MODULE valid
$$ SEQ_INST, 1
$^   ExtNotAllowed, 1
# This is a comment
A Bioseq "extension" is used for special classes of Bioseq. This class of
Bioseq should not have one but it does. This is probably a software error.

$^   ExtBadOrMissing, 2
This class of Bioseq requires an "extension" but it is missing or of the
wrong type. This is probably a software error.

$^   SeqDataNotFound, 3
No actual sequence data was found on this Bioseq. This is probably a
software problem.

$^   SeqDataNotAllowed, 4
The wrong type of sequence data was found on this Bioseq. This is probably a
software problem.

$^   ReprInvalid, 5
This Bioseq has an invalid representation class. This is probably a software
error.

$^   CircularProtein, 6
This protein Bioseq is represented as circular. Circular topology is
normally used only for certain DNA molecules, for example, plasmids.

$^   DSProtein, 7
This protein Bioseq has strandedness indicated. Strandedness is normally a
property only of DNA sequences. Please unset the strandedness.

$^   MolNotSet, 8
It is not clear whether this sequence is nucleic acid or protein. Please set
the appropriate molecule type (Bioseq.mol).

$^   MolOther, 9
Most sequences are either nucleic acid or protein. However, the molecule
type (Bioseq.mol) is set to "other". It should probably be set to nucleic
acid or a protein.

$^   FuzzyLen, 10
This sequence is marked as having an uncertain length, but the length is
known exactly.

$^   InvalidLen, 11
The length indicated for this sequence is invalid. This is probably a
software error.

$^   InvalidAlphabet, 12
This Bioseq has an invalid alphabet (e.g. protein codes on a nucleic acid or
vice versa). This is probably a software error.

$^   SeqDataLenWrong, 13
The length of this Bioseq does not agree with the length of the actual data.
This is probably a software error.

$^   SeqPortFail, 14
Something is very wrong with this entry. The validator cannot open a SeqPort
on the Bioseq. Further testing cannot be done.

$^   InvalidResidue, 15
Invalid residue codes were found in this Bioseq.

$^   StopInProtein, 16
Stop codon symbols were found in this protein Bioseq.

$^   PartialInconsistent, 17
This segmented sequence is described as complete or incomplete in several
places, but these settings are inconsistent.

$^   ShortSeq, 18
This Bioseq is unusually short (less than 4 amino acids or less than 11
nucleic acids). GenBank does not usually accept such short sequences.

$^   NoIdOnBioseq, 19
No SeqIds were found on this Bioseq. This is probably a software error.

$^   BadDeltaSeq, 20
Delta sequences should only be HTGS-1 or HTGS-2.

$^   LongHtgsSequence, 21
HTGS-1 or HTGS-2 sequences must be < 350 KB in length.

$^   LongLiteralSequence, 22
Delta literals must be < 350 KB in length.

$^   SequenceExceeds350kbp, 23
Individual sequences must be < 350 KB in length, unless they represent a single gene.

$^   ConflictingIdsOnBioseq, 24
Two SeqIds of the same class was found on this Bioseq. This is probably a software error.

$^   MolNuclAcid, 25
The specific type of this nucleic acid (DNA or RNA) is not set.

$^   ConflictingBiomolTech, 26
HTGS/STS/GSS records should be genomic DNA. There is a conflict between the
technique and expected molecule type.

$^   SeqIdNameHasSpace, 27
The Seq-id.name field should be a single word without any whitespace. This should be
fixed by the database staff.

$^   IdOnMultipleBioseqs, 28
There are multiple occurrences of the same Seq-id in this record. Sequence
identifiers must be unique within a record.

$^   DuplicateSegmentReferences, 29
The segmented sequence refers multiple times to the same Seq-id. This may be due
to a software error. Please consult with the database staff to fix this record.

$^   TrailingX, 30
The protein sequence ends with one or more X (unknown) amino acids.

$^   BadSeqIdFormat, 31
A nucleotide sequence identifier should be 1 letter plus 5 digits or 2 letters
plus 6 digits, and a protein sequence identifer should be 3 letters plus 5 digits.

$^   PartsOutOfOrder, 32
The parts inside a segmented set should correspond to the seq_ext of the segmented
bioseq.  A difference will affect how the flatfile is displayed.

$^   BadSecondaryAccn, 33
A secondary accession usually indicates a record replaced or subsumed by the current
record.  In this case, the current accession and secondary are the same.

$^   ZeroGiNumber, 34
GI numbers are assigned to sequences by NCBI's sequence tracking database.  0 is not
a legal value for a gi number.

$^   RnaDnaConflict, 35
The MolInfo biomol field is inconsistent with the Bioseq molecule type field.

$^   HistoryGiCollision, 36
The Bioseq history gi refers to this Bioseq, not to its predecessor or successor.

$^   GiWithoutAccession, 37
The Bioseq has a gi identifier but no GenBank/EMBL/DDBJ accession identifier.

$^   MultipleAccessions, 38
The Bioseq has a gi identifier and more than one GenBank/EMBL/DDBJ accession identifier.

$^   HistAssemblyMissing, 39
The Bioseq has a TPA identifier but does not have a Seq-hist.assembly alignment.  This
should be annotated or calculated by the database, resulting in a PRIMARY block visible
in the flatfile.

$^   TerminalNs, 40
The Bioseq has one or more N bases at the end.

$^   UnexpectedIdentifierChange, 41
The set of sequence identifiers on a Bioseq are not consistent with the previous version
of the record in the database.

$^   InternalNsInSeqLit, 42
There are runs of many Ns inside the SeqLit component of a delta Bioseq.

$^   SeqLitGapLength0, 43
A SeqLit component of a delta Bioseq can specify a gap, but it should not be a gap
of 0 length.

$^   TpaAssmeblyProblem, 44
Third party annotation records should have a TpaAssembly user object and a
Seq-hist.assembly alignment for the PRIMARY block.

$^   SeqLocLength, 45
A SeqLoc component of a delta Bioseq is suspiciously small.

$^   MissingGaps, 46
HTGS delta records should have gaps between each sequence segment.

$^   CompleteTitleProblem, 47
The sequence title has complete genome in it, but it is not marked as complete.

$^   CompleteCircleProblem, 48
This sequence has a circular topology, but it is not marked as complete.

$^   BadHTGSeq, 49
High throughput genomic sequences without gaps should have quality score graphs.

$^   GapInProtein, 50
Gap symbols found in this protein Bioseq.

$^   BadProteinStart, 51
A gap symbols was found at the start of this protein Bioseq.

$^   TerminalGap, 52
The Bioseq has a gap at the end.

$^   OverlappingDeltaRange, 53
The Bioseq has a gap at the end.

