForTSA",
940 "TSA records are expected to make use of a very limited set of MolInfo.biomol values: transcribed-RNA, mRNA, rRNA, ncRNA."} },
943 "More than one matching organism name"} },
945{
"ModifierTypeConflict",
946 "Resulting org-ref has more than one value for singleton modifier type"} },
948{
"AmbiguousModForward",
949 "Multiple modifier forwarding reaches incompatible targets"} },
951{
"AmbiguousTypeMaterial",
952 "Specified type material information belongs to unrelated taxa"} },
955 "Org-ref does not contain information to match"} },
957{
"HostIdenticalToOrganism",
958 "Specific host should not be identical to taxname"} } ,
960{
"MultipleStrains",
961 "A Biosource should only have one strain value"} } ,
964 "Orgmod variety should only be in plants, fungi, or cyanobacteria"} } ,
966{
"BadTypeMaterial",
967 "Bad value for type_material"} } ,
969{
"TaxonomyNoCommonAncestor",
970 "No common ancestor for input taxids in join request"} },
972{
"TaxonomyNoValidTaxids",
973 "All taxids in join request are invalid"} },
975{
"TaxonomyEmptyInput",
976 "No valid input to perform Taxonomy request"} } ,
978{
"ChromosomeWithoutLocation",
979 "Location should be chromosome if chromosome name is present"} },
981{
"TaxonomyBlankSample",
982 "Blank sample taxonomy should not coexist with sequence records"} },
984{
"NonViralSegment",
985 "Non-viral taxonomy should not have segment qualifier"} },
987{
"BadGeoLocNameCode",
988 "The geo_loc_name code (up to the first colon) is not on the approved list of countries."} },
990{
"LatLonGeoLocName",
991 "The lat_lon coordinate does not map to the indicated geo_loc_name."} },
993{
"ReplacedGeoLocNameCode",
994 "The geo_loc_name code (up to the first colon) is no longer on the approved list of countries."} },
996{
"BadGeoLocNameCapitalization",
997 "The geo_loc_name code does not use the correct capitalization."} },
999{
"BadInstitutionGeoLocName",
1000 "The institution (or institution: collection) code should not have a <geo_loc_name> modifier."} },
1002{
"MultipleIsolates",
1003 "A Biosource should only have one isolate value"} } ,
1005{
"BadGenomeRepresentation",
1006 "Genome Representation should not start with 'Partial' in structured comment"} },
1008{
"BadNullGeoLocName",
1009 "A null geo_loc_name should be be present on influenza or Sars virus records."} },
1011{
"BadNullCountry",
1012 "A null country should be be present on influenza or Sars virus records."} },
1014{
"BadNullCollectionDate",
1015 "A null collection date should be be present on influenza or Sars virus records."} },
1017{
"UnculturedGenome",
1018 "A genomic sequence should not have uncultured in its organism name"} },
1020{
"BadContigOrScaffoldChromosome",
1021 "Chromosome name should not contain contig or scaffold"}},
1023{
"HasStrainAndIsolate",
1024 "BioSource should not have both strain and isolate"}},
1026{
"TaxonomyIsMetagenome",
1027 "Taxonomy name should not be metagenome"}},
1034 "There is a non-ASCII type character in this entry."} },
1037 "There is a potentially misspelled word in this entry."} },
1039{
"AuthorListHasEtAl",
1040 "The author list contains et al, which should be replaced with the \ 1041 remaining author names."} },
1043{
"MissingPubInfo",
1044 "The publication is missing essential information, such as title or authors."} },
1046{
"UnnecessaryPubEquiv",
1047 "A nested Pub-equiv is not normally expected in a publication. This may prevent \ 1048 proper display of all publication information."} },
1050{
"BadPageNumbering",
1051 "The publication page numbering is suspect."} },
1053{
"MedlineEntryPub",
1054 "Publications should not be of type medline-entry. This has abstract and MeSH \ 1055 term information that does not appear in the GenBank flatfile. Type cit-art \ 1056 should be used instead."} },
1059 "There are bad values for month, day, or year in a date."} },
1061{
"StructuredCitGenCit",
1062 "The publication has title or journal embedded in the unstructured citgen.cit \ 1065{
"CollidingSerialNumbers",
1066 "Multiple publications have the same serial number explicitly recorded in the \ 1069{
"EmbeddedScript",
1070 "Script or other markup tags should not be used in sequence record fields."} },
1072{
"PublicationInconsistency",
1073 "Some fields in the publication should not be present with other fields."} },
1075{
"SgmlPresentInText",
1076 "SGML markup is embedded in text."} },
1078{
"UnexpectedPubStatusComment",
1079 "An unexpected publication status exists for a print, online-only, or ahead-of-print article : Content-Of-Pubdesc.comment-String."} },
1081{
"PastReleaseDate",
1082 "The record has is marked as hold-until-published, but the release anyway date has already passed."} },
1085 "The publication journal is missing an ISO journal title abbreviation."} },
1088 "The publication volume is missing."} },
1090{
"MissingVolumeEpub",
1091 "The electronic publication volume is missing."} },
1094 "The publication pages are missing."} },
1096{
"MissingPagesEpub",
1097 "The electronic publication pages are missing."} },
1099{
"BarcodeTooShort",
1100 "Barcode sequence is too short."} },
1102{
"BarcodeMissingPrimers",
1103 "Barcode sequence is missing primers."} },
1105{
"BarcodeMissingCountry",
1106 "Barcode sequence is missing country."} },
1108{
"BarcodeMissingVoucher",
1109 "Barcode sequence is missing voucher."} },
1111{
"BarcodeTooManyNs",
1112 "Barcode sequence contains too many Ns"} },
1114{
"BarcodeBadCollectionDate",
1115 "Barcode sequence has bad collection date"} } ,
1117{
"BarcodeMissingOrderAssignment",
1118 "Barcode sequence is missing order assignment."} },
1120{
"BarcodeLowTrace",
1121 "Barcode sequence has low trace."} },
1123{
"BarcodeFrameShift",
1124 "Barcode sequence has frame shift."} },
1126{
"BarcodeStructuredVoucher",
1127 "Barcode sequence has structured voucher problem."} },
1129{
"BarcodeTestFails",
1130 "Barcode test fails."} },
1132{
"BarcodeTestPasses",
1133 "Barcode test passes."} },
1136 "Invalid ASN.1"} },
1139 "Service failure prevented complete validation"} },
1142 "Colliding sequence identifiers prevented loading into the object manager."} },
1144{
"MissingPubRequirement",
1145 "The publication is missing essential information, such as title or authors."} },
1147{
"BadSubmissionAuthorName",
1148 "A submission author name field is invalid."} },
1150{
"BarcodeMissingGeoLocName",
1151 "Barcode sequence is missing geo_loc_name."} },
1154 "Bad author first name"} },
1157 "Bad author last name"} },
1160 "Bad affiliation state"} },
1166 "A protein is found in this entry, but the coding region has not been \ 1167 described. Please add a CdRegion feature to the nucleotide Bioseq."} },
1169{
"NucProtProblem",
1170 "Both DNA and protein sequences were expected, but one of the two seems to be \ 1171 missing. Perhaps this is the wrong package to use."} },
1174 "A segmented sequence was expected, but it was not found. Perhaps this is the \ 1175 wrong package to use."} },
1178 "No Bioseqs were found in this BioseqSet. Is that what was intended?"} },
1180{
"NucProtNotSegSet",
1181 "A nuc-prot set should not contain any other BioseqSet except segset."} },
1183{
"SegSetNotParts",
1184 "A segset should not contain any other BioseqSet except parts."} },
1186{
"SegSetMixedBioseqs",
1187 "A segset should not contain both nucleotide and protein Bioseqs."} },
1189{
"PartsSetMixedBioseqs",
1190 "A parts set should not contain both nucleotide and protein Bioseqs."} },
1192{
"PartsSetHasSets",
1193 "A parts set should not contain BioseqSets."} },
1195{
"FeaturePackagingProblem",
1196 "A feature should be packaged on its bioseq, or on a set containing the Bioseq."} },
1198{
"GenomicProductPackagingProblem",
1199 "The product of an mRNA feature in a genomic product set should point to a cDNA \ 1200 Bioseq packaged in the set, perhaps within a nuc-prot set. RefSeq records may \ 1201 however be referenced remotely."} },
1203{
"InconsistentMolInfoBiomols",
1204 "Mol-info.biomol is inconsistent within a segset, parts set, or pop/phy/mut/eco set."} },
1206{
"ArchaicFeatureLocation",
1207 "A feature location should refer to the accession or gi number, not a local or general ID."} },
1209{
"ArchaicFeatureProduct",
1210 "A feature product should refer to the accession or gi number, not a local or general ID."} },
1212{
"GraphPackagingProblem",
1213 "A graph should be packaged on its bioseq, or on a set containing the Bioseq."} },
1215{
"InternalGenBankSet",
1216 "An outer BioseqSet should not contain an internal BioseqSet of class genbank."} },
1219 "BioseqSet class should not be conset."} },
1222 "No Bioseqs were found in the entire record."} },
1224{
"INSDRefSeqPackaging",
1225 "INSD and RefSeq records should not be packaged together."} },
1227{
"GPSnonGPSPackaging",
1228 "Genomic product set records should not be packaged with other set types."} },
1231 "RefSeq records should not be packaged in a popset."} },
1233{
"BioseqSetClassNotSet",
1234 "The BioseqSet class field is not set."} },
1236{
"OrphanedProtein",
1237 "The Bioseq is an INSD or RefSeq protein erroneously not in a nuc-prot set."} },
1239{
"MissingSetTitle",
1240 "No title was found on a pop/phy/mut/eco set."} },
1242{
"NucProtSetHasTitle",
1243 "A title descriptor was found on a nuc-prot set."} },
1245{
"ComponentMissingTitle",
1246 "A title descriptor should be present on the components of a pop/phy/mut/eco set."} },
1249 "Only a single Bioseq was found in this BioseqSet. Is that what was intended?"} },
1251{
"MisplacedMolInfo",
1252 "Mol-info should not be on a pop/phy/mut/eco/wgs/genbank/genprod set."} },
1254{
"ImproperlyNestedSets",
1255 "A pop/phy/mut/eco/wgs set has an unexpected internal set other than nuc-prot, seg-set, or parts set."} },
1257{
"SeqSubmitWithWgsSet",
1258 "Seq-submit file is a wgs-set instead of a batch submission."} },
1260{
"InconsistentMoltypeSet",
1261 "Molecule types should be consistent within a pop/phy/mut/eco set"} },
1263{
"MissingAutodef",
1264 "Missing Autodef user object within a pop/phy/mut/eco set"} },
1266{
"InconsistentAutodef",
1267 "Inconsistent Autodef user objects within a pop/phy/mut/eco set"} },
1272{
"InvalidForType",
1273 "This feature type is illegal on this type of Bioseq."} },
1275{
"PartialProblem",
1276 "There are several places in an entry where a sequence can be described as \ 1277 either partial or complete. In this entry, these settings are inconsistent. \ 1278 Make sure that the location and product Seq-locs, the Bioseqs, and the \ 1279 SeqFeat partial flag all agree in describing this SeqFeat as partial or \ 1283 "A feature with an invalid type has been detected. This is most likely a \ 1284 software problem."} },
1287 "The coordinates describing the location of a feature do not fall within the \ 1288 sequence itself. A feature location or a product Seq-loc is out of range of \ 1289 the Bioseq it points to."} },
1292 "Mixed strands (plus and minus) have been found in the same location. While \ 1293 this is biologically possible, it is very unusual. Please check that this is \ 1294 really what you mean."} },
1296{
"AnticodonMixedStrand",
1297 "Mixed strands in Anticodon location"} } ,
1299{
"GenomeSetMixedStrand",
1300 "Mixed strands in feature location on small genome set - set trans-splicing exception if needed"} } ,
1303 "This location has intervals that are out of order. While whis is biologically \ 1304 possible, it is very unusual. Please check that this is really what you mean."} },
1307 "A fundamental error occurred in software while attempting to translate this \ 1308 coding region. It is either a software problem or sever data corruption."} },
1311 "An illegal start codon was used. Some possible explanations are: (1) the \ 1312 wrong genetic code may have been selected; (2) the wrong reading frame may \ 1313 be in use; or (3) the coding region may be incomplete at the 5' end, in \ 1314 which case a partial location should be indicated."} },
1317 "Internal stop codons are found in the protein sequence. Some possible \ 1318 explanations are: (1) the wrong genetic code may have been selected; (2) the \ 1319 wrong reading frame may be in use; (3) the coding region may be incomplete \ 1320 at the 5' end, in which case a partial location should be indicated; or (4) \ 1321 the CdRegion feature location is incorrect."} },
1324 "Normally a protein sequence is supplied. This sequence can then be compared \ 1325 with the translation of the coding region. In this entry, no protein Bioseq \ 1326 was found, and the comparison could not be made."} },
1329 "The protein sequence that was supplied is not identical to the translation \ 1330 of the coding region. Mismatching amino acids are found between these two \ 1334 "The protein sequence that was supplied is not the same length as the \ 1335 translation of the coding region. Please determine why they are different."} },
1338 "A coding region that is complete should have a stop codon at the 3'end. A \ 1339 stop codon was not found on this sequence, although one was expected."} },
1342 "An unparsed \transl_except qualifier was found. This indicates a parser \ 1345{
"MissingProteinName",
1346 "The name and description of the protein is missing from this entry. Every \ 1347 protein Bioseq must have one full-length Prot-ref feature to provide this \ 1350{
"NotSpliceConsensus",
1351 "Splice junctions typically have GT as the first two bases of the intron \ 1352 (splice donor) and AG as the last two bases of the intron (splice acceptor). \ 1353 This intron does not conform to that pattern."} },
1355{
"OrfCdsHasProduct",
1356 "A coding region flagged as orf has a protein product. There should be no \ 1357 protein product bioseq on an orf."} },
1359{
"GeneRefHasNoData",
1360 "A gene feature exists with no locus name or other fields filled in."} },
1362{
"ExceptInconsistent",
1363 "A coding region has an exception gbqual but the excpt flag is not set."} },
1365{
"ProtRefHasNoData",
1366 "A protein feature exists with no name or other fields filled in."} },
1368{
"GenCodeMismatch",
1369 "The genetic code stored in the BioSource is different than that for this CDS."} },
