1 embl_acc European Nucleotide Archive (was EMBL) accession \N 2 status Status \N 3 synonym Synonym \N 4 name Name Alternative/long name 5 type Type of feature \N 6 toplevel Top Level Top Level Non-Redundant Sequence Region 7 GeneCount Gene Count Total Number of Genes 10 SNPCount Short Variants Total Number of SNPs 11 codon_table Codon Table Alternate codon table 12 _selenocysteine Selenocysteine \N 13 bacend bacend \N 14 htg htg High Throughput phase attribute 15 miRNA Micro RNA Coordinates of the mature miRNA 16 non_ref Non Reference Non Reference Sequence Region 17 sanger_project Sanger Project name \N 18 clone_name Clone name \N 19 fish FISH location \N 21 org Sequencing centre \N 22 method Method \N 23 superctg Super contig id \N 24 inner_start Max start value \N 25 inner_end Min end value \N 26 state Current state of clone \N 27 organisation Organisation sequencing clone \N 28 seq_len Accession length \N 29 fp_size FP size \N 30 BACend_flag BAC end flags \N 31 fpc_clone_id fpc clone \N 32 KnwnPCCount protein_coding_KNOWN Number of Known Protein Coding 33 NovPCCount protein_coding_NOVEL Number of Novel Protein Coding 36 PredPCCount protein_coding_PREDICTED Number of Predicted Protein Coding 37 IGGeneCount IG_gene Number of IG Genes 38 IGPsGenCount IG_pseudogene Number of IG Pseudogenes 39 TotPsCount total_pseudogene Total Number of Pseudogenes 42 KnwnPCProgCount protein_coding_in_progress_KNOWN Number of Known Protein Coding in progress 43 NovPCProgCount protein_coding_in_progress_NOVEL Number of Novel Protein Coding in progress 44 AnnotSeqLength Annotated sequence length Annotated Sequence 45 TotCloneNum Total number of clones Total Number of Clones 46 NumAnnotClone Fully annotated clones Number of Fully Annotated Clones 47 ack Acknowledgement Acknowledgement for manual annotation 48 htg_phase High throughput phase High throughput genomic sequencing phase 49 description Description A general descriptive text attribute 50 chromosome Chromosome Chromosomal location for supercontigs that are not assembled 51 nonsense Nonsense Mutation Strain specific nonesense mutation 52 author Author Group resonsible for Vega annotation 53 author_email Author email address Author email address 54 remark Remark Annotation remark 55 transcr_class Transcript class Transcript class 57 ccds CCDS CCDS identifier 58 CCDS_PublicNote CCDS Public Note Public Note for CCDS identifier, provided by http://www.ncbi.nlm.nih.gov/CCDS 59 Frameshift Frameshift Frameshift modelled as intron 62 ncRNA Structure RNA secondary structure line 63 skip_clone skip clone Skip clone in align_by_clone_identity.pl \N 64 coding_cnt Coding genes Number of protein coding Genes 67 pseudogene_cnt Pseudogenes Number of pseudogenes 80 supercontig SuperContig name \N 81 well_name Well plate name \N 82 bacterial Bacterial \N 90 bacend_well_nam BACend well name \N 91 alt_well_name Alt well name \N 92 TranscriptEdge Transcript Edge \N 93 alt_embl_acc Alt European Nucleotide Archive (was EMBL) acc \N 94 alt_org Alt org \N 95 intl_clone_name International Clone Name \N 96 embl_version European Nucleotide Archive (was EMBL) Version \N 97 chr Chromosome Name Chromosome Name Contained in the Assembly 98 equiv_asm Equivalent EnsEMBL assembly For full chromosomes made from NCBI AGPs 109 HitSimilarity hit similarity percentage id to parent transcripts 110 HitCoverage hit coverage coverage of parent transcripts 111 PropNonGap proportion non gap proportion non gap 112 NumStops number of stops \N 113 GapExons gap exons number of gap exons 114 SourceTran source transcript source transcript 115 EndNotFound end not found end not found 116 StartNotFound start not found start not found 117 Frameshift Fra Frameshift modelled as intron \N 118 ensembl_name Ensembl name Name of equivalent Ensembl chromosome 119 NoAnnotation NoAnnotation Clones without manual annotation 120 hap_contig Haplotype contig Contig present on a haplotype 121 annotated Clone Annotation Status \N 122 keyword Clone Keyword \N 123 hidden_remark Hidden Remark \N 124 mRNA_start_NF mRNA start not found \N 125 mRNA_end_NF mRNA end not found \N 126 cds_start_NF CDS start not found \N 127 cds_end_NF CDS end not found \N 128 write_access Write access for Sequence Set 1 for writable , 0 for read-only 129 hidden