$^   LeadingX, 54
The protein sequence starts with one or more X (unknown) amino acids.

$^   InternalNsInSeqRaw, 55
There are runs of greater than 100 Ns within sequence.  Please describe
what these Ns represent with your sequence submission.

$^   InternalNsAdjacentToGap, 56
There are Ns directly adjacent to a SeqLit gap in a delta Bioseq.

$^   CaseDifferenceInSeqID, 57
Multiple Bioseqs have the same Seq-id except for capitalization. Sequence
identifiers must be unique in a case-insensitive manner within a record.

$^   DeltaComponentIsGi0, 58
Delta component refers to gi 0. This indicates an error in database processing of this record.

$^   FarFetchFailure, 59
Fetching of a far feature location or component bioseq was needed, but no fetch
function is registered in the program.

$^   InternalGapsInSeqRaw, 60
Raw sequences should not have gap characters.

$^   SelfReferentialSequence, 61
A delta sequence must refer to other components, not to itself.

$^   WholeComponent, 62
A delta sequence component should be described as a specific interval, not as
the whole of a sequence.

$^   TSAHistAssemblyMissing, 63
The Bioseq has a TSA MolInfo tech but does not have a Seq-hist.assembly alignment.

$^   ProteinsHaveGeneralID, 64
One or more protein Bioseqs have a general Seq-id.

$^   HighNContent, 65
This sequence contains too many Ns.

$^   SeqLitDataLength0, 66
A SeqLit component of a delta Bioseq must not have 0 length.

$^   DSmRNA, 67
This mRNA Bioseq is not single stranded.

$^   HighNContentStretch, 68
This sequence contains long stretches of Ns.

$^   HighNContentPercent, 69
This sequence contains a high percentage of Ns.

$^   BadSegmentedSeq, 70
Segmented sequences should have gap or virtual in between real components.

$^   SeqLitGapFuzzNot100, 71
Gap of unknown length should have standard length of 100.

$^   SeqGapProblem, 72
Inconsistent data in Seq-gap fields.


$$ SEQ_DESCR, 2

$^   BioSourceMissing, 1
The biological source of this sequence has not been described correctly.  A
Bioseq must have a BioSource descriptor that covers the entire molecule.
Additional BioSource features may also be added to recombinant molecules,
natural or otherwise, to designate the parts of the molecule. Please add the
source information.

$^   InvalidForType, 2
This descriptor cannot be used with this Bioseq. A descriptor placed at the
BioseqSet level applies to all of the Bioseqs in the set. Please make sure
the descriptor is consistent with every sequence to which it applies.

$^   FileOpenCollision, 3
FileOpen is unable to find a local file.  This is normal, and can be ignored.

$^   Unknown, 4
An unknown or "other" modifier was used.

$^   NoPubFound, 5
No publications were found in this entry which refer to this Bioseq. If a
publication descriptor is added to a BioseqSet, it will apply to all of the
Bioseqs in the set. A publication feature should be used if the publication
applies only to a subregion of a sequence.

$^   NoOrgFound, 6
This entry does not specify the organism that was the source of the sequence.
Please name the organism.

$^   MultipleBioSources, 7
There are multiple BioSource or OrgRef descriptors in the same chain with
the same taxonomic name. Their information should be combined into a single
BioSource descriptor.

$^   NoMolInfoFound, 8
This sequence does not have a Mol-info descriptor applying to it.  This indicates
genomic vs. message, sequencing technique, and whether the sequence is incomplete.

$^   BadCountryCode, 9
The country code (up to the first colon) is not on the approved list of countries.

$^   NoTaxonID, 10
The BioSource is missing a taxonID database identifier.  This will be inserted by
the automated taxonomy lookup called by Clean Up Record.

$^   InconsistentBioSources, 11
This population study has BioSource descriptors with different taxonomic names.
All members of a population study should be from the same organism.

$^   MissingLineage, 12
A BioSource should have a taxonomic lineage, which can be obtained from the
taxonomy network server.

$^   SerialInComment, 13
Comments that refer to the conclusions of a specific reference should not be
cited by a serial number inside brackets (e.g., [3]), but should instead be
attached as a REMARK on the reference itself.

$^   BioSourceNeedsFocus, 14
Focus must be set on a BioSource descriptor in records where there is a
BioSource feature with a different organism name.

$^   BadOrganelle, 15
Note that only Kinetoplastida have kinetoplasts, and that only Chlorarchniophyta
and Cryptophyta have nucleomorphs.

$^   MultipleChromosomes, 16
There are multiple chromosome qualifiers on this Bioseq.  With the exception of
some pseudoautosomal genes, this is likely to be a biological annotation error.

$^   BadSubSource, 17
Unassigned SubSource subtype.

$^   BadOrgMod, 18
Unassigned OrgMod subtype.

$^   InconsistentProteinTitle, 19
An instantiated protein title descriptor should normally be the same as the
automatically generated title.  This may be a curated exception, or it may
be out of synch with the current annotation.

$^   Inconsistent, 20
There are two descriptors of the same type which are inconsistent with each
other. Please make them consistent.

$^   ObsoleteSourceLocation, 21
There is a source location that is no longer legal for use in GenBank records.

$^   ObsoleteSourceQual, 22
There is a source qualifier that is no longer legal for use in GenBank records.

$^   StructuredSourceNote, 23
The name of a structured source field is present as text in a note.  The data
should probably be put into the appropriate field instead.

$^   UnnecessaryBioSourceFocus, 24
Focus should not be set on a BioSource descriptor in records where there is no
BioSource feature.

$^   RefGeneTrackingWithoutStatus, 25
The RefGeneTracking user object does not have the required Status field set.

$^   UnwantedCompleteFlag, 26
The Mol-info.completeness flag should not be set on a genomic sequence unless
the title also says it is a complete sequence or complete genome.

$^   CollidingPublications, 27
Multiple publication descriptors with the same PMID or MUID apply to a Bioseq.
The lower-level ones are redundant, and should be removed.

$^   TransgenicProblem, 28
A BioSource descriptor with /transgenic set must be accompanied by a BioSource
feature on the nucleotide record.

$^   TaxonomyLookupProblem, 29
A BioSource descriptor or feature has flags returned by taxonomy lookup that
are either inconsistent with the data or require a taxonomy consult.

$^   MultipleTitles, 30
There are multiple title descriptors in the same Bioseq or BioseqSet chain.

$^   RefGeneTrackingOnNonRefSeq, 31
The RefGeneTracking user object should only be in RefSeq records.

$^   BioSourceInconsistency, 32
There is an internal inconsistency with specific fields in the BioSource.