1372 "RNA type 0 (unknown RNA) should be type 255 (other)."} },
1374{
"UnknownImpFeatKey",
1375 "An import feature has an unrecognized key."} },
1377{
"UnknownImpFeatQual",
1378 "An import feature has an unrecognized qualifier."} },
1380{
"WrongQualOnImpFeat",
1381 "This qualifier is not legal for this feature."} },
1383{
"MissingQualOnImpFeat",
1384 "An essential qualifier for this feature is missing."} },
1386{
"PseudoCdsHasProduct",
1387 "A coding region flagged as pseudo has a protein product. There should be no \ 1388 protein product bioseq on a pseudo CDS."} },
1391 "The database in a cross-reference is not on the list of officially \ 1392 recognized database abbreviations."} },
1395 "The location has a reference to a bioseq that is not packaged in this record."} },
1398 "The intervals on this feature are identical to another feature of the same type, \ 1399 but the label or comment are different."} },
1401{
"UnnecessaryGeneXref",
1402 "This feature has a gene xref that is identical to the overlapping gene. This is \ 1403 redundant, and probably should be removed."} },
1405{
"TranslExceptPhase",
1406 "A \transl_except qualifier was not on a codon boundary."} },
1408{
"TrnaCodonWrong",
1409 "The tRNA codon recognized does not code for the indicated amino acid using the \ 1410 specified genetic code."} },
1413 "Feature location indicates that it is on both strands. This is not biologically \ 1414 possible for this kind of feature. Please indicate the correct strand (plus or \ 1415 minus) for this feature."} },
1418 "A CDS is overlapped by a gene feature, but is not completely contained by it. \ 1419 This may be an annotation error."} },
1422 "A CDS is overlapped by an mRNA feature, but the mRNA does not cover all \ 1423 intervals (i.e., exons) on the CDS. This may be an annotation error."} },
1425{
"OverlappingPeptideFeat",
1426 "The intervals on this processed protein feature overlap another protein feature. \ 1427 This may be caused by errors in originally annotating these features on DNA coordinates, \ 1428 where start or stop positions do not occur in between codon boundaries. These then \ 1429 appear as errors when the features are converted to protein coordinates by mapping \ 1430 through the CDS."} },
1432{
"SerialInComment",
1433 "Comments that refer to the conclusions of a specific reference should not be \ 1434 cited by a serial number inside brackets (e.g., [3]), but should instead be \ 1435 attached as a REMARK on the reference itself."} },
1437{
"MultipleCDSproducts",
1438 "More than one CDS feature points to the same protein product. This can happen with \ 1439 viral long terminal repeats (LTRs), but GenBank policy is to have each equivalent \ 1440 CDS point to a separately accessioned protein Bioseq."} },
1442{
"FocusOnBioSourceFeature",
1443 "The /focus flag is only appropriate on BioSource descriptors, not BioSource features."} },
1445{
"PeptideFeatOutOfFrame",
1446 "The start or stop positions of this processed peptide feature do not occur in between \ 1447 codon boundaries. This may incorrectly overlap other peptides when the features are \ 1448 converted to protein coordinates by mapping through the CDS."} },
1450{
"InvalidQualifierValue",
1451 "The value of this qualifier is constrained to a particular vocabulary of style. This \ 1452 value does not conform to those constraints. Please see the feature table documentation \ 1453 for more information."} },
1456 "An mRNA is overlapped by a gene feature, but is not completely contained by it. \ 1457 This may be an annotation error."} },
1460 "The mRNA sequence that was supplied is not the same length as the \ 1461 transcription of the mRNA feature. Please determine why they are different."} },
1463{
"TranscriptMismatches",
1464 "The mRNA sequence and the transcription of the mRNA feature are different. \ 1465 If the number is large, it may indicate incorrect intron/exon boundaries."} },
1467{
"CDSproductPackagingProblem",
1468 "The nucleotide location and protein product of the CDS are not packaged together \ 1469 in the same nuc-prot set. This may be an error in the software used to create \ 1472{
"DuplicateExonInterval",
1473 "The location has identical adjacent intervals, e.g., a duplicate exon reference."} },
1475{
"DuplicateAnticodonInterval",
1476 "The location has identical adjacent intervals, e.g., a duplicate exon reference."} },
1478{
"PolyAsiteNotPoint",
1479 "A polyA_site should be at a single nucleotide position."} },
1482 "An import feature loc field does not equal the feature location. This should be \ 1483 corrected, and then the loc field should be cleared."} },
1485{
"LocOnSegmentedBioseq",
1486 "Feature locations traditionally go on the individual parts of a segmented bioseq, not \ 1487 on the segmented sequence itself. These features are invisible in asn2ff reports, and \ 1488 are now being flagged for correction."} },
1490{
"UnnecessaryCitPubEquiv",
1491 "A set of citations on a feature should not normally have a nested Pub-equiv construct. \ 1492 This may prevent proper matching to the correct publication."} },
1494{
"ImpCDShasTranslation",
1495 "A CDS that has known translation errors cannot have a /translation qualifier."} },
1497{
"ImpCDSnotPseudo",
1498 "A CDS that has known translation errors must be marked as pseudo to suppress the \ 1501{
"MissingMRNAproduct",
1502 "The mRNA feature points to a cDNA product that is not packaged in the record. \ 1503 This is an error in the genomic product set."} },
1505{
"AbuttingIntervals",
1506 "The start of one interval is next to the stop of another. A single interval \ 1507 may be desirable in this case."} },
1509{
"MultiIntervalGene",
1510 "A gene feature on a single Bioseq should have a single interval spanning everything \ 1511 considered to be under that gene."} },
1513{
"FeatContentDup",
1514 "The intervals on this feature are identical to another feature of the same type, \ 1515 and the label and comment are also identical. This is likely to be an error in \ 1516 annotating the record. Note that GenBank format suppresses duplicate features, \ 1517 so use of Graphic view is recommended."} },
1519{
"BadProductSeqId",
1520 "The feature product refers to a database ID that has a locus name but no accession. \ 1521 This is probably an error in parsing of a submission."} },
1523{
"RnaProductMismatch",
1524 "The RNA feature product type does not correspond to the RNA feature type. These \ 1525 need to be consistent."} },
1527{
"MissingCDSproduct",
1528 "The CDS should have a product, but does not. Pseudo or short CDSs (less than 6 \ 1529 amino acids), or those marked with a rearrangement required for product exception, \ 1530 are exempt from needing a product."} },
1533 "The tRNA codon recognized is an illegal value."} },
1536 "The tRNA encoded amino acid is an illegal value."} },
1539 "There are gene xrefs but no gene features. Records should normally have single-interval \ 1540 gene features covering other biological features. Gene xrefs are used only to override \ 1541 the inheritance by overlap."} },
1543{
"UTRdoesNotAbutCDS",
1544 "The 5'UTR and 3'UTR features should exactly abut the CDS feature."} },
1546{
"BadConflictFlag",
1547 "The coding region conflict flag is set, but the translated product is the \ 1548 same as the instantiated product Bioseq."} },
1550{
"ConflictFlagSet",
1551 "The coding region conflict flag is appropriately set, but this record should \ 1552 be brought to the attention of the source database for possible correction."} },
1554{
"LocusTagProblem",
1555 "A gene locus_tag should be a single token, with no spaces."} },
1557{
"CollidingLocusTags",
1558 "Two gene features should not have the same locus_tag, which is supposed to be \ 1559 a unique identifer."} },
1561{
"AltStartCodonException",
1562 "An alternative start codon was used. This is rare, and it is expected that \ 1563 confirmatory evidence will be cited."} },
1565{
"PartialsInconsistent",
1566 "There are several places in an entry where a sequence can be described as \ 1567 either partial or complete. In this entry, these settings are inconsistent. \ 1568 Make sure that the location and product Seq-locs, the Bioseqs, and the \ 1569 SeqFeat partial flag all agree in describing this SeqFeat as partial or \ 1572{
"GenesInconsistent",
1573 "The gene on the genomic sequence of a genomic product set should be the \ 1574 same as the gene on the cDNA product of the mRNA feature."} },
1576{
"DuplicateTranslExcept",
1577 "There are multiple /transl_except qualifiers at the same location on this \ 1578 CDS but with different amino acids indicated."} },
1580{
"TranslExceptAndRnaEditing",
1581 "A CDS has both /exception=RNA editing and /transl_except qualifiers. RNA \ 1582 editing indicates post-transcriptional changes prior to translation. Use \ 1583 /transl_except for individual codon exceptions such as selenocysteine or \ 1584 other nonsense suppressors."} },
1586{
"NoNameForProtein",
1587 "A protein feature has a description, but no product name."} },
1589{
"TaxonDbxrefOnFeature",
1590 "A BioSource feature has a taxonID database identifier in the db_xref area \ 1591 common to all features. This db_xref should only exist within the separate \ 1592 BioSource xref list."} },
1594{
"UnindexedFeature",
1595 "The location of a feature does not allow it to be mapped to a single Bioseq, \ 1596 or to the segmented parent if on one or more part Bioseqs. It will not show \ 1597 up in flatfile and other formats, and should be corrected or removed."} },
1599{
"CDSmRNAmismatch",
1600 "There should usually be a one-to-one correspondence between mRNA and CDS \ 1601 under a given gene."} },
1603{
"UnnecessaryException",
1604 "The feature is marked with an exception qualifier, but the validator does \ 1605 not detect an error that needs to be suppressed."} },
1607{
"LocusTagProductMismatch",
1608 "In certain records a policy is that the locus_tag of the gene is expected to \ 1609 match the prefix of the general ID of the CDS or mRNA product Bioseq."} },
1612 "A fundamental error occurred in software while attempting to transcribe this \ 1613 messenger RNA. It is either a software problem or sever data corruption."} },
1615{
"PseudoCdsViaGeneHasProduct",
1616 "A coding region overlapped by a pseudo gene has a protein product. There \ 1617 should be no protein product bioseq on a pseudo CDS."} },
1619{
"MissingGeneXref",
1620 "This feature has multiple overlapping genes of the same length, but no \ 1621 xref to determine which one should be used for the /gene qualifier."} },
1623{
"FeatureCitationProblem",
1624 "This feature has a citation to a publication that needs to be repaired."} },
1626{
"NestedSeqLocMix",
1627 "A location should not have nested SEQLOC_MIX structures."} },
1629{
"WrongQualOnFeature",
1630 "This qualifier is not legal for this feature."} },
1632{
"MissingQualOnFeature",
1633 "An essential qualifier for this feature is missing."} },
1635{
"CodonQualifierUsed",
1636 "The codon qualifier should be replaced by individual transl_except code breaks, \ 1637 after checking to make sure the proper genetic code is being used."} },
1639{
"UnknownFeatureQual",
1640 "A feature has an unrecognized qualifier."} },
1642{
"BadCharInAuthorName",
1643 "An author name has illegal characters."} },
1646 "The mRNA feature has polyA tail added to make the mRNA sequence."} },
1648{
"ProteinNameEndsInBracket",
1649 "The protein name ends with a right square bracket, and may have been \ 1650 copied from another GenPept record, where the organism name is \ 1651 appended to the definition line and placed inside brackets."} },
1653{
"CDSwithMultipleMRNAs",
1654 "The CDS feature has more than one overlapping mRNA with the proper intervals and \ 1655 no other identification assigning it to a different coding region."} },
1657{
"MultipleEquivBioSources",
1658 "Multiple equivalent biosource features exist on the sequence. They should be \ 1659 fused into a single feature with multiple intervals."} },
1661{
"MultipleEquivPublications",
1662 "Multiple equivalent publication features exist on the sequence. They should be \ 1663 fused into a single feature with multiple intervals."} },
1665{
"BadFullLengthFeature",
1666 "A publication or biosource feature is on the full length the sequence. It should be \ 1667 converted to a publication or biosource descriptor."} },
1669{
"RedundantFields",
1670 "A comment or other field contains information that is redundant with the primary \ 1671 field on a feature."} },
1673{
"CDSwithNoMRNAOverlap",
1674 "The CDS feature has no overlapping mRNA with the proper intervals."} },
1677 "The CDS feature has no matching mRNA. Matches are identified via xref \ 1680{
"FeatureProductInconsistency",
1681 "The CDS feature has more than one overlapping mRNA with the proper intervals and \ 1682 no other identification assigning it to a different coding region."} },
1684{
"ImproperBondLocation",
1685 "Only bond features should have locations of type bond. Most other features should \ 1686 use interval or point locations."} },
1688{
"GeneXrefWithoutGene",
1689 "This feature has a gene xref, but there is no equivalent gene feature anywhere \ 1690 on the record."} },
1692{
"SeqFeatXrefProblem",
1693 "This feature has a seqfeat xref, but it has nothing in the id or data field."} },
1695{
"ProductFetchFailure",
1696 "Unable to fetch the Bioseq product of this feature. Remote fetching was requested, \ 1697 so this is likely due to a failure in a network sequence retrieval service."} },
1699{
"SuspiciousGeneXref",
1700 "This feature has a gene xref that is not expected for this organism."} },
1703 "The tRNA encoded amino acid is not set."} },
1705{
"CollidingFeatureIDs",
1706 "Multiple features have the same featureID. Feature ID must be unique within \ 1709{
"ExceptionProblem",
1710 "There is a problem with /exception text."} },
1712{
"PolyAsignalNotRange",
1713 "A polyA_signal should be at nucleotide range position, not a single point."} },
1715{
"OldLocusTagMismtach",
1716 "The old_locus_tag qualifier on a feature does not match that on the overlapping gene."} },