Hidden Sequence Set \N 130 vega_name Vega name Vega seq_region.name 131 vega_export_mod Export mode E (External), I (Internal) etc 132 vega_release Vega release Vega release number 133 atag_CLE Clone_left_end Clone_lef_end feature marked in GAP database 134 atag_CRE Clone_right_end Clone_right_end feature marked in GAP database 135 atag_Misc Misc miscellaneous feature marked in GAP database 136 atag_Unsure Unsure region of uncertain DNA sequence marked in GAP database 137 MultAssem Multiple Assembled seq region Part of Seq Region is part of more than one assembly 140 wgs WGS contig WGS contig integrated into the map 141 bac AGP clones tiling path of clones 142 GeneGC Gene GC Percentage GC content for this gene 143 TotAssemblyLeng Finished sequence length Length of the assembly not counting sequence gaps 144 amino_acid_sub Amino acid substitution Some translations have been manually curated for amino acid substitiutions. For example a stop codon may be changed to an amino acid in order to prevent premature truncation, or one amino acid can be substituted for another. 145 _rna_edit rna_edit RNA edit 146 kill_reason Kill Reason Reason why a transcript has been killed 147 strip_UTR Strip UTR Transcript needs bad UTR removing 148 TotAssLength Finished sequence length Finished Sequence 149 PsCount pseudogene Number of Pseudogenes 152 TotPTCount total_processed_transcript Total Number of Processed Transcripts 153 TotPCCount total_protein_coding Total Number of Protein Coding 156 PolyPsCount polymorphic_pseudogene Number of Polymorphic Pseudogenes 157 TotIGGeneCount total_IG_gene Total Number of IG Genes 158 ProcPsCount proc_pseudogene Number of Processed Pseudogenes 159 UnPsCount unproc_pseudogene Number of Unprocessed Pseudogenes 160 TPsCount transcribed_pseudogene Number of Transcribed Pseudogenes 161 TECCount TEC Number of TEC Genes 164 IsoPoint Isoelectric point Pepstats attributes 165 Charge Charge Pepstats attributes 166 MolecularWeight Molecular weight Pepstats attributes 167 NumResidues Number of residues Pepstats attributes 168 AvgResWeight Ave. residue weight Pepstats attributes 170 initial_met Initial methionine Set first amino acid to methionine 171 NonGapHCov NonGapHCov \N 172 otter_support otter support Evidence ID that was used as supporting feature for building a gene in Vega 173 enst_link enst link Code to link a OTTT with an ENST when they both share the CDS of ENST 174 upstream_ATG upstream ATG Alternative ATG found upstream of the defined as start ATG for the transcript 175 TPPsCount transcribed_processed_pseudogene Number of Transcribed Processed Pseudogenes 176 TUPsCount transcribed_unprocessed_pseudogene Number of Transcribed Unprocessed Pseudogenes 177 UniPsCount unitary_pseudogene Number of Unitary Pseudogenes 180 TUyPsCount transcribed_unitary_pseudogene Number of Transcribed Unitary Pseudogenes 181 PolyCount polymorphic Number of Polymorphic Genes 184 TRGeneCount TR_gene Number of TR Genes 185 TRPsCount TR_pseudo Number of TR Pseudogenes 186 tp_ott_support otter protein transcript support Evidence ID that was used as supporting feature for building a gene in Vega 187 td_ott_support otter dna transcript support Evidence ID that was used as supporting feature for building a gene in Vega 188 ep_ott_support otter protein exon support Evidence ID that was used as supporting feature for building a gene in Vega 189 ed_ott_support otter dna exon support Evidence ID that was used as supporting feature for building a gene in Vega 191 StopGained SNP causes stop codon to be gained This transcript has a variant that causes a stop codon to be gained in at least 10 percent of a HapMap population 192 StopLost SNP causes stop codon to be lost This transcript has a variant that causes a stop codon to be lost in at least 10 percent of a HapMap population 198 lost_frameshift lost_frameshift Frameshift on the query sequence is lost in the target sequence 199 AltThreePrime Alternate three prime end The position of other possible three prime ends for the transcript 216 GeneInLRG Gene in LRG This gene is contained within an LRG region 217 GeneOverlapLRG Gene overlaps LRG This gene is partially overlapped by a LRG region (start or end outside LRG) 218 readthrough_tra readthrough transcript Havana readthrough