$^   FastaBracketTitle, 33
Bracketed [...=...] information remains in the title.  This should have been parsed
out during sequence record generation to obtain qualifier values.

$^   MissingText, 34
Comments, regions, and other text descriptors need a descriptive text string.
The string provided with this descriptor is empty. If no text is desired, then
the descriptor should be removed.

$^   BadCollectionDate, 35
The collection date is not in the required format.

$^   BadPCRPrimerSequence, 36
The PCR primer sequence has illegal characters or non-IUPAC nucleotides.

$^   BadPunctuation, 37
The title ends with incorrect punctuation marks.

$^   BadPCRPrimerName, 38
The PCR primer name appears to be a sequence instead of an identifying label.

$^   BioSourceOnProtein, 39
A BioSource descriptor should not be placed on a protein that is in a nuc-prot set.

$^   BioSourceDbTagConflict, 40
Multiple db_xrefs with the same database should not appear on a single BioSource.

$^   DuplicatePCRPrimerSequence, 41
The PCR primer sequence has duplicate subsequences.

$^   MultipleNames, 42
There are multiple name descriptors in the same Bioseq or BioseqSet chain.

$^   MultipleComments, 43
There are multiple identical comment descriptors in the same Bioseq or BioseqSet chain.

$^   LatLonProblem, 44
There is a problem with the lat_lon qualifier in the BioSource.

$^   LatLonFormat, 45
The format of lat_lon should be dd.dd N|S ddd.dd E|W.

$^   LatLonRange, 46
Latitude or longitude is out of range.

$^   LatLonValue, 47
Latitude or longitude values appear to be in the wrong hemisphere or swapped.

$^   LatLonCountry, 48
The lat_lon coordinate does not map to the indicated country.

$^   LatLonState, 49
The lat_lon coordinate does not map to the indicated state or province.

$^   BadSpecificHost, 50
A BioSource descriptor or feature has a specific host value that may
require a taxonomy consult.

$^   RefGeneTrackingIllegalStatus, 51
The RefGeneTracking user object has an illegal Status value.

$^   ReplacedCountryCode, 52
The country code (up to the first colon) is no longer on the approved list of countries.

$^   BadInstitutionCode, 53
The institution (or institution: collection) code is not on the approved list.

$^   BadCollectionCode, 54
The institution code is recognized, but the collection is not on the approved list.

$^   BadVoucherID, 55
The voucher is missing a specific identifier.

$^   UnstructuredVoucher, 56
The voucher needs to be structured as "<institution-code>:[<collection-code>:]<culture_id>".

$^   ChromosomeLocation, 57
BioSource location is not usually chromosome.

$^   MultipleSourceQualifiers, 58
BioSource has unexpected multiple qualifiers of the same type.

$^   UnbalancedParentheses, 59
Qualifier should have matching ( and ) parentheses or [ and ] brackets.

$^   MultipleSourceVouchers, 60
BioSource has unexpected multiple bio_material/culture_collection/specimen_voucher
from the same institution.

$^   BadCountryCapitalization, 61
The country code does not use the correct capitalization.

$^   WrongVoucherType, 62
The institution (or institution: collection) code normally uses a different
bio_material/culture_collection/specimen_voucher type.

$^   UserObjectProblem, 63
The user object is missing required fields or has invalid data.

$^   TitleHasPMID, 64
The title has (PMID #####) embedded in it.

$^   BadKeyword, 65
The keyword is not appropriate in this record.

$^   NoOrganismInTitle, 66
A RefSeq record should have the organism name at the beginning of a nucleotide
title and bracketed at the end of a protein title.

$^   MissingChromosome, 67
An NC or AC RefSeq record should have a chromosome annotated.

$^   LatLonAdjacent, 68
The lat_lon coordinate may be in an adjacent country or in surrounding waters.

$^   BadStrucCommInvalidFieldName, 69
Structured comment is missing required fields or field values do not conform to correct format.

$^   BadStrucCommInvalidFieldValue, 70
Structured comment is missing required fields or field values do not conform to correct format.

$^   BadStrucCommMissingField, 71
Structured comment is missing required fields or field values do not conform to correct format.

$^   BadStrucCommFieldOutOfOrder, 72
Structured comment is missing required fields or field values do not conform to correct format.

$^   BadStrucCommMultipleFields, 73
Structured comment is missing required fields or field values do not conform to correct format.

$^   BioSourceNeedsChromosome, 74
Chromosome should be set on a BioSource descriptor in non-viral complete genomes.

$^   MolInfoConflictsWithBioSource, 75
Viral lineage information conflicts with MolInfo.

$^   MissingKeyword, 76
Expected keyword was not found.

$^   FakeStructuredComment, 77
Comment descriptor may have been formatted to look like structured comment.

$^   StructuredCommentPrefixOrSuffixMissing, 78
Structured comments should have a prefix or suffix.

$^   LatLonWater, 79
The lat_lon coordinate map in a body of water.

$^   LatLonOffshore, 80
The lat_lon coordinate is probably in a minor or unnamed body of water.

$^   MissingPersonalCollectionName, 81
The personal collection does not indicate the name of the collector.

$^   LatLonPrecision, 82
The precision of lat_lon should be dd.dd N|S ddd.dd E|W.

$^   DBLinkProblem, 83
Only one DBLink user object with approved databases should apply to each Bioseq.

$^   FinishedStatusForWGS, 84
WGS projects should not have the Genome-Assembly-Data structured comment current
finishing status set to Finished.

$^   BadTentativeName, 85
A structured comment descriptor or feature has a tentative name value that may
require a taxonomy consult.

$^   OrganismNotFound, 86
The indicated organism is not in the taxonomy database.

$^   TaxonomyIsSpeciesProblem, 87
Taxonomy lookup of the indicated organism reports an is_species_level problem.

$^   TaxonomyConsultRequired, 88
A taxonomy consult is required for the indicated organism.

$^   TaxonomyNucleomorphProblem, 89
Taxonomy lookup indicates that the nucleomorph flag should be set for this organism.


$$ GENERIC, 3

$^   NonAsciiAsn, 1
There is a non-ASCII type character in this entry.

$^   Spell, 2
There is a potentially misspelled word in this entry.

$^   AuthorListHasEtAl, 3
The author list contains et al, which should be replaced with the
remaining author names.

$^   MissingPubInfo, 4
The publication is missing essential information, such as title or authors.

$^   UnnecessaryPubEquiv, 5
A nested Pub-equiv is not normally expected in a publication.  This may prevent
proper display of all publication information.

$^   BadPageNumbering, 6
The publication page numbering is suspect.

$^   MedlineEntryPub, 7
Publications should not be of type medline-entry.  This has abstract and MeSH
term information that does not appear in the GenBank flatfile.  Type cit-art
should be used instead.