1718{
"DuplicateGeneOntologyTerm",
1719 "A feature has multiple identical Gene Ontology (GO) term specifications."} },
1721{
"InvalidInferenceValue",
1722 "The value of the inference qualifier is constrained by agreement of the international \ 1723 nucleotide sequence database collaboration. This value does not conform to those \ 1724 constraints. Please see the feature table documentation for more information."} },
1726{
"HypotheticalProteinMismatch",
1727 "There is a mismatch between the accession cited by the hypothetical protein claim \ 1728 and the actual accession of the record."} },
1730{
"FeatureRefersToAccession",
1731 "There is a mixture of features referring to sequence by gi numbers and by accession. \ 1732 This inconsistency is likely due to incomplete processing by software."} },
1734{
"SelfReferentialProduct",
1735 "A feature product points to the same sequence that the feature location does. \ 1736 The product must point to a different sequence that is the biological product \ 1737 of the first, due to transcription, translation, or peptide processing."} },
1739{
"ITSdoesNotAbutRRNA",
1740 "The internal transcribed spacer misc_RNA features should exactly abut the flanking rRNA features."} },
1742{
"FeatureSeqIDCaseDifference",
1743 "Feature location and referenced Bioseq have the same Seq-id except for capitalization. \ 1744 Sequence identifiers must be unique in a case-insensitive manner within a record."} },
1746{
"FeatureLocationIsGi0",
1747 "Feature location refers to gi 0. This indicates an error in database processing of this record."} },
1749{
"GapFeatureProblem",
1750 "Gap features must only cover gaps in the sequence, not actual bases."} },
1752{
"PseudoCdsHasProtXref",
1753 "A coding region flagged as pseudo has a protein cross reference. There should be no \ 1754 protein product bioseq or protein cross reference on a pseudo CDS."} },
1756{
"ErroneousException",
1757 "The feature is marked with a specific exception qualifier, but validation indicates \ 1758 that a different exception should be used."} },
1760{
"SegmentedGeneProblem",
1761 "A gene feature on the parts of a segmented Bioseq should map to a single interval on the \ 1762 segmented Bioseq's coordinate system."} },
1765 "Feature location is set to whole, the entirety of the parent sequence. Please specify \ 1766 exact intervals for this feature location."} },
1768{
"BadEcNumberFormat",
1769 "There is a problem with the format of the EC_number qualifier."} },
1771{
"BadEcNumberValue",
1772 "There is a problem with the value of the EC_number qualifier."} },
1774{
"EcNumberProblem",
1775 "There is a problem with the format of the EC_number qualifier."} },
1777{
"VectorContamination",
1778 "Contamination by cloning vector is annotated on this sequence. The underlying region \ 1779 should be removed from the sequence."} },
1781{
"MinusStrandProtein",
1782 "A feature on a protein indicates the minus strand, which does not exist."} },
1784{
"BadProteinName",
1785 "A protein feature has a name that conflicts with other information on the feature."} },
1787{
"GeneXrefWithoutLocus",
1788 "A feature has a gene xref with a locus_tag and no locus, but the gene with that locus_tag has a locus."} },
1790{
"UTRdoesNotExtendToEnd",
1791 "The UTR does not have the expected range."} },
1793{
"CDShasTooManyXs",
1794 "The CDS translation has greater than 50 percent ambiguous X residues."} },
1796{
"SuspiciousFrame",
1797 "The CDS has a frame greater than 1 that is not expected in this context."} },
1799{
"TerminalXDiscrepancy",
1800 "The CDS translation and protein product sequence have a different number of terminal Xs."} },
1802{
"UnnecessaryTranslExcept",
1803 "The CDS translates to the same amino acid as indicated by the transl_except code break."} },
1805{
"SuspiciousQualifierValue",
1806 "The value of this qualifier is constrained to a particular vocabulary of style. This \ 1807 value appears not to conform to those constraints. Please see the feature table documentation \ 1808 for more information."} },
1810{
"NotSpliceConsensusDonor",
1811 "Splice junctions typically have GT as the first two bases of the intron \ 1812 (splice donor) and AG as the last two bases of the intron (splice acceptor). \ 1813 This intron does not conform to that pattern."} },
1815{
"NotSpliceConsensusAcceptor",
1816 "Splice junctions typically have GT as the first two bases of the intron \ 1817 (splice donor) and AG as the last two bases of the intron (splice acceptor). \ 1818 This intron does not conform to that pattern."} },
1820{
"RareSpliceConsensusDonor",
1821 "Splice junctions typically have GT as the first two bases of the intron \ 1822 (splice donor) and AG as the last two bases of the intron (splice acceptor). \ 1823 This intron does not conform to that pattern."} },
1825{
"SeqFeatXrefNotReciprocal",
1826 "Feature xrefs between CDS and mRNA are not reciprocal."} },
1828{
"SeqFeatXrefFeatureMissing",
1829 "The feature referenced by a seqfeat xref cannot be found."} },
1831{
"FeatureInsideGap",
1832 "The feature is completely contained inside a sequence gap."} },
1834{
"FeatureCrossesGap",
1835 "The feature extends from actual sequence into a sequence gap."} },
1837{
"BadAuthorSuffix",
1838 "An author name has an unexpected suffix."} },
1840{
"BadAnticodonAA",
1841 "The tRNA encoded amino acid cannot be produced by any likely reverse complement \ 1842 and wobble expansion of the anticodon sequence."} },
1844{
"BadAnticodonCodon",
1845 "The tRNA indicated codon recognized cannot be produced by any likely reverse complement \ 1846 and wobble expansion of the anticodon sequence."} },
1848{
"AnticodonStrandConflict",
1849 "The tRNA feature location and anticodon location are not on the same strand."} },
1851{
"UndesiredGeneSynonym",
1852 "The gene synonym is uninformative."} },
1854{
"UndesiredProteinName",
1855 "The protein name is uninformative."} },
1857{
"FeatureBeginsOrEndsInGap",
1858 "The feature starts or stops within a sequence gap."} },
1860{
"GeneOntologyTermMissingGOID",
1861 "A Gene Ontology (GO) term is missing the GO Identifier."} },
1863{
"PseudoRnaHasProduct",
1864 "An RNA flagged as pseudo has a transcribed product. There should be no \ 1865 transcribed product bioseq on a pseudo RNA."} },
1867{
"PseudoRnaViaGeneHasProduct",
1868 "An RNA overlapped by a pseudo gene has a transcribed product. There \ 1869 should be no transcribed product bioseq on a pseudo RNA."} },
1871{
"BadRRNAcomponentOrder",
1872 "rRNA and ITS features are not in the expected order."} },
1874{
"BadRRNAcomponentOverlap",
1875 "rRNA and ITS or tRNA elements should not overlap."} },
1877{
"MissingGeneLocusTag",
1878 "If one gene in a record has a locus-tag value, all genes in the record \ 1879 should have a locus-tag value."} },
1881{
"MultipleProtRefs",
1882 "The name and description of the protein is missing from this entry. Every \ 1883 protein Bioseq must have one full-length Prot-ref feature to provide this \ 1886{
"BadInternalCharacter",
1887 "Biological names or labels should not end with question mark, \ 1888 exclamation point, or tilde."} },
1890{
"BadTrailingCharacter",
1891 "Biological names or labels should not contain underscore, period, \ 1892 comma, colon, or semicolon,"} },
1894{
"BadTrailingHyphen",
1895 "Biological names or labels should not end with a hyphen."} },
1897{
"MultipleGeneOverlap",
1898 "This genes completely contains two or more other genes."} },
1900{
"BadCharInAuthorLastName",
1901 "An author name has illegal characters."} },
1903{
"PseudoCDSmRNArange",
1904 "A pseudo CDS is overlapped by an mRNA feature, but the mRNA does not cover all \ 1905 intervals (i.e., exons) on the CDS. This may be an annotation error."} },
1907{
"ExtendablePartialProblem",
1908 "A partial end of this feature does not abut a gap and does not include the first \ 1909 or last nucleotide in the sequence, but it could be extended by one or two \ 1910 nucleotides to do so."} },
1912{
"GeneXrefNeeded",
1913 "This feature has multiple overlapping genes of the same length and same name, \ 1914 but no xref to determine which one should be used for the /gene qualifier."} },
1916{
"RubiscoProblem",
1917 "A protein name contains ribulose and bisphosphate but does not use \ 1918 the prefered formal naming convention."} },
1920{
"ProteinNameHasPMID",
1921 "The protein name has (PMID #####) embedded in it."} },
1923{
"BadGeneOntologyFormat",
1924 "A feature has incorrectly labeled fields in a Gene Ontology (GO) term specification."} },
1926{
"InconsistentGeneOntologyTermAndId",
1927 "The same GO term should apply to Gene Ontology (GO) term specifications with the same GO ID."} },
1929{
"DuplicateGeneConflictingLocusTag",
1930 "Two gene features with the same name are annotated at the same location."} },
1933 "Introns should be longer than 10 nt."} },
1935{
"GeneXrefStrandProblem",
1936 "This feature has a gene xref that points to a gene on the wrong strand."} },
1938{
"CDSmRNAXrefLocationProblem",
1939 "The CDS is not contained within the cross-referenced mRNA"} },
1941{
"LocusCollidesWithLocusTag",
1942 "A gene locus is identical with a gene locus_tag."} },
1944{
"IdenticalGeneSymbolAndSynonym",
1945 "The gene synonym is the same as the locus of a different gene."} },
1947{
"RptUnitRangeProblem",
1948 "The value of the rpt_unit_range qualifier is not inside the parent feature location."} },
1950{
"TooManyInferenceAccessions",
1951 "There are too many inference qualifier accessions to have their versions verified by network access."} },
1953{
"SgmlPresentInText",
1954 "SGML markup is embedded in text."} },
1956{
"MissingLocation",
1957 "A feature must specify its location."} },
1959{
"MultipleBioseqs",
1960 "Feature location refers to multiple near non-part bioseqs."} },
1962{
"DifferntIdTypesInSeqLoc",
1963 "All ids in a single seq-loc which refer to the same bioseq should be of the \ 1966{
"IntervalBeginsOrEndsInGap",
1967 "An internal interval of the feature starts or stops within a sequence gap."} },
1969{
"InconsistentRRNAstrands",
1970 "rRNA and ITS features are not on the same strand."} },
1972{
"CDSonMinusStrandMRNA",
1973 "Coding regions should be on the plus strand of mRNA molecules."} },
1976 "An mRNA feature has annotation indicating that it is really a tRNA."} },
1979 "The protein sequence that was supplied is not the same length as the translation of the coding region."} },
1981{
"InconsistentPseudogeneCounts",
1982 "There are pseudo features with and without pseudogene qualifiers."} },
1984{
"DeletedEcNumber",
1985 "The EC_number has been deleted."} },
1987{
"ReplacedEcNumber",
1988 "The EC_number has been replaced."} },
1991 "The EC_number has been split."} },
1993{
"PeptideFeatureLacksCDS",
1994 "The peptide feature cannot be assigned to a CDS parent, and thus cannot be mapped to the protein product."} },
1996{
"EcNumberDataMissing",
1997 "An EC_number qualifier data file is missing or unreadable."} },
2000 "Internal exon is too short."} } ,
2002{
"ExtraProteinFeature",
2003 "Protein sequence has multiple protein features that are not signal peptides, mature peptides, transit peptides, or preproteins."} } ,
2005{
"AssemblyGapAdjacentToNs",
2006 "Assembly_gap features must cover the entire contiguous sequence gaps."} },
2008{
"AssemblyGapCoversSequence",
2009 "Assembly_gap features must not cover actual bases in the sequence."} },
2011{
"FeatureBeginsOrEndsWithN",
2012 "The feature starts or stops with an N."} },
2014{
"FeatureIsMostlyNs",
2015 "The feature contains more than 50% of Ns."} },
2017{
"CDSonMinusStrandTranscribedRNA",
2018 "Coding regions should be on the plus strand of transcribed RNA molecules."} },
2020{
"MultipleGenCodes",
2021 "The genetic codes are the same for all CDS features on one Bioseq."} },
2024 "Incorrect use of Int-fuzz.lim"} },
2027 "Comment is inconsistent with content of feature."} },
2029{
"IntronIsStopCodon",
2030 "3 base intron actually contains a stop codon."} },
2032{
"InconsistentPseudogeneValue",
2033 "Pseudogene qualifiers do not match between a CDS or mRNA and the parent gene."} },
2035{
"MultiIntervalIntron",
2036 "Introns should only have a single interval."} },
2038{
"SeqLocTypeProblem",
2039 "A sequence location component is not the expected type."} },
2042 "The term RefSeq should not appear in a product name or a definition line."} },
2044{
"ColdShockProteinProblem",
2045 "A misc_feature containing cspA should not overlap a cold-shock protein CDS."} },
2048 "There is a problem with this feature location."} },
2050{
"GenCodeInvalid",
2051 "A coding region contains invalid genetic code."} },
2053{
"TranslExceptIsPartial",
2054 "A translation exception location should not be partial."} },
2056{
"GeneIdMismatch",
2057 "GeneID for parent and child features should match."} },
2059{
"ProductShouldBeWhole",
2060 "Feature products should be entire sequences."} },
2062{
"CDSmRNAMismatchProteinIDs",
2063 "A CDS-mRNA pair should hav matching protein_ids"} },
2065{
"CDSmRNAMissingProteinIDs",
2066 "A CDS-mRNA pair should have matching protein_ids"} },
2068{
"CDSmRNAMismatchTranscriptIDs",
2069 "A CDS-mRNA pair should hav matching transcript_ids"} },
2071{
"CDSmRNAmismatchCount",
2072 "A gene should contain the same number of mRNA features as coding region features"} },
2074{
"CDSmRNAMismatchLocation",
2075 "The coding region location should match the mRNA location"} },
2077{
"CDSmRNANotMatched",
2078 "Each mRNA feature should have a corresponding coding region feature"} },
2080{
"PartialProblemHasStop",
2081 "Feature has stop codon, but 3'end is labeled partial"} },
2083{
"PartialProblemMismatch3Prime",
2084 "Coding region should not be 3' partial if parent is 3' complete"} },
2086{
"PartialProblemMismatch5Prime",
2087 "Coding region should not be 5' partial if parent is 5' complete"} },
2089{
"PartialProblemNotSpliceConsensus3Prime",
2090 "3' partial is not at end of sequence, gap, or consensus splice site"} },
2092{
"PartialProblemNotSpliceConsensus5Prime",
2093 "5' partial is not at beginning of sequence, gap, or consensus splice site"} },