transcripts 300 CNE Constitutive exon An exon that is always included in the mature mRNA, even in different mRNA isoforms 301 CE Cassette exon One exon is spliced out of the primary transcript together with its flanking introns 302 IR Intron retention A sequence is spliced out as an intron or remains in the mature mRNA transcript 303 MXE Mutually exclusive exons In the simpliest case, one or two consecutive exons are retained but not both 304 A3SS Alternative 3' sites Two or more splice sites are recognized at the 5' end of an exon. An alternative 3' splice junction (acceptor site) is used, changing the 5' boundary of the downstream exon 305 A5SS Alternative 5' sites Two or more splice sites are recognized at the 3' end of an exon. An alternative 5' splice junction (donor site) is used, changing the 3' boundary of the upstream exon 306 AFE Alternative first exon The second exons of each variant have identical boundaries, but the first exons do not overlap 307 ALE Alternative last exon Penultimate exons of each splice variant have identical boundaries, but the last exons do not overlap 308 II Intron isoform Alternative donor or acceptor splice sites lead to truncation or extension of introns, respectively 309 EI Exon isoform Alternative donor or acceptor splice sites leads to truncation or extension of exons, respectively 310 AI Alternative initiation Alternative choice of promoters 311 AT Alternative termination Alternative choice of polyadenylation sites 312 patch_fix Assembly Patch Fix Assembly patch that will, in the next assembly release, replace the corresponding sequence found in the current assembly 313 patch_novel Assembly Patch Novel Assembly patch that will, in the next assembly release, be retained as an alternate non-reference sequence in a similar way to haplotypes 314 LRG Locus Reference Genomic Locus Reference Genomic sequence 315 NoEvidence Evidence for transcript removed Supporting evidence for this projected transcript has been removed 316 circular_seq Circular sequence Circular chromosome or plasmid molecule 317 external_db External database External database to which seq_region name may be linked 318 split_tscript split_tscript split_tscript 319 Threep Three prime end Alternate three prime end 320 gene_cluster Gene cluster Havana annotated gene cluster 328 _rib_frameshift Ribosomal Frameshift Position and magnitude of frameshift 345 vega_ref_chrom Vega reference chromosome Haplotypes reference a regular chromosome (indicated in the value of the attribute) 346 PutPCCount protein_coding_PUTATIVE Number of Putative Protein Coding 347 proj_alt_seq Projection altered sequence Projected sequence differs from original 348 hav_gene_type Havana gene biotype Gene biotype assigned by Havana 353 noncoding_cnt Non coding genes Number of non coding genes 358 PHIbase_mutant PHI-base mutant PHI-base phenotype of the mutants 360 ncrna_host ncrna_host Havana ncrna_host gene 361 peptide-class Peptide classification The classification of the gene or transcript based on alignment to NR (values: TE WH NH) 362 working-set Working Gene Set High-confidence set of genes, composed of evidence-based genes and non-overlapping protein-coding ab initio gene models 363 filtered-set Filtered Gene Set v1 Working genes that are screened for TE content and orthology with sorghum and rice 364 super-set Super Working Gene Set Set of all working gene set loci from both Builds 4a and 5a 365 projected4a2 Projected by alignment Temporary (Monday, August 23, 2010) 366 merged Merged species \N 367 karyotype_rank Rank in the karyotype For a given seq_region, if it is part of the species karyotype, will indicate its rank 368 noncoding_acnt Non coding genes Number of non coding genes on alternate sequences 369 coding_acnt Coding genes Number of protein coding genes on alternate sequences 370 pseudogene_acnt Pseudogenes Number of pseudogenes on alternate sequences 371 clone_end Clone end Side of the contig on which a vector lies (enum:RIGHT, LEFT) 372 contig_scaffold Contig Scaffold Scaffold that contains mutually ordered contigs 373 current_version Current Accession Version Identifies the most recent version of an accession 374 seq_status Sequence Status Sequence status. 375 clone_vector Vector sequence A clone-end vector associated with a contig (enum:SP6, T7). 