$^   BadDate, 8
There are bad values for month, day, or year in a date.

$^   StructuredCitGenCit, 9
The publication has title or journal embedded in the unstructured citgen.cit
field.

$^   CollidingSerialNumbers, 10
Multiple publications have the same serial number explicitly recorded in the
data.

$^   EmbeddedScript, 11
Script or other markup tags should not be used in sequence record fields.


$^   PublicationInconsistency, 12
Some fields in the publication should not be present with other fields.

$^ SgmlPresentInText, 13
SGML markup is embedded in text.

$^ UnexpectedPubStatusComment, 14
An unexpected publication status exists for a print, online-only,
or ahead-of-print article : Content-Of-Pubdesc.comment-String.

$^ PastReleaseDate, 15
The record has is marked as hold-until-published, but the release
anyway date has already passed.

$^   MissingISOJTA, 16
The publication journal is missing an ISO journal title abbreviation.

$$ SEQ_PKG, 4

$^   NoCdRegionPtr, 1
A protein is found in this entry, but the coding region has not been
described. Please add a CdRegion feature to the nucleotide Bioseq.

$^   NucProtProblem, 2
Both DNA and protein sequences were expected, but one of the two seems to be
missing. Perhaps this is the wrong package to use.

$^   SegSetProblem, 3
A segmented sequence was expected, but it was not found. Perhaps this is the
wrong package to use.

$^   EmptySet, 4
No Bioseqs were found in this BioseqSet. Is that what was intended?

$^   NucProtNotSegSet, 5
A nuc-prot set should not contain any other BioseqSet except segset.

$^   SegSetNotParts, 6
A segset should not contain any other BioseqSet except parts.

$^   SegSetMixedBioseqs, 7
A segset should not contain both nucleotide and protein Bioseqs.

$^   PartsSetMixedBioseqs, 8
A parts set should not contain both nucleotide and protein Bioseqs.

$^   PartsSetHasSets, 9
A parts set should not contain BioseqSets.

$^   FeaturePackagingProblem, 10
A feature should be packaged on its bioseq, or on a set containing the Bioseq.

$^   GenomicProductPackagingProblem, 11
The product of an mRNA feature in a genomic product set should point to a cDNA
Bioseq packaged in the set, perhaps within a nuc-prot set.  RefSeq records may
however be referenced remotely.

$^   InconsistentMolInfoBiomols, 12
Mol-info.biomol is inconsistent within a segset, parts set, or pop/phy/mut/eco set.

$^   ArchaicFeatureLocation, 13
A feature location should refer to the accession or gi number, not a local or general ID.

$^   ArchaicFeatureProduct, 14
A feature product should refer to the accession or gi number, not a local or general ID.

$^   GraphPackagingProblem, 15
A graph should be packaged on its bioseq, or on a set containing the Bioseq.

$^   InternalGenBankSet, 16
An outer BioseqSet should not contain an internal BioseqSet of class genbank.

$^   ConSetProblem, 17
BioseqSet class should not be conset.

$^   NoBioseqFound, 18
No Bioseqs were found in the entire record.

$^   INSDRefSeqPackaging, 19
INSD and RefSeq records should not be packaged together.

$^   GPSnonGPSPackaging, 20
Genomic product set records should not be packaged with other set types.

$^   RefSeqPopSet, 21
RefSeq records should not be packaged in a popset.

$^   BioseqSetClassNotSet, 22
The BioseqSet class field is not set.

$^   OrphanedProtein, 23
The Bioseq is an INSD or RefSeq protein erroneously not in a nuc-prot set.

$^   MissingSetTitle, 24
No title was found on a pop/phy/mut/eco set.

$^   NucProtSetHasTitle, 25
A title descriptor was found on a nuc-prot set.

$^   ComponentMissingTitle, 26
A title descriptor should be present on the components of a
pop/phy/mut/eco set.

$^   SingleItemSet, 27
Only a single Bioseq was found in this BioseqSet. Is that what was intended?

$^   MisplacedMolInfo, 28
Mol-info should not be on a pop/phy/mut/eco/wgs/genbank/genprod set.

$^   ImproperlyNestedSets, 29
A pop/phy/mut/eco/wgs set has an unexpected internal set other than nuc-prot,
seg-set, or parts set.


$$ SEQ_FEAT, 5

$^   InvalidForType, 1
This feature type is illegal on this type of Bioseq.

$^   PartialProblem, 2
There are several places in an entry where a sequence can be described as
either partial or complete. In this entry, these settings are inconsistent.
Make sure that the location and product Seq-locs, the Bioseqs, and the
SeqFeat partial flag all agree in describing this SeqFeat as partial or
complete.

$^   InvalidType, 3
A feature with an invalid type has been detected. This is most likely a
software problem.

$^   Range, 4
The coordinates describing the location of a feature do not fall within the
sequence itself. A feature location or a product Seq-loc is out of range of
the Bioseq it points to.

$^   MixedStrand, 5
Mixed strands (plus and minus) have been found in the same location. While
this is biologically possible, it is very unusual. Please check that this is
really what you mean.

$^   SeqLocOrder, 6
This location has intervals that are out of order. While whis is biologically
possible, it is very unusual. Please check that this is really what you mean.

$^   CdTransFail, 7
A fundamental error occurred in software while attempting to translate this
coding region. It is either a software problem or sever data corruption.

$^   StartCodon, 8
An illegal start codon was used. Some possible explanations are: (1) the
wrong genetic code may have been selected; (2) the wrong reading frame may
be in use; or (3) the coding region may be incomplete at the 5' end, in
which case a partial location should be indicated.

$^   InternalStop, 9
Internal stop codons are found in the protein sequence. Some possible
explanations are: (1) the wrong genetic code may have been selected; (2) the
wrong reading frame may be in use; (3) the coding region may be incomplete
at the 5' end, in which case a partial location should be indicated; or (4)
the CdRegion feature location is incorrect.

$^   NoProtein, 10
Normally a protein sequence is supplied. This sequence can then be compared
with the translation of the coding region. In this entry, no protein Bioseq
was found, and the comparison could not be made.

$^   MisMatchAA, 11
The protein sequence that was supplied is not identical to the translation
of the coding region. Mismatching amino acids are found between these two
sequences.

$^   TransLen, 12
The protein sequence that was supplied is not the same length as the
translation of the coding region. Please determine why they are different.

$^   NoStop, 13
A coding region that is complete should have a stop codon at the 3'end.  A
stop codon was not found on this sequence, although one was expected.

$^   TranslExcept, 14
An unparsed \transl_except qualifier was found. This indicates a parser
problem.

