A 64 bit positive integer that is uniquely and forever assigned to this RefSNP object

The date the RefSNP was last updated or create_date if never updated

The id of the last dbSNP build in which this RefSNP was created or updated

Record of one RefSNP merging into another. Due to curatorial changes or a change in input alignment data sets, a RefSNP may change anchor such that it now coincides with second RefSNP. Only one 'live' RefSNP is allowed at a given anchor. To resolve this conflict, dbSNP chooses one RefSNP as 'live', and merges the data from the other RefSNP into it. dbSNP gives preference to the clinical RefSNP and if that is not sufficient it chooses the oldest RefSNP, the one with the lowest ID.

this field is for dbsnp1 merge only. Record of each time another RefSNP objects merged into this RefSNP because the RsAnchors of each were the same. If the recipient of a merge then merges into yet a third RefSNP, the list is flattened.

The RefSNP ID of the RefSNP object that was merged into the now live RefSNP

Set of PubMed IDs (PMIDs) for this RefSNP or its supporting submissions

For recording the movement of an observation that was in this RefSNP in the previous release, but no longer in the current

present_obs_movements

The record of movements between the previous and current release for observations mapped to this RefSNP by the Alignment Data Set used in this release

DbSnpIds of the supporting data where this particular observation is found (SubSnpId, ClinVarSnpId, etc.

[ subsnp, frequency, clinvar ] - The kind of supporting data. This list can expand.

A single contextual allele in SPDI notation. Contextual allele means that applying the Blossom Precision Correction Algorithm would leave the fields unchanged.

The RefSeq/Genbank Accession.Version for the reference sequence

The 0-based boundary position where the deletion starts. That is, position 0 starts the deletion immediately before the first nucleotide and position 1 starts the deletion between the first and second nucleotides.

The IUPAC sequence of nucleotides/amino-acids to delete from the reference. This can be empty, which is how a pure insertion is represented.

The IUPAC sequence of nucleotides/amino-acids to insert after perforing the deletion. Amino-acids use the single character encoding. All nucleotide codes including the ones for ambiguity are allowed.

The RSIDs of any other RefSnps that contain this observation in the current release. Can only be non-empty for the identity allele.

The characteristics of an observation that allow one to find it in the previous release. Should only be used when the observation described was present in the previous release.

A single contextual allele in SPDI notation. Contextual allele means that applying the Blossom Precision Correction Algorithm would leave the fields unchanged.

The ids of the RefSnps that contained a particular observation in the previous release. Only identity alleles can belong to more than one RefSnp, so this can only have more than one entry if the observation maps to the identity allele. The PreviousRelease struct should only be used when the observation was present in the previous release, so this field should not be empty.

The most recent release in which this observation started being associated with this RSID. If the historical membership for this observation is release1:rs1 release2:rs2 release3:rs1 release4:rs1, this will hold "release3". Note that because of a change to the dbSNP data model between builds 151 and 152, if the most recent release is prior to 152 then the observation may have been added to this RefSNP before the build listed. For example, if it says 140, it is possible that it was really added in 130. But it cannot have been added after build 140. If it says 152, then it was last added in build 152 and not before or after that.

Data specific to primary snapshots; cannot be present at the same time as merged_snapshot_data or nosnppos_snapshot_data

List of all placements, each containing a list of the alleles in the context of that reference region. Includes both nucleotide and protein placements. For all placements, the list of alleles is the same length and in the same order. They represent the alleles on the preferred top level placement (PTLP) in sorted order. So, on a given placement, the first allele is how the first allele on the PTLP appears upon mapping to the given placement. Similarly for the second allele, and so on.

For nucleotide placements, each allele in this placement is stored as a SPDI. Each SPDI contains a reference sequence identifier. For the set of alleles in SPDI syntax, they must all have the same reference sequence identifier, that matches the seq_id attribute. For protein placements, the allele is either in SPDI syntax, or gives a general description of a frameshift.

True if this placement is the preferred top level placement (PTLP) under the alignment data set which generated this RefSnp cluster

[ refseq_chromosome, refseq_contig, gpipe_chromosome, contig, refseq_genomic, refseq_mrna, refseq_mrna_pred, mrna, refseq_ncrna, refseq_ncrna_pred, ncrna, refseq_prot, genbank, embl, ddbj ]

True if this sequence is aligned reverse to the PTLP sequence. Thus, the PTLP sequence's is_aln_opposite_orientation attribute is always false.

True if this sequence's residues are different than the PTLP sequence at this locus. Thus, the PTLP sequence's is_mismatch attribute is always false

A RefSnp can describe 1 to N alleles. While for the PTLP, all alleles (in SPDI syntax) are the same type and length, non-PTLP Placements (i.e. all other Placements), the allele in SPDI syntax may have different types, lengths and start positions, and in some rare cases, may not even overlap. But they are all on this placement's Sequence.

deleted_sequence

inserted_sequence str

Each element holds the annotations associated with a particular variant. This list of annotation lists has the same order and length as the list of alleles in each placement. This order associates each allele with its corresponding annotation list. If an allele was not associated with any annotations, the corresponding annotation set will have only empty lists.

assembly_annotation