376 creation_date Creation date Creation date of annotation 377 update_date Update date Last update date of annotation 378 seq_date Sequence date Sequence date 379 has_stop_codon Contains stop codon Translation attribute 380 havana_cv Havana CV term Controlled vocabulary terms from Havana 381 TlPPsCount translated_processed_pseudogene Number of Translated Processed Pseudogenes 382 NoTransRefError No translations due to reference error This gene is believed to include protein coding transcripts, but no transcript has a translation due to a reference assembly error making specifying the translation impossible. 383 parent_exon_key parent_exon_key The exon key to identify a projected transcript's parent transcript. 386 parent_sid parent_sid The parent stable ID to identify a projected transcript's parent transcript. For internal statistics use only since this method does not work in all cases. 387 noncoding_acnt_s Small non coding genes Number of small non coding genes on alternate sequences 388 noncoding_acnt_m Misc non coding genes Number of unclassified (miscellaneous) non coding genes on alternate sequences 389 noncoding_cnt_s Small non coding genes Number of small non coding genes 390 noncoding_cnt_l Long non coding genes Number of long non coding genes 391 TlUPsCount translated_unprocessed_pseudogene Number of Translated Unprocessed Pseudogenes 393 AFFYMETRIXCount AFFYMETRIX Count Total Number of AFFYMETRIX features 394 RFLPCount RFLP Count Total Number of RFLP features 395 xref_id Xref ID ID of associated database reference 396 vega_chr_type Vega chrom type Type of chromosome - haplotype, other, etc 398 genscan Genscan gene predictions Number of prediction genes generated by Genscan 399 gsc GSC gene prediction Number of prediction genes generated by gsc 400 snap Snap gene prediction Number of prediction genes generated by Snap 401 fgenesh FGENESH gene prediction Number of prediction genes generated by FGENESH 402 genefinder Genefinder gene prediction Number of prediction genes generated by Genefinder 403 transcript_cnt Gene transcripts Number of transcripts 404 transcript_acnt Gene transcripts Number of transcripts on the alternate sequences 405 ref_length Golden Path Length Length of the primary assembly 406 total_length Base Pairs Total length of the assembly 407 refseq_compare refseq_compare This attribute can be applied to both gene and transcript. It is supposed to give an indication of whether the annotation in the ensembl database is matched by annotation that we have imported from refseq. At the gene level, the match is unlikely to be an exact match because all or some of the transcripts may differ. Also, the biotype e.g. coding potential may differ. therefore, matching is a bit fuzzy and is done primarily on genomic location and then also takes gene length and gene name into consideration. 408 coding_rcnt Readthrough coding genes Number of readthrough coding genes 409 coding_racnt Readthrough coding genes Number of readthrough coding genes on alternate sequences 410 noncoding_racnt_l Readthrough long non coding genes Number of readthrough long non coding genes on alternate sequences 411 noncoding_racnt_s Readthrough small non coding genes Number of readthrough small non coding genes on alternate sequences 412 noncoding_rcnt_s Readthrough small non coding genes Number of readthrough small non coding genes 413 noncoding_rcnt_l Readthrough long non coding genes Number of readthrough long non coding genes 414 pseudogene_rcnt Readthrough pseudogenes Number of readthrough pseudogenes 415 pseudogene_racnt Readthrough pseudogenes Number of readthrough pseudogenes on alternate sequences 416 gencode_level GENCODE annotation level level 1 (verified loci), level 2 (manually annotated loci), level 3 (automatically annotated loci) 417 gencode_basic GENCODE basic annotation GENCODE Basic is a view provided by UCSC for users. It includes a subset of the GENCODE transcripts. In general, for protein coding genes it will show only the full length models (unless a protein coding gene has no full-length models, in which case other rules apply). For noncoding genes, it will also only show the full-length (mRNA start and end found) models (unless there are no full-length models, in which case other rules apply). 