$^   NoProtRefFound, 15
The name and description of the protein is missing from this entry. Every
protein Bioseq must have one full-length Prot-ref feature to provide this
information.

$^   NotSpliceConsensus, 16
Splice junctions typically have GT as the first two bases of the intron
(splice donor) and AG as the last two bases of the intron (splice acceptor).
This intron does not conform to that pattern.

$^ OrfCdsHasProduct, 17
A coding region flagged as orf has a protein product.  There should be no
protein product bioseq on an orf.

$^ GeneRefHasNoData, 18
A gene feature exists with no locus name or other fields filled in.

$^ ExceptInconsistent, 19
A coding region has an exception gbqual but the excpt flag is not set.

$^ ProtRefHasNoData, 20
A protein feature exists with no name or other fields filled in.

$^ GenCodeMismatch, 21
The genetic code stored in the BioSource is different than that for this CDS.

$^ RNAtype0, 22
RNA type 0 (unknown RNA) should be type 255 (other).

$^ UnknownImpFeatKey, 23
An import feature has an unrecognized key.

$^ UnknownImpFeatQual, 24
An import feature has an unrecognized qualifier.

$^ WrongQualOnImpFeat, 25
This qualifier is not legal for this feature.

$^ MissingQualOnImpFeat, 26
An essential qualifier for this feature is missing.

$^ PseudoCdsHasProduct, 27
A coding region flagged as pseudo has a protein product.  There should be no
protein product bioseq on a pseudo CDS.

$^ IllegalDbXref, 28
The database in a cross-reference is not on the list of officially
recognized database abbreviations.

$^ FarLocation, 29
The location has a reference to a bioseq that is not packaged in this record.

$^ DuplicateFeat, 30
The intervals on this feature are identical to another feature of the same type,
but the label or comment are different.

$^ UnnecessaryGeneXref, 31
This feature has a gene xref that is identical to the overlapping gene.  This is
redundant, and probably should be removed.

$^   TranslExceptPhase, 32
A \transl_except qualifier was not on a codon boundary.

$^   TrnaCodonWrong, 33
The tRNA codon recognized does not code for the indicated amino acid using the
specified genetic code.

$^   BothStrands, 34
Feature location indicates that it is on both strands. This is not biologically
possible for this kind of feature. Please indicate the correct strand (plus or
minus) for this feature.

$^   CDSgeneRange, 35
A CDS is overlapped by a gene feature, but is not completely contained by it.
This may be an annotation error.

$^   CDSmRNArange, 36
A CDS is overlapped by an mRNA feature, but the mRNA does not cover all
intervals (i.e., exons) on the CDS. This may be an annotation error.

$^ OverlappingPeptideFeat, 37
The intervals on this processed protein feature overlap another protein feature.
This may be caused by errors in originally annotating these features on DNA coordinates,
where start or stop positions do not occur in between codon boundaries.  These then
appear as errors when the features are converted to protein coordinates by mapping
through the CDS.

$^ SerialInComment, 38
Comments that refer to the conclusions of a specific reference should not be
cited by a serial number inside brackets (e.g., [3]), but should instead be
attached as a REMARK on the reference itself.

$^ MultipleCDSproducts, 39
More than one CDS feature points to the same protein product.  This can happen with
viral long terminal repeats (LTRs), but GenBank policy is to have each equivalent
CDS point to a separately accessioned protein Bioseq.

$^ FocusOnBioSourceFeature, 40
The /focus flag is only appropriate on BioSource descriptors, not BioSource features.

$^ PeptideFeatOutOfFrame, 41
The start or stop positions of this processed peptide feature do not occur in between
codon boundaries.  This may incorrectly overlap other peptides when the features are
converted to protein coordinates by mapping through the CDS.

$^ InvalidQualifierValue, 42
The value of this qualifier is constrained to a particular vocabulary of style.  This
value does not conform to those constraints.  Please see the feature table documentation
for more information.

$^ MultipleMRNAproducts, 43
More than one mRNA feature points to the same cDNA product.  This is an error in the
genomic product set.  Each mRNA feature should have a unique product Bioseq.

$^   mRNAgeneRange, 44
An mRNA is overlapped by a gene feature, but is not completely contained by it.
This may be an annotation error.

$^   TranscriptLen, 45
The mRNA sequence that was supplied is not the same length as the
transcription of the mRNA feature. Please determine why they are different.

$^   TranscriptMismatches, 46
The mRNA sequence and the transcription of the mRNA feature are different.
If the number is large, it may indicate incorrect intron/exon boundaries.

$^   CDSproductPackagingProblem, 47
The nucleotide location and protein product of the CDS are not packaged together
in the same nuc-prot set.  This may be an error in the software used to create
the record.

$^   DuplicateInterval, 48
The location has identical adjacent intervals, e.g., a duplicate exon reference.

$^   PolyAsiteNotPoint, 49
A polyA_site should be at a single nucleotide position.

$^   ImpFeatBadLoc, 50
An import feature loc field does not equal the feature location.  This should be
corrected, and then the loc field should be cleared.

$^   LocOnSegmentedBioseq, 51
Feature locations traditionally go on the individual parts of a segmented bioseq, not
on the segmented sequence itself.  These features are invisible in asn2ff reports, and
are now being flagged for correction.

$^   UnnecessaryCitPubEquiv, 52
A set of citations on a feature should not normally have a nested Pub-equiv construct.
This may prevent proper matching to the correct publication.

$^   ImpCDShasTranslation, 53
A CDS that has known translation errors cannot have a /translation qualifier.

$^   ImpCDSnotPseudo, 54
A CDS that has known translation errors must be marked as pseudo to suppress the
translation.

$^   MissingMRNAproduct, 55
The mRNA feature points to a cDNA product that is not packaged in the record.
This is an error in the genomic product set.

$^   AbuttingIntervals, 56
The start of one interval is next to the stop of another.  A single interval
may be desirable in this case.

$^   CollidingGeneNames, 57
Two gene features should not have the same name.

$^   MultiIntervalGene, 58
A gene feature on a single Bioseq should have a single interval spanning everything
considered to be under that gene.

$^ FeatContentDup, 59
The intervals on this feature are identical to another feature of the same type,
and the label and comment are also identical. This is likely to be an error in
annotating the record.  Note that GenBank format suppresses duplicate features,
so use of Graphic view is recommended.

$^   BadProductSeqId, 60
The feature product refers to a database ID that has a locus name but no accession.
This is probably an error in parsing of a submission.

$^   RnaProductMismatch, 61
The RNA feature product type does not correspond to the RNA feature type.  These
need to be consistent.

$^   MissingCDSproduct, 62
The CDS should have a product, but does not.  Pseudo or short CDSs (less than 6
amino acids), or those marked with a rearrangement required for product exception,
are exempt from needing a product.