2095{
"PartialProblemmRNASequence5Prime",
2096 "Start does not include first/last residue of mRNA sequence"} },
2098{
"PartialProblemmRNASequence3Prime",
2099 "Stop does not include first/last residue of mRNA sequence"} },
2101{
"PartialProblemOrganelle5Prime",
2102 "Start does not include first/last residue of organelle sequence (organelle does not use standard splice site convention)"} },
2104{
"PartialProblemOrganelle3Prime",
2105 "Stop does not include first/last residue of organelle sequence (organelle does not use standard splice site convention)"} },
2107{
"PartialProblem5Prime",
2108 "Start does not include first/last residue of sequence"} },
2110{
"PartialProblem3Prime",
2111 "Stop does not include first/last residue of sequence"} },
2113{
"PartialsInconsistentCDSProtein",
2114 "Coding region and protein feature partials conflict"} },
2116{
"InvalidPseudoQualifier",
2117 "Pseudogene qualifier has a controlled vocabulary"} },
2119{
"InvalidRptUnitRange",
2120 "/rpt_unit_range should be a base range"} },
2122{
"InvalidRptUnitSeqCharacters",
2123 "/rpt_unit_seq has illegal characters"} },
2125{
"InvalidRepeatUnitLength",
2126 "Length of rpt_unit_seq should be equal to or shorter than feature length"} },
2128{
"MismatchedAllele",
2129 "allele qualifiers on features and genes should match"} },
2131{
"InvalidOperonMatchesGene",
2132 "Operon name should not match gene name"} },
2134{
"InvalidPunctuation",
2135 "Other than /replace, a qualifier should contain more than just quotation marks"} },
2137{
"InvalidAlleleDuplicates",
2138 "Do not add redundant allele qualifiers to features for which the gene has an allele"} },
2140{
"InvalidCompareRefSeqAccession",
2141 "Do not use RefSeq accessions for qualifier compare"} },
2143{
"RepeatSeqDoNotMatch",
2144 "repeat_region /rpt_unit and underlying sequence should match"} },
2146{
"RecombinationClassOtherNeedsNote",
2147 "If recombination_class is 'other' a note should be present"} },
2149{
"RegulatoryClassOtherNeedsNote",
2150 "If regulatory_class is 'other' a note should be present"} },
2152{
"UnparsedtRNAAnticodon",
2153 "Unparsed anticodon qualifier in tRNA"} },
2155{
"UnparsedtRNAProduct",
2156 "Unparsed product qualifier in tRNA"} },
2158{
"rRNADoesNotHaveProduct",
2159 "An rRNA feature should have a product name"} },
2161{
"InvalidCompareMissingVersion",
2162 "/compare should have both an accession and a version"} },
2164{
"InvalidCompareBadAccession",
2165 "/compare should include a valid accession"} },
2167{
"MobileElementInvalidQualifier",
2168 "/mobile_element has a controlled vocabulary"} },
2170{
"InvalidReplace",
2171 "A /replace qualifier should only be composed of nucleotide or amino acid characters"} },
2173{
"InvalidVariationReplace",
2174 "A variation qualifier should should only be composed of acgt unambiguous nucleotide bases"} },
2176{
"InvalidNumberQualifier",
2177 "Number qualifiers should not contain spaces"} },
2179{
"InvalidProductOnGene",
2180 "A product qualifier is not used on a gene feature"} },
2182{
"InvalidMatchingReplace",
2183 "The value of a /replace qualifier should be different from the underlying sequence"} },
2185{
"InvalidCodonStart",
2186 "A codon_start value should be 1, 2, or 3"} },
2188{
"WrongQualOnCDS",
2189 "A gene_synonym value should go on a gene, rather than a coding region feature"} },
2191{
"EcNumberInCDSComment",
2192 "Enzyme Commission Numbers should not be placed in coding region comments; they should be placed in the protein feature EC field"} },
2194{
"EcNumberInProteinName",
2195 "Enzyme Commission Numbers should not be placed in protein names; they should be placed in the protein feature EC field"} },
2197{
"EcNumberInProteinComment",
2198 "Enzyme Commission Numbers should not be placed in protein comments; they should be placed in the protein feature EC field"} },
2201 "EC number field should not be blank"} },
2203{
"GeneLocusCollidesWithLocusTag",
2204 "A locus value for one gene should not be reused for a locus-tag on another gene"} },
2206{
"LocusTagGeneLocusMatch",
2207 "A gene locus and a gene locus-tag should be different values"} },
2209{
"LocusTagHasSpace",
2210 "Gene locus tags should not have spaces"} },
2212{
"OldLocusTagBadFormat",
2213 "old-locus-tag values should not contain commas. Multiple old_locus_tags should be split into separate qualifiers."} },
2215{
"OldLocusTagWithoutLocusTag",
2216 "A feature should not have an old-locus-tag value if it does not have a locus-tag value"} },
2218{
"BadRRNAcomponentOverlapRRNA",
2219 "Internal transcribed spacers should not overlap adjacent rRNA components"} },
2221{
"BadRRNAcomponentOverlapAndOrder",
2222 "rRNA components should appear in the correct order and not overlap"} },
2224{
"BadRRNAcomponentOverlapTRNA",
2225 "rRNA features should not overlap tRNA features"} },
2227{
"NotSpliceConsensusAcceptorTerminalIntron",
2228 "Introns should end with a splice consensus acceptor"} },
2230{
"NotSpliceConsensusDonorTerminalIntron",
2231 "Introns should begin with a splice consensus donor"} },
2233{
"IdenticalMRNAtranscriptIDs",
2234 "Identical transcript IDs should not appear on multiple mRNAs"} },
2236{
"InvalidFeatureForMRNA",
2237 "mRNA feature should not appear on an mRNA (cDNA) Bioseq."} },
2239{
"InvalidFeatureForNucleotide",
2240 "Invalid feature for a nucleotide Bioseq."} },
2242{
"InvalidFeatureForProtein",
2243 "Invalid feature for a protein Bioseq."} },
2245{
"InvalidRNAFeature",
2246 "RNA feature should be converted to the appropriate RNA feature subtype"} },
2248{
"InvalidTRNAdata",
2249 "tRNA data structure should not appear on a non-tRNA feature"} },
2251{
"mRNAUnnecessaryException",
2252 "mRNA should not have unqualified transcribed product replaced exception"} },
2254{
"AssemblyGapFeatureProblem",
2255 "An assembly_gap feature should only be on a contig record"} },
2257{
"ExceptionMissingText",
2258 "Exception flag is set, but exception text is empty"} },
2260{
"MiscFeatureNeedsNote",
2261 "A note or other qualifier is required for a misc_feature"} },
2263{
"MissingExceptionFlag",
2264 "Exception text is present, but exception flag is not set"} },
2266{
"NoCDSbetweenUTRs",
2267 "Gene has both 5'UTR and 3'UTR but does not have a coding region"} },
2269{
"RepeatRegionNeedsNote",
2270 "A repeat_region feature should have qualifiers or a note"} },
2273 "A code-break location should fall inside the coding region feature location"} } ,
2276 "An anticodon location should fall inside the tRNA feature location"} } ,
2278{
"ExceptionRequiresLocusTag",
2279 "Genes with an exception indicating that the gene was split must have a locus-tag value"} },
2281{
"BadTranssplicedInterval",
2282 "a trans-spliced feature should have multiple intervals"} },
2284{
"TRNAinsideTMRNA",
2285 "tRNA should not be contained within tmRNA"} },
2287{
"IncorrectQualifierCapitalization",
2288 "The qualifier name is incorrectly capitalized"} },
2290{
"CDSdoesNotMatchVDJC",
2291 "The CDS does not have a parent VDJ or C segment"} },
2293{
"GeneOnNucPositionOfPeptide",
2294 "Peptide under CDS matches small Gene"} },
2296{
"ShortTRNAIntron",
2297 "Bacterial tRNA intron less than 100 bp"} },
2299{
"BadCDScomponentOverlapTRNA",
2300 "CDS features should not overlap tRNA features"} },
2303 "Feature location uses strand other"} },
2309 "The seqence referenced by an alignment SeqID is not packaged in the record."} },
2312 "Please contact the sequence database for further help with this error."} },
2314{
"DensegLenStart",
2315 "Please contact the sequence database for further help with this error."} },
2317{
"StartLessthanZero",
2318 "Please contact the sequence database for further help with this error."} },
2320{
"StartMorethanBiolen",
2321 "Please contact the sequence database for further help with this error."} },
2323{
"EndLessthanZero",
2324 "Please contact the sequence database for further help with this error."} },
2326{
"EndMorethanBiolen",
2327 "Please contact the sequence database for further help with this error."} },
2329{
"LenLessthanZero",
2330 "Please contact the sequence database for further help with this error."} },
2332{
"LenMorethanBiolen",
2333 "Please contact the sequence database for further help with this error."} },
2336 "Please contact the sequence database for further help with this error."} },
2338{
"AlignDimSeqIdNotMatch",
2339 "Please contact the sequence database for further help with this error."} },
2341{
"SegsDimSeqIdNotMatch",
2342 "Please contact the sequence database for further help with this error."} },
2345 "Please contact the sequence database for further help with this error."} },
2348 "Please contact the sequence database for further help with this error."} },
2351 "Please contact the sequence database for further help with this error."} },
2354 "Please contact the sequence database for further help with this error."} },
2357 "Please contact the sequence database for further help with this error."} },
2360 "Please contact the sequence database for further help with this error."} },
2363 "BLAST alignments are not desired in records submitted to the sequence database."} },
2365{
"PercentIdentity",
2366 "An acceptable percent identity score is 75 percent or higher."} },
2369 "Alignment is shorter than expected."} },
2371{
"UnexpectedAlignmentType",
2372 "Only DenseSeg alignments are expected."} },
2375{
"SegsDimMismatch",
2376 "Please contact the sequence database for further help with this error."} },
2378{
"SegsNumsegMismatch",
2379 "Please contact the sequence database for further help with this error."} },
2381{
"SegsStartsMismatch",
2382 "Please contact the sequence database for further help with this error."} },
2384{
"SegsPresentMismatch",
2385 "Please contact the sequence database for further help with this error."} },
2387{
"SegsPresentStartsMismatch",
2388 "Please contact the sequence database for further help with this error."} },
2390{
"SegsPresentStrandsMismatch",
2391 "Please contact the sequence database for further help with this error."} },
2393{
"NucProtMixture",
2394 "The alignment refers to a mixture of nucleotides and proteins."} },
2401 "The graph minimum value is outside of the 0-100 range."} },
2404 "The graph maximum value is outside of the 0-100 range."} },
2407 "Some quality scores are below the stated graph minimum value."} },
2410 "Some quality scores are above the stated graph maximum value."} },
2413 "The number of bytes in the quality graph does not correspond to the \ 2414 stated length of the graph."} },
2416{
"GraphOutOfOrder",
2417 "The quality graphs are not packaged in order - may be due to an old fa2htgs bug."} },
2419{
"GraphBioseqLen",
2420 "The length of the quality graph does not correspond to the length of the Bioseq."} },
2422{
"GraphSeqLitLen",
2423 "The length of the quality graph does not correspond to the length of the \ 2424 delta Bioseq literal component."} },
2426{
"GraphSeqLocLen",
2427 "The length of the quality graph does not correspond to the length of the \ 2428 delta Bioseq location component."} },
2430{
"GraphStartPhase",
2431 "The quality graph does not start or stop on a sequence segment boundary."} },
2433{
"GraphStopPhase",
2434 "The quality graph does not start or stop on a sequence segment boundary."} },
2436{
"GraphDiffNumber",
2437 "The number quality graph does not equal the number of sequence segments."} },
2439{
"GraphACGTScore",
2440 "Quality score values for known bases should be above 0."} },
2443 "Quality score values for unknown bases should not be above 0."} },
2446 "Gap positions should not have quality scores above 0."} },
2449 "Quality graphs overlap - may be due to an old fa2htgs bug."} },
2452 "Quality graph does not map to Bioseq in record."} },
2454{
"GraphACGTScoreMany",
2455 "Quality score values for known bases should be above 0."} },
2457{
"GraphNScoreMany",
2458 "Quality score values for unknown bases should not be above 0."} },
2460{
"GraphLocInvalid",
2461 "Location for quality score values extends beyond end of sequence."} },
2468 "Seq-annot.data.ids should only be used for communication between programs."} },
2471 "Seq-annot.data.locs should only be used for communication between programs."} },
2477 "Exception was caught while performing validation. Vaidation terminated."} }
2490 const string&
msg,
2491 const string& desc,
2496 const intseq_offset)
2524 stringdesc =
"FEATURE: ";
2567 returnsc_ErrStrsMap.size();
2573 static const stringkSeqInst =
"SEQ_INST";
2574 static const stringkSeqDescr =
"SEQ_DESCR";
2575 static const stringkGeneric =
"GENERIC";
2576 static const stringkSeqPkg =
"SEQ_PKG";
2577 static const stringkSeqFeat =
"SEQ_FEAT";
2578 static const stringkSeqAlign =
"SEQ_ALIGN";
2579 static const string kSeqGraph=
"SEQ_GRAPH";
2580 static const stringkSeqAnnot =
"SEQ_ANNOT";
2581 static const stringkInternal =
"INTERNAL";
2582 static const string kUnknown=
"UNKNOWN";
2586 #define IS_IN(x) (errIndex > ERR_CODE_BEGIN(x)) && (errIndex < ERR_CODE_END(x)) 2588 if((errIndex <
eErr_MAX) && (errIndex > 0)) {
2589 if(
IS_IN(SEQ_INST) ) {
2591}
else if(
IS_IN(SEQ_DESCR) ) {
2593}
else if(
IS_IN(GENERIC) ) {
2595}
else if(
IS_IN(SEQ_PKG) ) {
2597}
else if(
IS_IN(SEQ_FEAT) ) {
2599}
else if(
IS_IN(SEQ_ALIGN) ) {
2601}
else if(
IS_IN(SEQ_GRAPH) ) {
2603}
else if(
IS_IN(SEQ_ANNOT) ) {
2605}
else if(
IS_IN(INTERNAL) ) {
2626 if(err_it != sc_ErrStrsMap.end()) {
2627 returnerr_it->second.second;
2630 returnsc_ErrStrsMap.find(
eErr_UNKNOWN)->second.second;
2655 "Info",
"Warning",
"Error",
"Critical",
"Fatal",
"Trace" 2658 returnstr_sev[sev];
2667 if(err_it != sc_ErrStrsMap.end()) {
2668 returnerr_it->second.first;
2671 returnsc_ErrStrsMap.find(
eErr_UNKNOWN)->second.first;
2679 while(err_it != sc_ErrStrsMap.end()) {
2681 returnerr_it->first;
2685 returnerr_it->first;
static const TErrTypStrs sc_ErrStrs[]
SStaticPair< unsigned int, TErrStrs > TErrTypStrs
SStaticPair< const char *, const char * > TErrStrs
CStaticArrayMap< unsigned int, pair< string, string > > TErrTypeStrsMap
DEFINE_STATIC_ARRAY_MAP_WITH_COPY(TErrTypeStrsMap, sc_ErrStrsMap, sc_ErrStrs)
User-defined methods of the data storage class.