418 struct_var Structural variants Total Number of structural variants 419 genblast GenBlastG gene predictions Number of prediction genes generated by GenBlastG 420 syn_gene_pairs Syntenic gene pairs Syntenic gene relationship from Gramene pipeline 421 vectorbase_maker_pre VectorBase gene predictions Number of prediction genes generated with MAKER, by VectorBase. 422 trnascan tRNAscan-SE predictions Number of predicted tRNA genes generated by tRNAscan-SE 423 tgac_pred_supp7 T. turgidum RNA-seq alignments Number of T. turgidum RNA-seq alignments from Krasileva et al. 424 tgac_pred_supp17 T. aestivum RNA-seq alignments Number of T. aestivum RNA-seq alignments from Krasileva et al. 425 genome_component Genome Component Name For polyploid genome, the genome component name the seq_region belongs to 426 transcript_whl RNA-seq transcripts RNA-seq transcripts from EchinoBase 427 appris APPRIS APPRIS is a system that deploys a range of computational methods to provide value to the annotations of the human genome. APPRIS also selects one of the CDS for each gene as the principal isoform. APPRIS defines the principal variant by combining protein structural and functional information and information from the conservation of related species. principal1 - APPRIS principal isoform. principal2 - APPRIS candidate isoform (CCDS). principal3 - APPRIS candidate isoform (earliest CCDS). principal4 - APPRIS candidate isoform (longest CCDS). principal5 - APPRIS candidate isoform (longest coding sequence). alternative1 - APPRIS candidate isoform that is conserved in at least three tested species. alternative2 - APPRIS candidate isoform that appears to be conserved in fewer than three tested species 428 TSL Transcript Support Level Transcription Support Level (TSL) is a method to highlight the well-supported and poorly-supported transcript models for users. The method relies on the primary data that can support full-length transcript structure and data are provided by UCSC. The following categories are assigned to each of the evaluated annotations. tsl1 - all splice junctions of the transcript are supported by at least one non-suspect mRNA. tsl2 - the best supporting mRNA is flagged as suspect or the support is from multiple ESTs. tsl3 - the only support is from a single EST. tsl4 - the best supporting EST is flagged as suspect. tsl5 - no single transcript supports the model structure. tslNA - the transcript was not analyzed for one of the following reasons: pseudogene annotation, including transcribed pseudogenes.Human leukocyte antigen (HLA) transcript. Immunoglobin gene transcript. T-cell receptor transcript. Single-exon transcript (will be included in a future version) 429 protein_coverage Protein Coverage Protein coverage for this gene derived from geneTree in compara 430 consensus_coverage Consensus Coverage Consensus coverage for this gene derived from geneTree in compara 431 has_start_codon Contains start codon Translation attribute 437 lncRNACount lncRNA_Count Number of lncRNAs 438 ncRNACount ncRNA_Count Number of ncRNAs 439 UnclassPTCount UnclassPT_Count Number of Unclassified Processed Transcripts 444 noncoding_cnt_m Misc non coding genes Number of unclassified (miscellaneous) non coding genes 445 noncoding_rcnt_m Readthrough misc non coding genes Number of readthrough unclassified (miscellaneous) non coding genes 446 noncoding_racnt_m Readthrough misc non coding genes Number of readthrough unclassified (miscellaneous) non coding genes on alternate sequences 447 noncoding_acnt_l Long non coding genes Number of long non coding genes on alternate sequences 448 noncoding_racnt Readthrough non coding genes Number of readthrough non coding genes on alternate sequences 449 noncoding_rcnt Readthrough non coding genes Number of readthrough non coding genes 450 rseq_mrna_match RefSeq model genomic seq to mRNA match This is a transcript attribute that signifies an exact match between the underlying genomic sequence of the RefSeq transcript with the corresponding RefSeq mRNA sequence the model was built from (based on a match between the transcript stable id and an accession in the RefSeq mRNA file). An exact match occurs when the underlying genomic sequence of the model can be perfectly aligned to the mRNA sequence post polyA clipping. 