$^   BadTrnaCodon, 63
The tRNA codon recognized is an illegal value.

$^   BadTrnaAA, 64
The tRNA encoded amino acid is an illegal value.

$^   OnlyGeneXrefs, 65
There are gene xrefs but no gene features.  Records should normally have single-interval
gene features covering other biological features.  Gene xrefs are used only to override
the inheritance by overlap.

$^   UTRdoesNotAbutCDS, 66
The 5'UTR and 3'UTR features should exactly abut the CDS feature.

$^   BadConflictFlag, 67
The coding region conflict flag is set, but the translated product is the
same as the instantiated product Bioseq.

$^   ConflictFlagSet, 68
The coding region conflict flag is appropriately set, but this record should
be brought to the attention of the source database for possible correction.

$^   LocusTagProblem, 69
A gene locus_tag should be a single token, with no spaces.

$^   CollidingLocusTags, 70
Two gene features should not have the same locus_tag, which is supposed to be
a unique identifer.

$^   AltStartCodon, 71
An alternative start codon was used. This is rare, and it is expected that
confirmatory evidence will be cited.

$^   PartialsInconsistent, 72
There are several places in an entry where a sequence can be described as
either partial or complete. In this entry, these settings are inconsistent.
Make sure that the location and product Seq-locs, the Bioseqs, and the
SeqFeat partial flag all agree in describing this SeqFeat as partial or
complete.

$^   GenesInconsistent, 73
The gene on the genomic sequence of a genomic product set should be the
same as the gene on the cDNA product of the mRNA feature.

$^   DuplicateTranslExcept, 74
There are multiple /transl_except qualifiers at the same location on this
CDS but with different amino acids indicated.

$^   TranslExceptAndRnaEditing, 75
A CDS has both /exception=RNA editing and /transl_except qualifiers.  RNA
editing indicates post-transcriptional changes prior to translation.  Use
/transl_except for individual codon exceptions such as selenocysteine or
other nonsense suppressors.

$^   NoNameForProtein, 76
A protein feature has a description, but no product name.

$^   TaxonDbxrefOnFeature, 77
A BioSource feature has a taxonID database identifier in the db_xref area
common to all features. This db_xref should only exist within the separate
BioSource xref list.

$^   UnindexedFeature, 78
The location of a feature does not allow it to be mapped to a single Bioseq,
or to the segmented parent if on one or more part Bioseqs. It will not show
up in flatfile and other formats, and should be corrected or removed.

$^   CDSmRNAmismatch, 79
There should usually be a one-to-one correspondence between mRNA and CDS
under a given gene.

$^   UnnecessaryException, 80
The feature is marked with an exception qualifier, but the validator does
not detect an error that needs to be suppressed.

$^   LocusTagProductMismatch, 81
In certain records a policy is that the locus_tag of the gene is expected to
match the prefix of the general ID of the CDS or mRNA product Bioseq.

$^   MrnaTransFail, 82
A fundamental error occurred in software while attempting to transcribe this
messenger RNA. It is either a software problem or sever data corruption.

$^ PseudoCdsViaGeneHasProduct, 83
A coding region overlapped by a pseudo gene has a protein product.  There
should be no protein product bioseq on a pseudo CDS.

$^ MissingGeneXref, 84
This feature has multiple overlapping genes of the same length, but no
xref to determine which one should be used for the /gene qualifier.

$^ FeatureCitationProblem, 85
This feature has a citation to a publication that needs to be repaired.

$^ NestedSeqLocMix, 86
A location should not have nested SEQLOC_MIX structures.

$^ WrongQualOnFeature, 87
This qualifier is not legal for this feature.

$^ MissingQualOnFeature, 88
An essential qualifier for this feature is missing.

$^ CodonQualifierUsed, 89
The codon qualifier should be replaced by individual transl_except code breaks,
after checking to make sure the proper genetic code is being used.

$^ UnknownFeatureQual, 90
A feature has an unrecognized qualifier.

$^ BadCharInAuthorName, 91
An author name has illegal characters.

$^ PolyATail, 92
The mRNA feature has polyA tail added to make the mRNA sequence.

$^ ProteinNameEndsInBracket, 93
The protein name ends with a right square bracket, and may have been
copied from another GenPept record, where the organism name is
appended to the definition line and placed inside brackets.

$^ CDSwithMultipleMRNAs, 94
The CDS feature has more than one overlapping mRNA with the proper intervals and
no other identification assigning it to a different coding region.

$^ MultipleEquivBioSources, 95
Multiple equivalent biosource features exist on the sequence. They should be
fused into a single feature with multiple intervals.

$^ MultipleEquivPublications, 96
Multiple equivalent publication features exist on the sequence. They should be
fused into a single feature with multiple intervals.

$^ BadFullLengthFeature, 97
A publication or biosource feature is on the full length the sequence. It should be
converted to a publication or biosource descriptor.

$^ RedundantFields, 98
A comment or other field contains information that is redundant with the primary
field on a feature.

$^ CDSwithNoMRNAOverlap, 99
The CDS feature has more than one overlapping mRNA with the proper intervals and
no other identification assigning it to a different coding region.

$^ FeatureProductInconsistency, 100
The CDS feature has more than one overlapping mRNA with the proper intervals and
no other identification assigning it to a different coding region.

$^ ImproperBondLocation, 101
Only bond features should have locations of type bond. Most other features should
use interval or point locations.

$^ GeneXrefWithoutGene, 102
This feature has a gene xref, but there is no equivalent gene feature anywhere
on the record.

$^ SeqFeatXrefProblem, 103
This feature has a seqfeat xref, but it has nothing in the id or data field.

$^ ProductFetchFailure, 104
Unable to fetch the Bioseq product of this feature.  Remote fetching was requested,
so this is likely due to a failure in a network sequence retrieval service.

$^ SuspiciousGeneXref, 105
This feature has a gene xref that is not expected for this organism.

$^ MissingTrnaAA, 106
The tRNA encoded amino acid is not set.

$^ CollidingFeatureIDs, 107
Multiple features have the same featureID.  Feature ID must be unique within
a record.

$^ ExceptionProblem, 108
There is a problem with /exception text.

$^   PolyAsignalNotRange, 109
A polyA_signal should be at nucleotide range position, not a single point.

$^   OldLocusTagMismtach, 110
The old_locus_tag qualifier on a feature does not match that on the overlapping gene.

$^   DuplicateGeneOntologyTerm, 111
A feature has multiple identical Gene Ontology (GO) term specifications.