@ eErr_SEQ_ALIGN_SegsDimSeqIdNotMatch
@ eErr_SEQ_PKG_PartsSetMixedBioseqs
@ eErr_SEQ_DESCR_StructuredCommentPrefixOrSuffixMissing
@ eErr_SEQ_DESCR_DBLinkBadBioSample
@ eErr_SEQ_FEAT_WrongQualOnImpFeat
@ eErr_SEQ_FEAT_NotSpliceConsensusAcceptor
@ eErr_SEQ_DESCR_BadPlastidName
@ eErr_SEQ_DESCR_ObsoleteSourceQual
@ eErr_SEQ_FEAT_PartialProblemMismatch5Prime
@ eErr_SEQ_FEAT_rRNADoesNotHaveProduct
@ eErr_SEQ_GRAPH_GraphACGTScoreMany
@ eErr_SEQ_DESCR_MissingEnvironmentalSample
@ eErr_SEQ_INST_HighNContent
@ eErr_SEQ_DESCR_ObsoleteSourceLocation
@ eErr_SEQ_FEAT_CDSmRNAmismatch
@ eErr_SEQ_INST_HTGS_STS_GSS_WGSshouldNotBeRNA
@ eErr_SEQ_INST_BadDeltaSeq
@ eErr_SEQ_DESCR_TaxonomyConsultRequired
@ eErr_GENERIC_BadFirstName
@ eErr_SEQ_DESCR_InconsistentBioSources_ConLocation
@ eErr_SEQ_INST_FarFetchFailure
@ eErr_SEQ_FEAT_WholeLocation
@ eErr_SEQ_FEAT_mRNAgeneRange
@ eErr_SEQ_FEAT_SegmentedGeneProblem
@ eErr_SEQ_DESCR_BINDoesNotMatch
@ eErr_SEQ_DESCR_MissingPlasmidLocation
@ eErr_SEQ_DESCR_FinishedStatusForWGS
@ eErr_SEQ_DESCR_InconsistentTaxName
@ eErr_GENERIC_MissingPubRequirement
@ eErr_GENERIC_MissingVolume
@ eErr_SEQ_DESCR_DBLinkBadCapitalization
@ eErr_SEQ_PKG_InconsistentMolInfoBiomols
@ eErr_SEQ_FEAT_MobileElementInvalidQualifier
@ eErr_SEQ_FEAT_EcNumberProblem
@ eErr_SEQ_FEAT_TRNAinsideTMRNA
@ eErr_SEQ_FEAT_DuplicateAnticodonInterval
@ eErr_SEQ_INST_CompleteGenomeHasGaps
@ eErr_SEQ_INST_BadSeqIdCharacter
@ eErr_SEQ_FEAT_CDShasTooManyXs
@ eErr_SEQ_FEAT_ShortTRNAIntron
@ eErr_SEQ_FEAT_TranslExceptPhase
@ eErr_SEQ_FEAT_MinusStrandProtein
@ eErr_SEQ_FEAT_NotSpliceConsensusDonor
@ eErr_GENERIC_AuthorListHasEtAl
@ eErr_SEQ_INST_CompleteTitleProblem
@ eErr_SEQ_INST_HistoryGiCollision
@ eErr_SEQ_DESCR_BadNullCountry
@ eErr_SEQ_DESCR_UnwantedCompleteFlag
@ eErr_SEQ_INST_mRNAshouldBeSingleStranded
@ eErr_SEQ_FEAT_GeneXrefWithoutLocus
@ eErr_SEQ_FEAT_MultipleGenCodes
@ eErr_SEQ_DESCR_DBLinkBadAssembly
@ eErr_SEQ_FEAT_BadLocation
@ eErr_SEQ_DESCR_InvalidTissueType
@ eErr_SEQ_ALIGN_LenLessthanZero
@ eErr_SEQ_FEAT_GenesInconsistent
@ eErr_SEQ_DESCR_BadStrucCommInvalidSuffix
@ eErr_SEQ_DESCR_WGSmasterLacksBioProject
@ eErr_SEQ_DESCR_LatLonWater
@ eErr_SEQ_FEAT_FeatureRefersToAccession
@ eErr_SEQ_INST_HighNContentStretch
@ eErr_SEQ_PKG_NoBioseqFound
@ eErr_SEQ_DESCR_TaxonomyServiceProblem
@ eErr_SEQ_INST_HighNcontent3Prime
@ eErr_SEQ_INST_TerminalGap
@ eErr_SEQ_FEAT_PseudoRnaHasProduct
@ eErr_SEQ_FEAT_EcNumberDataMissing
@ eErr_SEQ_DESCR_InconsistentBioSources
@ eErr_SEQ_GRAPH_GraphDiffNumber
@ eErr_SEQ_FEAT_InvalidProductOnGene
@ eErr_SEQ_INST_MultipleAccessions
@ eErr_GENERIC_PastReleaseDate
@ eErr_SEQ_DESCR_BioSourceDbTagConflict
@ eErr_SEQ_DESCR_MultipleDBLinkObjects
@ eErr_SEQ_INST_BadProteinStart
@ eErr_SEQ_FEAT_BadRRNAcomponentOverlapTRNA
@ eErr_SEQ_FEAT_mRNAUnnecessaryException
@ eErr_SEQ_FEAT_UnknownImpFeatQual
@ eErr_SEQ_FEAT_DuplicateExonInterval
@ eErr_GENERIC_UnnecessaryPubEquiv
@ eErr_SEQ_FEAT_PartialProblem3Prime
@ eErr_SEQ_DESCR_BadGenomeRepresentation
@ eErr_SEQ_FEAT_ProductShouldBeWhole
@ eErr_SEQ_DESCR_InconsistentMolTypeBiomol
@ eErr_GENERIC_InvalidAsn
@ eErr_SEQ_INST_ProteinShouldNotHaveGaps
@ eErr_SEQ_GRAPH_GraphNScore
@ eErr_SEQ_INST_ESTshouldBemRNA
@ eErr_SEQ_DESCR_TaxonomyBlankSample
@ eErr_SEQ_DESCR_MissingPersonalCollectionName
@ eErr_SEQ_FEAT_InvalidCodonStart
@ eErr_SEQ_DESCR_BadKeywordUnverified
@ eErr_SEQ_FEAT_ITSdoesNotAbutRRNA
@ eErr_SEQ_DESCR_BioSourceOnProtein
@ eErr_SEQ_DESCR_LatLonRange
@ eErr_SEQ_DESCR_MultipleBioSources
@ eErr_SEQ_FEAT_SuspiciousFrame
@ eErr_SEQ_DESCR_InconsistentProteinTitle
@ eErr_SEQ_FEAT_InvalidCompareBadAccession
@ eErr_SEQ_FEAT_UnnecessaryTranslExcept
@ eErr_SEQ_DESCR_InvalidMolInfo
@ eErr_SEQ_FEAT_InvalidFeatureForNucleotide
@ eErr_SEQ_DESCR_InconsistentMolInfoTechnique
@ eErr_GENERIC_BarcodeStructuredVoucher
@ eErr_SEQ_GRAPH_GraphBioseqId
@ eErr_SEQ_FEAT_InvalidCompareMissingVersion
@ eErr_SEQ_DESCR_NoOrganismInTitle
@ eErr_SEQ_FEAT_InvalidRptUnitRange
@ eErr_SEQ_DESCR_LatLonPrecision
@ eErr_SEQ_DESCR_InconsistentMolInfo
@ eErr_SEQ_FEAT_MixedStrand
@ eErr_SEQ_INST_TSAMasterLacksStrucComm
@ eErr_SEQ_DESCR_BadAssemblyName
@ eErr_SEQ_INST_WholeComponent
@ eErr_SEQ_FEAT_BadRRNAcomponentOrder
@ eErr_SEQ_DESCR_DuplicatePCRPrimerSequence
@ eErr_SEQ_FEAT_BadGeneOntologyFormat
@ eErr_SEQ_INST_ReprInvalid
@ eErr_SEQ_INST_GenomeSeqGapProblem
@ eErr_SEQ_DESCR_LatLonCountry
@ eErr_GENERIC_MissingPubInfo
@ eErr_SEQ_PKG_NucProtSetHasTitle
@ eErr_SEQ_DESCR_RefGeneTrackingOnNucProtSet
@ eErr_SEQ_INST_TSAseqGapProblem
@ eErr_SEQ_FEAT_IllegalDbXref
@ eErr_SEQ_ALIGN_AlignDimSeqIdNotMatch
@ eErr_SEQ_FEAT_MultipleBioseqs
@ eErr_SEQ_DESCR_StrucCommMissingUserObject
@ eErr_GENERIC_SgmlPresentInText
@ eErr_GENERIC_DuplicateIDs
@ eErr_SEQ_DESCR_LatLonAdjacent
@ eErr_SEQ_ALIGN_SeqIdProblem
@ eErr_SEQ_INST_HTGS_STS_GSS_WGSshouldBeGenomic
@ eErr_GENERIC_MissingPagesEpub
@ eErr_GENERIC_MissingISOJTA
@ eErr_SEQ_FEAT_PartialsInconsistentCDSProtein
@ eErr_SEQ_DESCR_BadStrucCommInvalidFieldName
@ eErr_SEQ_PKG_SegSetProblem
@ eErr_SEQ_DESCR_EmptyOrgInput
@ eErr_SEQ_INST_SeqLitDataLength0
@ eErr_SEQ_FEAT_BadAnticodonAA
@ eErr_SEQ_FEAT_MissingCDSproduct
@ eErr_SEQ_DESCR_BadStrucCommInvalidFieldValue
@ eErr_SEQ_GRAPH_GraphOverlap
@ eErr_SEQ_INST_CircBactGenomeProblem
@ eErr_SEQ_FEAT_RnaProductMismatch
@ eErr_SEQ_DESCR_UnstructuredVoucher
@ eErr_SEQ_INST_WGSMasterLacksStrucComm
@ eErr_SEQ_DESCR_TaxonomyIsMetagenome
@ eErr_SEQ_DESCR_BadVariety
@ eErr_SEQ_FEAT_FeatureBeginsOrEndsInGap
@ eErr_SEQ_DESCR_BadInstitutionGeoLocName
@ eErr_SEQ_FEAT_TranslExceptAndRnaEditing
@ eErr_SEQ_DESCR_LatLonOffshore
@ eErr_SEQ_ALIGN_SegsStartsMismatch
@ eErr_SEQ_DESCR_TaxonomyNucleomorphProblem
@ eErr_SEQ_INST_ContigsTooShort
@ eErr_GENERIC_BarcodeTooManyNs
@ eErr_SEQ_FEAT_EcNumberInProteinName
@ eErr_SEQ_GRAPH_GraphByteLen
@ eErr_SEQ_DESCR_BadTypeMaterial
@ eErr_SEQ_FEAT_InvalidTRNAdata
@ eErr_SEQ_PKG_BioseqSetClassNotSet
@ eErr_SEQ_FEAT_SuspiciousGeneXref
@ eErr_SEQ_DESCR_NoMolInfoFound
@ eErr_SEQ_DESCR_OrgModMissingValue
@ eErr_SEQ_FEAT_UnnecessaryException
@ eErr_SEQ_DESCR_SerialInComment
@ eErr_SEQ_FEAT_AssemblyGapFeatureProblem
@ eErr_SEQ_FEAT_OldLocusTagWithoutLocusTag
@ eErr_SEQ_PKG_OrphanedProtein
@ eErr_SEQ_DESCR_NoOrgFound
@ eErr_SEQ_FEAT_NotSpliceConsensusAcceptorTerminalIntron
@ eErr_SEQ_INST_SeqGapBadLinkage
@ eErr_SEQ_FEAT_AnticodonMixedStrand
@ eErr_SEQ_FEAT_PartialProblemMismatch3Prime
@ eErr_SEQ_DESCR_BadPunctuation
@ eErr_SEQ_FEAT_UnparsedtRNAProduct
@ eErr_SEQ_FEAT_MissingProteinName
@ eErr_SEQ_DESCR_BadPCRPrimerSequence
@ eErr_SEQ_FEAT_InconsistentPseudogeneValue
@ eErr_SEQ_FEAT_GeneXrefWithoutGene
@ eErr_SEQ_ALIGN_PercentIdentity
@ eErr_SEQ_INST_SelfReferentialSequence
@ eErr_SEQ_DESCR_TransgenicProblem
@ eErr_SEQ_INST_DeltaComponentIsGi0
@ eErr_GENERIC_BarcodeLowTrace
@ eErr_SEQ_FEAT_ReplacedEcNumber
@ eErr_SEQ_PKG_MissingSetTitle
@ eErr_SEQ_DESCR_UnnecessaryBioSourceFocus
@ eErr_SEQ_FEAT_PartialsInconsistent
@ eErr_SEQ_FEAT_InvalidQualifierValue
@ eErr_SEQ_FEAT_CDSmRNANotMatched
@ eErr_GENERIC_BadPageNumbering
@ eErr_SEQ_FEAT_FeatContentDup
@ eErr_SEQ_INST_MolNotSet
@ eErr_SEQ_DESCR_WGSMasterLacksBothBioSampleBioProject
@ eErr_SEQ_INST_GiWithoutAccession