451 rseq_mrna_nonmatch RefSeq model genomic seq to mRNA non-match This is a transcript attribute that signifies a non-match between the underlying genomic sequence of the RefSeq transcript with the corresponding RefSeq mRNA sequence the model was built from. A non-match is deemed to have occurred if the underlying genomic sequence does not have a perfect alignment to the mRNA sequence post polyA clipping. It can also signify that no comparison was possible as the model stable id may not have had a corresponding entry in the RefSeq mRNA file (sometimes happens when accessions are retired or changed). When a non-match occurs one or several of the following transcript attributes will also be present to provide more detail on the nature of the non-match: rseq_5p_mismatch, rseq_cds_mismatch, rseq_3p_mismatch, rseq_nctran_mismatch, rseq_no_comparison 452 rseq_5p_mismatch RefSeq model genomic seq (5' UTR) to mRNA mismatch This is a transcript attribute that signifies a mismatch between the underlying genomic sequence of the RefSeq transcript with the corresponding RefSeq mRNA sequence the model was built from. Specifically, there is a mismatch in the 5' UTR of the RefSeq model. Information about the mismatch can be found in the value field of the transcript attribute. 453 rseq_cds_mismatch RefSeq model genomic seq (CDS) to mRNA mismatch This is a transcript attribute that signifies a mismatch between the underlying genomic sequence of the RefSeq transcript with the corresponding RefSeq mRNA sequence the model was built from. Specifically, there is a mismatch in the CDS of the RefSeq model. Information about the mismatch can be found in the value field of the transcript attribute. 454 rseq_3p_mismatch RefSeq model genomic seq (3' UTR) to mRNA mismatch This is a transcript attribute that signifies a mismatch between the underlying genomic sequence of the RefSeq transcript with the corresponding RefSeq mRNA sequence the model was built from. Specifically, there is a mismatch in the 3' UTR of the RefSeq model. Information about the mismatch can be found in the value field of the transcript attribute. 455 rseq_nctran_mismatch RefSeq model genomic seq (non-coding) to mRNA mismatch This is a transcript attribute that signifies a mismatch between the underlying genomic sequence of the RefSeq transcript with the corresponding RefSeq mRNA sequence the model was built from. This is a comparison between the entire underlying genomic sequence of the RefSeq model to the mRNA in the case of RefSeq models that are non-coding. Information about the mismatch can be found in the value field of the transcript attribute. 456 rseq_no_comparison RefSeq model no comparison made to mRNA This is a transcript attribute that signifies that no alignment was carried out between the underlying genomic sequence of RefSeq model and a corresponding RefSeq mRNA. The reason for this is generally that no corresponding, unversioned accession was found in the RefSeq mRNA file for the transcript stable id. This sometimes happens when accessions are retired or replaced. A second possibility is that the sequences were too long and problematic to align (though this is rare). The value field gives more information about the reason no comparison was possible. 457 rseq_ens_match_wt RefSeq model to overlapping Ensembl model whole transcript match This is a transcript attribute that signifies that for the RefSeq transcript there is an overlapping Ensembl model that is identical across the whole transcript. A whole transcript match is defined as follows: 1) In the case that both models are coding, the transcript, CDS and peptide sequences are all identical and the genomic coordinates of every exon match. 2) In the case that both transcripts are non-coding the transcript sequences and the genomic coordinates of every exon are identical. No comparison is made between a coding and a non-coding transcript. Useful related attributes are: rseq_ens_match_cds and rseq_ens_no_match. 458 rseq_ens_match_cds RefSeq model to overlapping Ensembl model CDS match This is a transcript attribute that signifies that for the RefSeq transcript there is an overlapping Ensembl model that is identical across the CDS region only. A CDS match is defined as follows: the CDS and peptide sequences are identical and the genomic coordinates of every translatable exon match. Useful related attributes are: rseq_ens_match_wt and rseq_ens_no_match. 