$^   InvalidInferenceValue, 112
The value of the inference qualifier is constrained by agreement of the international
nucleotide sequence database collaboration.  This value does not conform to those
constraints.  Please see the feature table documentation for more information.

$^ HpotheticalProteinMismatch, 113
There is a mismatch between the accession cited by the hypothetical protein claim
and the actual accession of the record.

$^ FeatureRefersToAccession, 114
There is a mixture of features referring to sequence by gi numbers and by accession.
This inconsistency is likely due to incomplete processing by software.

$^ SelfReferentialProduct, 115
A feature product points to the same sequence that the feature location does.
The product must point to a different sequence that is the biological product
of the first, due to transcription, translation, or peptide processing.

$^ ITSdoesNotAbutRRNA, 116
The internal transcribed spacer misc_RNA features should exactly abut the flanking rRNA features.

$^ FeatureSeqIDCaseDifference, 117
Feature location and referenced Bioseq have the same Seq-id except for capitalization.
Sequence identifiers must be unique in a case-insensitive manner within a record.

$^ FeatureLocationIsGi0, 118
Feature location refers to gi 0. This indicates an error in database processing of this record.

$^ GapFeatureProblem, 119
Gap features must only cover gaps in the sequence, not actual bases.

$^ PseudoCdsHasProtXref, 120
A coding region flagged as pseudo has a protein cross reference.  There should be no
protein product bioseq or protein cross reference on a pseudo CDS.

$^ ErroneousException, 121
The feature is marked with a specific exception qualifier, but validation indicates
that a different exception should be used.

$^ SegmentedGeneProblem, 122
A gene feature on the parts of a segmented Bioseq should map to a single interval on the
segmented Bioseq's coordinate system.

$^   WholeLocation, 123
Feature location is set to whole, the entirety of the parent sequence.  Please specify
exact intervals for this feature location.

$^ BadEcNumberFormat, 124
There is a problem with the format of the EC_number qualifier.

$^ BadEcNumberValue, 125
There is a problem with the value of the EC_number qualifier.

$^ EcNumberProblem, 126
There is a problem with the format of the EC_number qualifier.

$^ VectorContamination, 127
Contamination by cloning vector is annotated on this sequence. The underlying region
should be removed from the sequence.

$^ MinusStrandProtein, 128
A feature on a protein indicates the minus strand, which does not exist.

$^ BadProteinName, 129
A protein feature has a name that conflicts with other information on the feature.

$^ GeneXrefWithoutLocus, 130
A feature has a gene xref with a locus_tag and no locus, but the gene with that locus_tag has a locus.

$^ UTRdoesNotExtendToEnd, 131
The UTR does not have the expected range.

$^ CDShasTooManyXs, 132
The CDS translation has greater than 50 percent ambiguous X residues.

$^ SuspiciousFrame, 133
The CDS has a frame greater than 1 that is not expected in this context.

$^ TerminalXDiscrepancy, 134
The CDS translation and protein product sequence have a different number of terminal Xs.

$^ UnnecessaryTranslExcept, 135
The CDS translates to the same amino acid as indicated by the transl_except code break.

$^ SuspiciousQualifierValue, 136
The value of this qualifier is constrained to a particular vocabulary of style.  This
value appears not to conform to those constraints.  Please see the feature table documentation
for more information.

$^ NotSpliceConsensusDonor, 137
Splice junctions typically have GT as the first two bases of the intron
(splice donor) and AG as the last two bases of the intron (splice acceptor).
This intron does not conform to that pattern.

$^ NotSpliceConsensusAcceptor, 138
Splice junctions typically have GT as the first two bases of the intron
(splice donor) and AG as the last two bases of the intron (splice acceptor).
This intron does not conform to that pattern.

$^ RareSpliceConsensusDonor, 139
Splice junctions typically have GT as the first two bases of the intron
(splice donor) and AG as the last two bases of the intron (splice acceptor).
This intron does not conform to that pattern.

$^ SeqFeatXrefNotReciprocal, 140
Feature xrefs between CDS and mRNA are not reciprocal.

$^ SeqFeatXrefFeatureMissing, 141
The feature referenced by a seqfeat xref cannot be found.

$^ FeatureInsideGap, 142
The feature is completely contained inside a sequence gap.

$^ FeatureCrossesGap, 143
The feature extends from actual sequence into a sequence gap.

$^ BadAuthorSuffix, 144
An author name has an unexpected suffix.

$^   BadAnticodonAA, 145
The tRNA encoded amino acid cannot be produced by any likely reverse complement
and wobble expansion of the anticodon sequence.

$^   BadAnticodonCodon, 146
The tRNA indicated codon recognized cannot be produced by any likely reverse complement
and wobble expansion of the anticodon sequence.

$^   BadAnticodonStrand, 147
The tRNA feature location and anticodon location are not on the same strand.

$^   UndesiredGeneSynonym, 148
The gene synonym is uninformative.

$^   UndesiredProteinName, 149
The protein name is uninformative.

$^ FeatureBeginsOrEndsInGap, 150
The feature starts or stops within a sequence gap.

$^ GeneOntologyTermMissingGOID, 151
A Gene Ontology (GO) term is missing the GO Identifier.

$^ PseudoRnaHasProduct, 152
An RNA flagged as pseudo has a transcribed product.  There should be no
transcribed product bioseq on a pseudo RNA.

$^ PseudoRnaViaGeneHasProduct, 153
An RNA overlapped by a pseudo gene has a transcribed product.  There
should be no transcribed product bioseq on a pseudo RNA.

$^ BadRRNAcomponentOrder, 154
rRNA and ITS features are not in the expected order.

$^ BadRRNAcomponentOverlap, 155
rRNA and ITS or tRNA elements should not overlap.

$^ MissingGeneLocusTag, 156
If one gene in a record has a locus-tag value, all genes in the record
should have a locus-tag value.

$^ MultipleProtRefs, 157
The name and description of the protein is missing from this entry. Every
protein Bioseq must have one full-length Prot-ref feature to provide this
information.

$^   BadInternalCharacter, 158
Biological names or labels should not end with question mark,
exclamation point, or tilde.

$^   BadTrailingCharacter, 159
Biological names or labels should not contain underscore, period,
comma, colon, or semicolon, 

$^   BadTrailingHyphen, 160
Biological names or labels should not end with a hyphen.

$^   MultipleGeneOverlap, 161
This genes completely contains two or more other genes.

$^ BadCharInAuthorLastName, 162
An author name has illegal characters.

$^   PseudoCDSmRNArange, 163
A pseudo CDS is overlapped by an mRNA feature, but the mRNA does not cover all
intervals (i.e., exons) on the CDS. This may be an annotation error.