@ eErr_SEQ_DESCR_RefGeneTrackingIllegalStatus
@ eErr_SEQ_DESCR_TitleMissingText
@ eErr_SEQ_FEAT_GeneOntologyTermMissingGOID
@ eErr_SEQ_FEAT_DuplicateGeneOntologyTerm
@ eErr_SEQ_FEAT_ProtRefHasNoData
@ eErr_SEQ_GRAPH_GraphSeqLocLen
@ eErr_SEQ_ANNOT_AnnotIDs
@ eErr_SEQ_INST_MissingGaps
@ eErr_SEQ_FEAT_SeqLocTypeProblem
@ eErr_SEQ_FEAT_NotSpliceConsensusDonorTerminalIntron
@ eErr_SEQ_DESCR_InvalidForType
@ eErr_SEQ_PKG_PartsSetHasSets
@ eErr_SEQ_DESCR_LatLonValue
@ eErr_SEQ_FEAT_BadRRNAcomponentOverlapRRNA
@ eErr_SEQ_DESCR_FastaBracketTitle
@ eErr_SEQ_FEAT_InternalStop
@ eErr_SEQ_FEAT_FeatureCitationProblem
@ eErr_SEQ_FEAT_MisMatchAA
@ eErr_SEQ_DESCR_OrganismIsUndefinedSpecies
@ eErr_SEQ_INST_StopInProtein
@ eErr_SEQ_DESCR_TaxonomyPlastidsProblem
@ eErr_SEQ_DESCR_IdenticalInstitutionCode
@ eErr_SEQ_PKG_ImproperlyNestedSets
@ eErr_SEQ_FEAT_BadTrnaAA
@ eErr_SEQ_DESCR_BacteriaMissingSourceQualifier
@ eErr_GENERIC_MissingPages
@ eErr_SEQ_INST_UnknownLengthGapNot100
@ eErr_SEQ_FEAT_WrongQualOnFeature
@ eErr_SEQ_DESCR_BadCountryCapitalization
@ eErr_SEQ_FEAT_MultipleProtRefs
@ eErr_SEQ_GRAPH_GraphGapScore
@ eErr_GENERIC_MedlineEntryPub
@ eErr_SEQ_FEAT_ProductFetchFailure
@ eErr_SEQ_FEAT_MultipleEquivPublications
@ eErr_SEQ_ALIGN_DensegLenStart
@ eErr_SEQ_PKG_SeqSubmitWithWgsSet
@ eErr_SEQ_FEAT_InconsistentPseudogeneCounts
@ eErr_SEQ_PKG_InconsistentMoltypeSet
@ eErr_SEQ_INST_ConflictingBiomolTech
@ eErr_SEQ_FEAT_MismatchedAllele
@ eErr_SEQ_FEAT_RepeatSeqDoNotMatch
@ eErr_SEQ_DESCR_DBLinkProblem
@ eErr_SEQ_FEAT_MissingQualOnImpFeat
@ eErr_SEQ_FEAT_InvalidRptUnitSeqCharacters
@ eErr_GENERIC_BarcodeMissingCountry
@ eErr_SEQ_PKG_INSDRefSeqPackaging
@ eErr_SEQ_FEAT_GenCodeMismatch
@ eErr_SEQ_FEAT_TranscriptLen
@ eErr_SEQ_FEAT_RubiscoProblem
@ eErr_SEQ_FEAT_InvalidAlleleDuplicates
@ eErr_SEQ_FEAT_ImpCDSnotPseudo
@ eErr_SEQ_FEAT_LocusCollidesWithLocusTag
@ eErr_SEQ_INST_InvalidLen
@ eErr_SEQ_FEAT_PseudoCdsHasProduct
@ eErr_SEQ_DESCR_TPAassemblyWithoutTPAKeyword
@ eErr_SEQ_PKG_GPSnonGPSPackaging
@ eErr_SEQ_DESCR_InvalidForTypeGIBB
@ eErr_SEQ_FEAT_InvalidFeatureForProtein
@ eErr_SEQ_FEAT_BadCDScomponentOverlapTRNA
@ eErr_SEQ_FEAT_BadEcNumberValue
@ eErr_SEQ_FEAT_EcNumberEmpty
@ eErr_SEQ_INST_HighNContentPercent
@ eErr_SEQ_DESCR_RefGeneTrackingOnNonRefSeq
@ eErr_SEQ_DESCR_BadCollectionDate
@ eErr_SEQ_DESCR_BadContigOrScaffoldChromosome
@ eErr_SEQ_FEAT_ImpCDShasTranslation
@ eErr_SEQ_FEAT_IdenticalGeneSymbolAndSynonym
@ eErr_SEQ_FEAT_MultipleEquivBioSources
@ eErr_SEQ_FEAT_ProductLength
@ eErr_SEQ_FEAT_CdTransFail
@ eErr_SEQ_FEAT_BadCDScomment
@ eErr_SEQ_INST_HighNcontent5Prime
@ eErr_SEQ_DESCR_StrainContainsTaxInfo
@ eErr_SEQ_FEAT_CDSwithNoMRNAOverlap
@ eErr_SEQ_DESCR_BadInstitutionCode
@ eErr_SEQ_FEAT_NoProtein
@ eErr_SEQ_FEAT_MultipleCDSproducts
@ eErr_SEQ_FEAT_PeptideFeatOutOfFrame
@ eErr_SEQ_INST_TSAshouldBNotBeDNA
@ eErr_SEQ_DESCR_MissingChromosome
@ eErr_SEQ_FEAT_ProteinNameHasPMID
@ eErr_SEQ_FEAT_ImpFeatBadLoc
@ eErr_SEQ_FEAT_EcNumberInCDSComment
@ eErr_SEQ_DESCR_MoltypeUnknown
@ eErr_SEQ_FEAT_MissingQualOnFeature
@ eErr_SEQ_FEAT_ShortExon
@ eErr_SEQ_INST_BadProteinMoltype
@ eErr_SEQ_FEAT_PolyAsiteNotPoint
@ eErr_SEQ_FEAT_RepeatRegionNeedsNote
@ eErr_SEQ_DESCR_BadAltitude
@ eErr_SEQ_FEAT_StartCodon
@ eErr_SEQ_FEAT_FeatureLocationIsGi0
@ eErr_SEQ_DESCR_NucleotideTechniqueOnProtein
@ eErr_SEQ_PKG_InconsistentAutodef
@ eErr_SEQ_FEAT_SuspiciousQualifierValue
@ eErr_SEQ_FEAT_GeneXrefStrandProblem
@ eErr_SEQ_FEAT_NotSpliceConsensus
@ eErr_GENERIC_BarcodeFrameShift
@ eErr_SEQ_INST_CompleteCircleProblem
@ eErr_SEQ_DESCR_LatLonGeoLocName
@ eErr_SEQ_FEAT_PolyATail
@ eErr_SEQ_FEAT_MissingTrnaAA
@ eErr_SEQ_DESCR_TaxonomyNoCommonAncestor
@ eErr_GENERIC_NonAsciiAsn
@ eErr_SEQ_FEAT_CDSwithMultipleMRNAs
@ eErr_SEQ_FEAT_CDSmRNAMismatchProteinIDs
@ eErr_SEQ_GRAPH_GraphNScoreMany
@ eErr_SEQ_FEAT_InvalidOperonMatchesGene
@ eErr_SEQ_FEAT_UnparsedtRNAAnticodon
@ eErr_SEQ_FEAT_CollidingFeatureIDs
@ eErr_SEQ_DESCR_TitleHasPMID
@ eErr_SEQ_FEAT_RefSeqInText
@ eErr_SEQ_DESCR_IncorrectlyFormattedVoucherID
@ eErr_SEQ_DESCR_StrainWithEnvironSample
@ eErr_SEQ_FEAT_OrfCdsHasProduct
@ eErr_SEQ_DESCR_BadStrucCommMultipleFields
@ eErr_SEQ_FEAT_CDSmRNAMismatchTranscriptIDs
@ eErr_SEQ_FEAT_PartialProblemOrganelle3Prime
@ eErr_SEQ_ALIGN_AlignDimOne
@ eErr_SEQ_FEAT_ErroneousException
@ eErr_SEQ_FEAT_ImproperBondLocation
@ eErr_SEQ_FEAT_InvalidPseudoQualifier
@ eErr_SEQ_PKG_GraphPackagingProblem
@ eErr_SEQ_FEAT_ExtendablePartialProblem
@ eErr_SEQ_FEAT_FeatureSeqIDCaseDifference
@ eErr_SEQ_DESCR_BadNullCollectionDate
@ eErr_SEQ_FEAT_SeqFeatXrefFeatureMissing
@ eErr_SEQ_INST_OverlappingDeltaRange
@ eErr_SEQ_FEAT_BadProductSeqId
@ eErr_SEQ_FEAT_PeptideFeatureLacksCDS
@ eErr_SEQ_FEAT_InvalidCompareRefSeqAccession
@ eErr_SEQ_FEAT_OverlappingPeptideFeat
@ eErr_SEQ_DESCR_BadKeywordNoTechnique
@ eErr_SEQ_DESCR_OrganismNotFound
@ eErr_SEQ_FEAT_BadTranssplicedInterval
@ eErr_SEQ_FEAT_InvalidReplace
@ eErr_SEQ_FEAT_ExtraProteinFeature
@ eErr_SEQ_INST_SeqLocLength
@ eErr_SEQ_INST_FarLocationExcludesFeatures
@ eErr_SEQ_DESCR_InconsistentVirusMoltype
@ eErr_SEQ_ALIGN_SegsDimOne
@ eErr_SEQ_DESCR_MultipleTaxonIDs
@ eErr_SEQ_INST_IdOnMultipleBioseqs
@ eErr_SEQ_FEAT_GeneOnNucPositionOfPeptide
@ eErr_SEQ_DESCR_MoltypeOtherGenetic
@ eErr_SEQ_DESCR_BadKeyword
@ eErr_SEQ_INST_HighNpercent3Prime
@ eErr_SEQ_INST_SeqPortFail
@ eErr_SEQ_FEAT_UnknownImpFeatKey
@ eErr_SEQ_FEAT_DuplicateTranslExcept
@ eErr_SEQ_INST_BadSecondaryAccn
@ eErr_SEQ_DESCR_NoPubFound
@ eErr_SEQ_DESCR_BadInstitutionCountry
@ eErr_SEQ_DESCR_MissingPlasmidName
@ eErr_SEQ_INST_InvalidAlphabet
@ eErr_SEQ_FEAT_IdenticalMRNAtranscriptIDs
@ eErr_SEQ_ALIGN_LenMorethanBiolen
@ eErr_SEQ_FEAT_CDSonMinusStrandMRNA
@ eErr_SEQ_DESCR_UnculturedNeedsEnvSample
@ eErr_SEQ_DESCR_BadTentativeName
@ eErr_SEQ_PKG_SegSetNotParts
@ eErr_SEQ_INST_MolNuclAcid
@ eErr_SEQ_DESCR_MoltypeOther
@ eErr_SEQ_DESCR_BadPlasmidChromosomeLinkageName
@ eErr_SEQ_GRAPH_GraphSeqLitLen
@ eErr_SEQ_DESCR_Inconsistent
@ eErr_SEQ_INST_ExtNotAllowed
@ eErr_GENERIC_BadAffilState
@ eErr_SEQ_DESCR_BadTextInSourceQualifier
@ eErr_SEQ_DESCR_SuspectedContaminatedCellLine
@ eErr_SEQ_DESCR_InconsistentRefSeqMoltype
@ eErr_SEQ_PKG_ArchaicFeatureLocation
@ eErr_SEQ_GRAPH_GraphMax
@ eErr_SEQ_FEAT_PartialProblemHasStop
@ eErr_SEQ_DESCR_AmbiguousSpecificHost
@ eErr_SEQ_DESCR_StrucCommMissingPrefixOrSuffix
@ eErr_SEQ_DESCR_TaxonomyNoValidTaxids
@ eErr_SEQ_DESCR_BadGeoLocNameCapitalization
@ eErr_SEQ_FEAT_AssemblyGapCoversSequence
@ eErr_GENERIC_BarcodeTestFails
@ eErr_SEQ_FEAT_PseudoCdsViaGeneHasProduct
@ eErr_SEQ_FEAT_CodonQualifierUsed
@ eErr_SEQ_FEAT_PartialProblem5Prime
@ eErr_SEQ_FEAT_NestedSeqLocMix
@ eErr_SEQ_FEAT_ShortIntron
@ eErr_SEQ_ALIGN_BlastAligns
@ eErr_SEQ_INST_LongHtgsSequence
@ eErr_SEQ_ALIGN_SegsNumsegMismatch
@ eErr_SEQ_FEAT_SplitEcNumber
@ eErr_SEQ_FEAT_AssemblyGapAdjacentToNs
@ eErr_SEQ_FEAT_InvalidPunctuation
@ eErr_SEQ_FEAT_RareSpliceConsensusDonor
@ eErr_SEQ_FEAT_LocusTagProductMismatch
@ eErr_SEQ_FEAT_CDSmRNAMismatchLocation
@ eErr_SEQ_FEAT_UnknownFeatureQual
@ eErr_SEQ_DESCR_ChromosomeWithoutLocation
@ eErr_SEQ_ALIGN_UnexpectedAlignmentType
@ eErr_SEQ_DESCR_MultipleChromosomes
@ eErr_SEQ_FEAT_ExceptionRequiresLocusTag