459 rseq_ens_no_match RefSeq model to overlapping Ensembl model no match This is a transcript attribute that signifies that for the RefSeq transcript there is no overlapping Ensembl model that is identical across either the whole transcript or the CDS. This is caused by differences between the transcript, CDS or peptide sequences or between the exon genomic coordinates. Useful related attributes are: rseq_ens_match_wt and rseq_ens_match_cds. 468 ccds_transcript CCDS transcript This attribute signifies that a transcript has a matching CCDS transcript (the accession of which will be in the value column of the transcript_attrib entry). A match occurs when the genomic coordinates of all coding exons of the transcript are identical to the genomic coordinate of all coding exons in the overlapping CCDS model. 469 SO_accession SO accession Sequence Ontology accession 470 SO_term SO term Sequence Ontology term 471 display_term display term Ensembl display term 472 NCBI_term NCBI term NCBI term 473 feature_SO_term feature SO term Sequence Ontology term for the associated feature 474 rank rank Relative severity of this variation consequence 475 polyphen_prediction polyphen prediction PolyPhen-2 prediction 476 sift_prediction sift prediction SIFT prediction 477 short_name Short name A shorter name for an instance, e.g. a VariationSet 478 dbsnp_clin_sig dbSNP/ClinVar clinical significance The clinical significance of a variant as reported by ClinVar and dbSNP 479 dgva_clin_sig DGVa clinical significance The clinical significance of a structural variant as reported by DGVa 480 clinvar_clin_sig ClinVar clinical significance The clinical significance of a variant as reported by ClinVar 481 prot_func_analysis Protein function analysis The program used to make protein function predictions 482 associated_gene Associated gene ID of gene(s) linked by phenotype association 483 risk_allele Risk allele Risk allele in phenotype association 484 p_value P-value P-value denoting significance of an observed phenotype annotation 485 variation_names Variation names Variant ID(s) linked with a phenotype association 486 sample_id Sample ID Sample ID for source of phenotype association 487 strain_id Strain ID Strain ID for source of phenotype association 488 lod_score LOD score Log Of Odds score 489 variance Variance Variance statistic 490 inheritance_type Inheritance type Inheritance type of a trait 491 external_id External ID External identifier for an entity 492 odds_ratio Odds ratio Odds ratio used to denote significance of an observed phenotype annotation 493 beta_coef Beta coefficient Beta coefficient (or standardized coefficient) used to denote significance of an observed phenotype annotation 494 allele_symbol Allele symbol Allele symbol linked with phenotype association 495 allele_accession_id Allele accession ID Allele accession ID linked with phenotype association 496 marker_accession_id Marker accession ID Marker ID linked with phenotype association 497 evidence Variant evidence status Evidence status for a variant 498 review_status ClinVar review_status ClinVar review_status for assertation 499 based_on Evidence type used for protein impact prediction Evidence type used for a PolyPhen protein impact prediction 500 conservation_score Sift conservation score Median conservation va in an alignment used to make a Sift prediction 501 sequence_number Number of sequences in alignment Number of protein sequences in the alignment use to make a protein impact prediction 502 otter_truncated Otter truncated feature This feature extends beyond the slice, but has been trimmed. (For use in otter client-server communications.) 503 trans_spliced Trans-spliced transcript A single RNA transcript derived from multiple precursor mRNAs. 505 genebuild_msu7_tes TE-related Gene (MSU) Number of TE-related genes predicted by MSU through a process of automatic and manual curation 506 ibsc_low_confidence PGSB low-confidence Number of low-confidence genes annotated by the International Barley Sequencing Consortium 507 pubmed_id PubMed ID PubMed identifier