$^   ExtendablePartialProblem, 164
A partial end of this feature does not abut a gap and does not include the first
or last nucleotide in the sequence, but it could be extended by one or two
nucleotides to do so.

$^ GeneXrefNeeded, 165
This feature has multiple overlapping genes of the same length and same name,
but no xref to determine which one should be used for the /gene qualifier.

$^ RubiscoProblem, 166
A protein name contains ribulose and bisphosphate but does not use
the prefered formal naming convention.

$^ UnqualifiedException, 167
The feature is marked with an automatically supplied exception qualifier
that should be replaced or supplemented with more informative information.

$^   ProteinNameHasPMID, 168
The protein name has (PMID #####) embedded in it.

$^   BadGeneOntologyFormat, 169
A feature has incorrectly labeled fields in a Gene Ontology (GO) term specification.

$^   InconsistentGeneOntologyTermAndId, 170
The same GO term should apply to Gene Ontology (GO) term specifications with the same GO ID.

$^   MultiplyAnnotatedGenes, 171
Two gene features with the same name are annotated at the same location.

$^   ReplicatedGeneSequence, 172
Two gene features with the same name are annotated at different locations, but the
underlying sequence is identical.

$^   ShortIntron, 173
Introns should be longer than 10 nt.

$^ GeneXrefStrandProblem, 174
This feature has a gene xref that points to a gene on the wrong strand.

$^ CDSmRNAXrefLocationProblem, 175
The CDS is not contained within the cross-referenced mRNA.

$^ LocusCollidesWithLocusTag, 176
A gene locus is identical with a gene locus_tag.

$^   IdenticalGeneSymbolAndSynonym, 177
The gene synonym is the same as the locus of a different gene.

$^   NeedsNote, 178
A misc_feature requires a note.

$^ RptUnitRangeProblem, 179
The value of the rpt_unit_range qualifier is not inside the parent feature location.

$^ TooManyInferenceAccessions, 180
There are too many inference qualifier accessions to have their versions verified by
network access.

$^ IntervalBeginsOrEndsInGap, 181
An internal interval of the feature starts or stops within a sequence gap.

$^ InconsistentRRNAstrands, 182
rRNA and ITS features are not on the same strand.

$^ CDSonMinusStrandMRNA, 183
Coding regions should be on the plus strand of mRNA molecules.

$^ tRNAmRNAmixup, 184
An mRNA feature has annotation indicating that it is really a tRNA.

$^ ProductLength, 185
The protein sequence that was supplied is not the same length as the
translation of the coding region.

$^ InconsistentPseudogeneCounts, 186
There are pseudo features with and without pseudogene qualifiers.

$^ DeletedEcNumber, 187
The EC_number has been deleted.

$^ ReplacedEcNumber, 188
The EC_number has been replaced.

$^ SplitEcNumber, 189
The EC_number has been split.

$$ SEQ_ALIGN, 6

$^   SeqIdProblem, 1
The seqence referenced by an alignment SeqID is not packaged in the record.

$^   StrandRev, 2
Please contact the sequence database for further help with this error.

$^   DensegLenStart, 3
Please contact the sequence database for further help with this error.

$^   StartLessthanZero, 4
Please contact the sequence database for further help with this error.

$^   StartMorethanBiolen, 5
Please contact the sequence database for further help with this error.

$^   EndLessthanZero, 6
Please contact the sequence database for further help with this error.

$^   EndMorethanBiolen, 7
Please contact the sequence database for further help with this error.

$^   LenLessthanZero, 8
Please contact the sequence database for further help with this error.

$^   LenMorethanBiolen, 9
Please contact the sequence database for further help with this error.

$^   SumLenStart, 10
Please contact the sequence database for further help with this error.

$^   AlignDimSeqIdNotMatch, 11
Please contact the sequence database for further help with this error.

$^   SegsDimSeqIdNotMatch, 12
Please contact the sequence database for further help with this error.

$^   FastaLike, 13
Please contact the sequence database for further help with this error.

$^   NullSegs, 14
Please contact the sequence database for further help with this error.

$^   SegmentGap, 15
Please contact the sequence database for further help with this error.

$^   SegsDimOne, 16
Please contact the sequence database for further help with this error.

$^   AlignDimOne, 17
Please contact the sequence database for further help with this error.

$^   Segtype, 18
Please contact the sequence database for further help with this error.

$^   BlastAligns, 19
BLAST alignments are not desired in records submitted to the sequence database.

$^   PercentIdentity, 20
An acceptable percent identity score is 75 percent or higher.

$^   ShortAln, 21
Alignment is shorter than expected.

$^   UnexpectedAlignmentType 22
Only DenseSeg alignments are expected.

$$ SEQ_GRAPH, 7

$^   GraphMin, 1
The graph minimum value is outside of the 0-100 range.

$^   GraphMax, 2
The graph maximum value is outside of the 0-100 range.

$^   GraphBelow, 3
Some quality scores are below the stated graph minimum value.

$^   GraphAbove, 4
Some quality scores are above the stated graph maximum value.

$^   GraphByteLen, 5
The number of bytes in the quality graph does not correspond to the
stated length of the graph.

$^   GraphOutOfOrder, 6
The quality graphs are not packaged in order - may be due to an old fa2htgs bug.

$^   GraphBioseqLen, 7
The length of the quality graph does not correspond to the length of the Bioseq.

$^   GraphSeqLitLen, 8
The length of the quality graph does not correspond to the length of the
delta Bioseq literal component.

$^   GraphSeqLocLen, 9
The length of the quality graph does not correspond to the length of the
delta Bioseq location component.

$^   GraphStartPhase, 10
The quality graph does not start or stop on a sequence segment boundary.

$^   GraphStopPhase, 11
The quality graph does not start or stop on a sequence segment boundary.

$^   GraphDiffNumber, 12
The number quality graph does not equal the number of sequence segments.

$^   GraphACGTScore, 13
Quality score values for known bases should be above 0.

$^   GraphNScore, 14
Quality score values for unknown bases should not be above 0.

$^   GraphGapScore, 15
Gap positions should not have quality scores above 0.

$^   GraphOverlap, 16
Quality graphs overlap - may be due to an old fa2htgs bug.

$^   GraphBioseqId, 17
Quality graph does not map to Bioseq in record.

$^   GraphACGTScoreMany, 18
Quality score values for known bases should be above 0.

$^   GraphNScoreMany, 19
Quality score values for unknown bases should not be above 0.

$^   GraphLocInvalid, 20
Location for quality score values extends beyond end of sequence.

$$ SEQ_ANNOT, 8

$^   AnnotIDs, 1
Seq-annot.data.ids should only be used for communication between programs.

$^   AnnotLOCs, 2
Seq-annot.data.locs should only be used for communication between programs.