@ eErr_SEQ_GRAPH_GraphLocInvalid
@ eErr_SEQ_DESCR_StructuredSourceNote
@ eErr_GENERIC_BarcodeBadCollectionDate
@ eErr_SEQ_FEAT_TranscriptMismatches
@ eErr_SEQ_FEAT_InconsistentGeneOntologyTermAndId
@ eErr_SEQ_INST_TrailingX
@ eErr_SEQ_DESCR_InvalidMatingType
@ eErr_SEQ_PKG_MisplacedMolInfo
@ eErr_GENERIC_EmbeddedScript
@ eErr_SEQ_DESCR_InconsistentDates
@ eErr_GENERIC_BarcodeTestPasses
@ eErr_SEQ_GRAPH_GraphAbove
@ eErr_SEQ_ALIGN_SegmentGap
@ eErr_SEQ_FEAT_IncorrectQualifierCapitalization
@ eErr_SEQ_FEAT_InvalidNumberQualifier
@ eErr_SEQ_GRAPH_GraphBioseqLen
@ eErr_SEQ_INST_CircularProtein
@ eErr_SEQ_DESCR_WrongBiomolForTSA
@ eErr_SEQ_INST_NoIdOnBioseq
@ eErr_SEQ_FEAT_FeatureInsideGap
@ eErr_SEQ_DESCR_AmbiguousModForward
@ eErr_SEQ_FEAT_DifferntIdTypesInSeqLoc
@ eErr_SEQ_DESCR_BadStrucCommMissingField
@ eErr_SEQ_DESCR_BadSubSource
@ eErr_SEQ_FEAT_InvalidRNAFeature
@ eErr_SEQ_FEAT_tRNArange
@ eErr_SEQ_FEAT_GeneIdMismatch
@ eErr_SEQ_ALIGN_SumLenStart
@ eErr_SEQ_INST_PartsOutOfOrder
@ eErr_GENERIC_StructuredCitGenCit
@ eErr_SEQ_FEAT_MissingMRNAproduct
@ eErr_SEQ_FEAT_tRNAmRNAmixup
@ eErr_SEQ_DESCR_DBLinkOnSet
@ eErr_SEQ_FEAT_BadFullLengthFeature
@ eErr_SEQ_ALIGN_NullSegs
@ eErr_SEQ_FEAT_LocOnSegmentedBioseq
@ eErr_SEQ_DESCR_InconsistentGenBankblocks
@ eErr_SEQ_FEAT_BadCharInAuthorName
@ eErr_SEQ_DESCR_MultipleStrains
@ eErr_SEQ_ALIGN_StrandRev
@ eErr_SEQ_FEAT_UndesiredProteinName
@ eErr_SEQ_FEAT_MissingGeneLocusTag
@ eErr_GENERIC_BarcodeMissingOrderAssignment
@ eErr_SEQ_FEAT_FarLocation
@ eErr_SEQ_INST_MolinfoOther
@ eErr_SEQ_FEAT_SgmlPresentInText
@ eErr_SEQ_DESCR_BadGeoLocNameCode
@ eErr_SEQ_INST_BadSeqIdLength
@ eErr_SEQ_FEAT_MrnaTransFail
@ eErr_SEQ_INST_SeqDataNotAllowed
@ eErr_SEQ_GRAPH_GraphStopPhase
@ eErr_SEQ_GRAPH_GraphStartPhase
@ eErr_SEQ_INST_BadHTGSeq
@ eErr_SEQ_DESCR_InvalidSexQualifier
@ eErr_SEQ_FEAT_InvalidFuzz
@ eErr_SEQ_FEAT_InvalidInferenceValue
@ eErr_SEQ_FEAT_GeneXrefNeeded
@ eErr_SEQ_FEAT_PartialProblemOrganelle5Prime
@ eErr_SEQ_FEAT_InvalidType
@ eErr_SEQ_FEAT_BadAuthorSuffix
@ eErr_SEQ_DESCR_TaxonomyAmbiguousName
@ eErr_SEQ_FEAT_SerialInComment
@ eErr_SEQ_DESCR_NoKeywordHasTechnique
@ eErr_SEQ_INST_UnexpectedIdentifierChange
@ eErr_SEQ_INST_WGSseqGapProblem
@ eErr_SEQ_DESCR_TitleNotAppropriateForSet
@ eErr_SEQ_DESCR_MultipleStrucComms
@ eErr_SEQ_FEAT_InconsistentRRNAstrands
@ eErr_SEQ_FEAT_PartialProblemNotSpliceConsensus5Prime
@ eErr_SEQ_FEAT_AltStartCodonException
@ eErr_SEQ_DESCR_LatLonState
@ eErr_SEQ_PKG_ArchaicFeatureProduct
@ eErr_GENERIC_UnexpectedPubStatusComment
@ eErr_SEQ_DESCR_MultipleSourceQualifiers
@ eErr_SEQ_FEAT_WrongQualOnCDS
@ eErr_SEQ_FEAT_BadRRNAcomponentOverlapAndOrder
@ eErr_SEQ_FEAT_LocusTagHasSpace
@ eErr_SEQ_INST_LongLiteralSequence
@ eErr_SEQ_FEAT_BadRRNAcomponentOverlap
@ eErr_SEQ_FEAT_BadTrailingCharacter
@ eErr_SEQ_GRAPH_GraphACGTScore
@ eErr_SEQ_DESCR_DBLinkBadFormat
@ eErr_SEQ_PKG_ConSetProblem
@ eErr_SEQ_FEAT_InvalidForType
@ eErr_SEQ_FEAT_IntervalBeginsOrEndsInGap
@ eErr_SEQ_FEAT_GeneLocusCollidesWithLocusTag
@ eErr_SEQ_ALIGN_NucProtMixture
@ eErr_SEQ_FEAT_ProteinNameEndsInBracket
@ eErr_SEQ_DESCR_UserObjectNoType
@ eErr_SEQ_DESCR_WrongVoucherType
@ eErr_SEQ_FEAT_CDSgeneRange
@ eErr_SEQ_INST_MitoMetazoanTooLong
@ eErr_SEQ_INST_ProteinsHaveGeneralID
@ eErr_SEQ_GRAPH_GraphOutOfOrder
@ eErr_SEQ_FEAT_BadInternalCharacter
@ eErr_SEQ_FEAT_TranslExceptIsPartial
@ eErr_SEQ_DESCR_HasStrainAndIsolate
@ eErr_GENERIC_BarcodeMissingGeoLocName
@ eErr_SEQ_DESCR_CompleteGenomeLacksBioProject
@ eErr_SEQ_DESCR_NoSourceDescriptor
@ eErr_SEQ_DESCR_CollidingPubMedID
@ eErr_SEQ_FEAT_DuplicateFeat
@ eErr_SEQ_FEAT_PseudoCdsHasProtXref
@ eErr_SEQ_DESCR_BadCollectionCode
@ eErr_SEQ_FEAT_BadProteinName
@ eErr_SEQ_INST_ExtBadOrMissing
@ eErr_SEQ_FEAT_FeatureProductInconsistency
@ eErr_SEQ_DESCR_SyntheticConstructWrongMolType
@ eErr_GENERIC_PublicationInconsistency
@ eErr_GENERIC_BadSubmissionAuthorName
@ eErr_GENERIC_CollidingSerialNumbers
@ eErr_SEQ_PKG_ComponentMissingTitle
@ eErr_SEQ_FEAT_DuplicateGeneConflictingLocusTag
@ eErr_SEQ_DESCR_DBLinkMissingUserObject
@ eErr_SEQ_INST_TSAHistAssemblyMissing
@ eErr_SEQ_FEAT_MissingLocation
@ eErr_SEQ_DESCR_TaxonomyLookupProblem
@ eErr_SEQ_DESCR_FileOpenCollision
@ eErr_SEQ_DESCR_AmbiguousName
@ eErr_SEQ_ALIGN_SegsPresentMismatch
@ eErr_SEQ_PKG_InternalGenBankSet
@ eErr_SEQ_DESCR_BadStrucCommFieldOutOfOrder
@ eErr_SEQ_DESCR_BadStrucCommInvalidPrefix
@ eErr_SEQ_DESCR_DBLinkBadBioProject
@ eErr_SEQ_FEAT_MultiIntervalGene
@ eErr_SEQ_DESCR_BioSourceMissing
@ eErr_SEQ_FEAT_ExceptionMissingText
@ eErr_SEQ_FEAT_BadAnticodonCodon
@ eErr_SEQ_FEAT_BadTrailingHyphen
@ eErr_SEQ_FEAT_OldLocusTagMismtach
@ eErr_SEQ_DESCR_MolInfoConflictsWithBioSource
@ eErr_SEQ_INST_InstantiatedGapMismatch
@ eErr_SEQ_FEAT_UTRdoesNotAbutCDS
@ eErr_SEQ_ALIGN_FastaLike
@ eErr_SEQ_INST_PartialInconsistent
@ eErr_SEQ_FEAT_PseudoRnaViaGeneHasProduct
@ eErr_SEQ_DESCR_BadNullGeoLocName
@ eErr_SEQ_DESCR_NoTaxonID
@ eErr_SEQ_FEAT_ConflictFlagSet
@ eErr_SEQ_FEAT_FeatureBeginsOrEndsWithN
@ eErr_SEQ_DESCR_LatLonFormat
@ eErr_SEQ_FEAT_StrandOther
@ eErr_SEQ_FEAT_UnnecessaryGeneXref
@ eErr_SEQ_FEAT_CollidingLocusTags
@ eErr_SEQ_PKG_FeaturePackagingProblem
@ eErr_SEQ_DESCR_MultipleNames
@ eErr_SEQ_FEAT_PartialProblemNotSpliceConsensus3Prime
@ eErr_SEQ_FEAT_DeletedEcNumber
@ eErr_SEQ_FEAT_FeatureIsMostlyNs
@ eErr_SEQ_ALIGN_SegsDimMismatch
@ eErr_SEQ_INST_BadSeqIdFormat
@ eErr_SEQ_FEAT_InvalidMatchingReplace
@ eErr_SEQ_PKG_GenomicProductPackagingProblem
@ eErr_SEQ_INST_CaseDifferenceInSeqID
@ eErr_SEQ_PKG_SegSetMixedBioseqs
@ eErr_SEQ_FEAT_NoCDSbetweenUTRs
@ eErr_SEQ_INST_ZeroGiNumber
@ eErr_INTERNAL_Exception
@ eErr_SEQ_FEAT_BadEcNumberFormat
@ eErr_SEQ_DESCR_DBLinkBadSRAaccession
@ eErr_SEQ_DESCR_MissingText
@ eErr_SEQ_FEAT_BothStrands
@ eErr_SEQ_INST_ConflictingIdsOnBioseq
@ eErr_SEQ_FEAT_UnindexedFeature
@ eErr_SEQ_FEAT_CDSonMinusStrandTranscribedRNA
@ eErr_SEQ_DESCR_WrongOrganismFor16SrRNA
@ eErr_SEQ_INST_HistAssemblyMissing
@ eErr_SEQ_FEAT_ExceptionProblem
@ eErr_SEQ_FEAT_CDSproductPackagingProblem
@ eErr_SEQ_DESCR_FakeStructuredComment
@ eErr_SEQ_FEAT_OldLocusTagBadFormat
@ eErr_SEQ_DESCR_MissingLineage
@ eErr_SEQ_FEAT_RedundantFields
@ eErr_SEQ_PKG_NoCdRegionPtr
@ eErr_SEQ_INST_InternalNsInSeqRaw
@ eErr_SEQ_DESCR_BadOrgMod
@ eErr_SEQ_DESCR_BadSpecificHost
@ eErr_SEQ_INST_TerminalNs
@ eErr_SEQ_DESCR_BadPCRPrimerName
@ eErr_SEQ_ALIGN_StartLessthanZero
@ eErr_SEQ_FEAT_ColdShockProteinProblem
@ eErr_SEQ_DESCR_OrgModValueInvalid
@ eErr_GENERIC_BarcodeMissingPrimers
@ eErr_SEQ_DESCR_BadOrganelleLocation
@ eErr_SEQ_FEAT_TrnaCodonWrong
@ eErr_SEQ_FEAT_NoNameForProtein
@ eErr_SEQ_FEAT_SeqFeatXrefProblem
@ eErr_SEQ_INST_PrimaryAndThirdPartyMixture
@ eErr_SEQ_ALIGN_StartMorethanBiolen
@ eErr_SEQ_FEAT_RptUnitRangeProblem
@ eErr_SEQ_FEAT_InvalidVariationReplace
@ eErr_SEQ_FEAT_SeqFeatXrefNotReciprocal
@ eErr_SEQ_DESCR_BadKeywordForStrucComm
@ eErr_SEQ_FEAT_SeqLocOrder
@ eErr_SEQ_DESCR_TaxonomyIsSpeciesProblem
@ eErr_SEQ_DESCR_EnvironSampleMissingQualifier
@ eErr_SEQ_FEAT_CDSdoesNotMatchVDJC
@ eErr_SEQ_FEAT_CDSmRNAXrefLocationProblem
@ eErr_SEQ_FEAT_AnticodonStrandConflict
@ eErr_SEQ_DESCR_InconsistentTaxNameSet
@ eErr_SEQ_PKG_SingleItemSet
@ eErr_GENERIC_BarcodeTooShort
@ eErr_SEQ_DESCR_MultipleIsolates
@ eErr_SEQ_DESCR_BadCountryCode
@ eErr_SEQ_ALIGN_SegsPresentStartsMismatch
@ eErr_SEQ_FEAT_InvalidRepeatUnitLength
@ eErr_SEQ_DESCR_ChromosomeLocation
@ eErr_SEQ_DESCR_InconsistentMolType
@ eErr_SEQ_FEAT_CDSmRNAMissingProteinIDs
@ eErr_SEQ_DESCR_BioSourceNeedsChromosome
@ eErr_SEQ_DESCR_WGSmasterLacksBioSample
@ eErr_SEQ_FEAT_VectorContamination
@ eErr_SEQ_FEAT_AbuttingIntervals
@ eErr_SEQ_FEAT_BadConflictFlag
@ eErr_SEQ_FEAT_EcNumberInProteinComment
@ eErr_SEQ_FEAT_MultiIntervalIntron
@ eErr_SEQ_DESCR_InconsistentTPA
@ eErr_SEQ_FEAT_LocusTagProblem
@ eErr_SEQ_DESCR_AmbiguousTypeMaterial
@ eErr_SEQ_DESCR_BioSourceInconsistency
@ eErr_SEQ_GRAPH_GraphMin
@ eErr_SEQ_FEAT_CDSmRNArange
@ eErr_SEQ_DESCR_TaxonomyEmptyInput
@ eErr_SEQ_FEAT_OnlyGeneXrefs
@ eErr_SEQ_DESCR_ModifierTypeConflict
@ eErr_SEQ_FEAT_UnnecessaryCitPubEquiv
@ eErr_SEQ_INST_HighNpercent5Prime
@ eErr_SEQ_FEAT_TranslExcept
@ eErr_SEQ_DESCR_HostIdenticalToOrganism
@ eErr_SEQ_FEAT_ExceptInconsistent
@ eErr_SEQ_DESCR_BadBioSourceFrequencyValue
@ eErr_SEQ_DESCR_ScaffoldLacksBioProject
@ eErr_SEQ_PKG_NucProtNotSegSet
@ eErr_SEQ_INST_InternalNsAdjacentToGap
@ eErr_SEQ_FEAT_PartialProblem
@ eErr_SEQ_DESCR_MultipleComments
@ eErr_SEQ_INST_SeqDataNotFound
@ eErr_SEQ_INST_InternalGapsInSeqRaw
@ eErr_SEQ_DESCR_ReplacedCountryCode
@ eErr_SEQ_FEAT_MultipleGeneOverlap
@ eErr_SEQ_FEAT_RegulatoryClassOtherNeedsNote
@ eErr_SEQ_FEAT_GeneRefHasNoData
@ eErr_SEQ_INST_DuplicateSegmentReferences
@ eErr_SEQ_FEAT_TooManyInferenceAccessions
@ eErr_SEQ_FEAT_LocusTagGeneLocusMatch
@ eErr_GENERIC_MissingVolumeEpub
@ eErr_SEQ_DESCR_InconsistentWGSFlags
@ eErr_SEQ_FEAT_TerminalXDiscrepancy
@ eErr_SEQ_DESCR_ReplacedGeoLocNameCode
@ eErr_SEQ_FEAT_CDSmRNAmismatchCount
@ eErr_SEQ_ALIGN_SegsPresentStrandsMismatch
@ eErr_SEQ_FEAT_MiscFeatureNeedsNote
@ eErr_SEQ_DESCR_UserObjectNoData
@ eErr_SEQ_FEAT_UTRdoesNotExtendToEnd
@ eErr_SEQ_DESCR_RegionMissingText
@ eErr_SEQ_INST_SeqLitGapLength0
@ eErr_SEQ_INST_SeqIdNameHasSpace
@ eErr_SEQ_DESCR_UnbalancedParentheses
@ eErr_SEQ_DESCR_RefGeneTrackingWithoutStatus
@ eErr_SEQ_DESCR_MultipleTitles
@ eErr_SEQ_FEAT_FocusOnBioSourceFeature
@ eErr_SEQ_DESCR_ProteinTechniqueOnNucleotide
@ eErr_SEQ_FEAT_PolyAsignalNotRange
@ eErr_SEQ_ALIGN_ShortAln
@ eErr_SEQ_DESCR_CommentMissingText
@ eErr_SEQ_PKG_RefSeqPopSet
@ eErr_SEQ_DESCR_BioSourceNeedsFocus
@ eErr_SEQ_DESCR_CollidingPublications
@ eErr_SEQ_FEAT_PartialProblemmRNASequence3Prime
@ eErr_SEQ_PKG_NucProtProblem
@ eErr_SEQ_FEAT_UndesiredGeneSynonym
@ eErr_SEQ_FEAT_GenomeSetMixedStrand
@ eErr_SEQ_INST_InternalNsInSeqLit
@ eErr_SEQ_FEAT_BadTrnaCodon
@ eErr_SEQ_FEAT_GenCodeInvalid
@ eErr_SEQ_INST_SeqDataLenWrong
@ eErr_GENERIC_BadLastName
@ eErr_SEQ_ALIGN_EndMorethanBiolen
@ eErr_SEQ_FEAT_PseudoCDSmRNArange
@ eErr_SEQ_ANNOT_AnnotLOCs
@ eErr_SEQ_INST_GapInProtein
@ eErr_SEQ_INST_SeqGapProblem
@ eErr_SEQ_INST_InvalidResidue
@ eErr_SEQ_FEAT_BadCharInAuthorLastName
@ eErr_SEQ_FEAT_PartialProblemmRNASequence5Prime
@ eErr_SEQ_GRAPH_GraphBelow
@ eErr_SEQ_INST_RnaDnaConflict
@ eErr_SEQ_FEAT_InvalidFeatureForMRNA
@ eErr_SEQ_FEAT_FeatureCrossesGap
@ eErr_SEQ_FEAT_SelfReferentialProduct
@ eErr_SEQ_DESCR_MissingMetagenomicQualifier
@ eErr_SEQ_FEAT_CDSwithNoMRNA
@ eErr_SEQ_FEAT_GapFeatureProblem
@ eErr_SEQ_FEAT_HypotheticalProteinMismatch
@ eErr_SEQ_DESCR_SyntheticConstructNeedsArtificial
@ eErr_SEQ_INST_TpaAssemblyProblem
@ eErr_SEQ_PKG_MissingAutodef
@ eErr_GENERIC_DeltaSeqError
@ eErr_SEQ_FEAT_MissingGeneXref
@ eErr_GENERIC_BarcodeMissingVoucher
@ eErr_SEQ_ALIGN_EndLessthanZero
@ eErr_SEQ_FEAT_RecombinationClassOtherNeedsNote
@ eErr_SEQ_DESCR_NonViralSegment
@ eErr_SEQ_FEAT_MissingExceptionFlag
@ eErr_SEQ_DESCR_UnculturedGenome
@ eErr_SEQ_FEAT_TaxonDbxrefOnFeature
@ eErr_SEQ_FEAT_IntronIsStopCodon
Base class for all serializable objects.
class CStaticArrayMap<> provides access to a static array in much the same way as CStaticArraySet<>,...
TBase::const_iterator const_iterator
void SetFeatureObjDescFromFields()
static const string & ConvertSeverity(EDiagSev sev)
static size_t GetErrCount()
static const string & ConvertErrCode(unsigned int)
const string GetErrCode() const
CConstRef< CSerialObject > m_Object
const string GetVerbose() const
const CSerialObject & GetObject() const
CConstRef< CSeq_entry > m_Ctx
static unsigned int ConvertToErrCode(const string &str)
const string GetErrGroup() const
static const string & ConvertErrGroup(unsigned int)
void SetObject(const CSerialObject &obj)
static const char * str(char *buf, int n)
EDiagSev
Severity level for the posted diagnostics.
@ eDiagSevMax
Verbosity level for max. severity.
void Reset(void)
Reset reference object.
bool NotEmpty(void) const THROWS_NONE
Check if CConstRef is not empty â pointing to an object and has a non-null value.
#define END_NCBI_SCOPE
End previously defined NCBI scope.
#define BEGIN_NCBI_SCOPE
Define ncbi namespace.
static bool EndsWith(const CTempString str, const CTempString end, ECase use_case=eCase)
Check if a string ends with a specified suffix value.
static string IntToString(int value, TNumToStringFlags flags=0, int base=10)
Convert int to string.
static bool Equal(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2, ECase use_case=eCase)
Test for equality of a substring with another string.
TObjDesc & SetObjDesc(void)
Assign a value to ObjDesc data member.
TErrorGroup & SetErrorGroup(void)
Assign a value to ErrorGroup data member.
bool IsSetFeatureId(void) const
Check if a value has been assigned to FeatureId data member.
TMsg & SetMsg(void)
Assign a value to Msg data member.
bool IsSetLocation(void) const
Check if a value has been assigned to Location data member.
const TProduct_loc & GetProduct_loc(void) const
Get the Product_loc member data.
const TObj_content & GetObj_content(void) const
Get the Obj_content member data.
const TLocation & GetLocation(void) const
Get the Location member data.
TSev & SetSev(void)
Assign a value to Sev data member.
TErrIndex & SetErrIndex(void)
Assign a value to ErrIndex data member.
bool IsSetObj_content(void) const
Check if a value has been assigned to Obj_content data member.
TErrorName & SetErrorName(void)
Assign a value to ErrorName data member.
TAccession & SetAccession(void)
Assign a value to Accession data member.
bool IsSetProduct_loc(void) const
Check if a value has been assigned to Product_loc data member.
const TBioseq & GetBioseq(void) const
Get the Bioseq member data.
TAccnver & SetAccnver(void)
Assign a value to Accnver data member.
TSeqOffset & SetSeqOffset(void)
Assign a value to SeqOffset data member.
TErrIndex GetErrIndex(void) const
Get the ErrIndex member data.
const TFeatureId & GetFeatureId(void) const
Get the FeatureId member data.
bool IsSetBioseq(void) const
Check if a value has been assigned to Bioseq data member.
TVersion & SetVersion(void)
Assign a value to Version data member.
static const char * kSeqGraph
static SLJIT_INLINE sljit_ins msg(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)
Template structure SStaticPair is simlified replacement of STL pair<> Main reason of introducing this...
static const char * kUnknown
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