A consensus sequence contains a sequence of IUPAC nucleotides and novel variants. The nucleotides are specified in the DNA alphabet. The DNA alphabet consists of primary nucleotides (A, C, G, T). Wildcard IUPAC nucleotides (M, R, W, S, Y, K, V, H, D, B, X, N) may be used if they are acceptable in the context in which they appear. The default is to use all upper case letters. The full specification of the IUPAC codes may be found here: (http://nar.oxfordjournals.org/content/13/9/3021.short) Cornish-Bowden A. Nomenclature for incompletely specified bases in nucleic acid sequences: recommendations 1984. Nucleic Acids Res. 1985; 13:3021-3030. Children: -------- - sequence: (required, qty: 1) Nucleotide data for the consensus block. - variant: (optional, 0 or more) If region-match is false, variant is expected to refer to the novel-variants. - sequence-quality: (optional, qty: 0 or more) A score for a sub-sequence specified by start and end (includes 'start', excludes 'end') that indicates the quality of the read. Attributes: ---------- - reference-sequence-id: (required) Reference to a unique reference-sequence defined in this document under "consensus-sequence". IDREF must exactly match the ID for the reference-sequence. - start: (required) Start position of a targeted region on contig, 0-based or space-counted coordinate system, closed-open range - end: (required) End position of a targeted region on contig, 0-based or space-counted coordinate system, closed-open range - strand: (optional) String value (eg. one of "-1", "1", "-", "+"); defaults to "+" if unspecified - phasing-group: Phasing group identifier - DEPRECATED. Use "phase-set". - phase-set: Phase set identifier (string, optional) - continuity: (optional) True if this represents a continuous read, false if not continuous. - expected-copy-number: (optional) Integer for how many copies of the sequence block were expected (0 to n). - description: (optional) Text description of the targeted region, like "HLA-A exon 3" - xs:anyAttribute: Custom use attribute for additional sequence information. (optional) |
| QName | Type | Fixed | Default | Use | Inheritable | Annotation |
|---|---|---|---|---|---|---|
| continuity | xs:boolean | optional | ||||
| description | restriction of xs:string | optional | ||||
| end | position-type | optional | ||||
| expected-copy-number | restriction of xs:int | optional | ||||
| phase-set | xs:string | optional | ||||
| phasing-group | xs:string | optional | ||||
| reference-sequence-id | xs:IDREF | required | ||||
| start | position-type | optional | ||||
| strand | restriction of xs:string | optional | ||||
| Wildcard: ANY attribute from ANY namespace | ||||||
| Complex Type | consensus-sequence |
<xs:element name="consensus-sequence-block"> <xs:annotation> <xs:documentation>A consensus sequence contains a sequence of IUPAC nucleotides and novel variants. The nucleotides are specified in the DNA alphabet. The DNA alphabet consists of primary nucleotides (A, C, G, T). Wildcard IUPAC nucleotides (M, R, W, S, Y, K, V, H, D, B, X, N) may be used if they are acceptable in the context in which they appear. The default is to use all upper case letters. The full specification of the IUPAC codes may be found here: (http://nar.oxfordjournals.org/content/13/9/3021.short) Cornish-Bowden A. Nomenclature for incompletely specified bases in nucleic acid sequences: recommendations 1984. Nucleic Acids Res. 1985; 13:3021-3030. Children: -------- - sequence: (required, qty: 1) Nucleotide data for the consensus block. - variant: (optional, 0 or more) If region-match is false, variant is expected to refer to the novel-variants. - sequence-quality: (optional, qty: 0 or more) A score for a sub-sequence specified by start and end (includes 'start', excludes 'end') that indicates the quality of the read. Attributes: ---------- - reference-sequence-id: (required) Reference to a unique reference-sequence defined in this document under "consensus-sequence". IDREF must exactly match the ID for the reference-sequence. - start: (required) Start position of a targeted region on contig, 0-based or space-counted coordinate system, closed-open range - end: (required) End position of a targeted region on contig, 0-based or space-counted coordinate system, closed-open range - strand: (optional) String value (eg. one of "-1", "1", "-", "+"); defaults to "+" if unspecified - phasing-group: Phasing group identifier - DEPRECATED. Use "phase-set". - phase-set: Phase set identifier (string, optional) - continuity: (optional) True if this represents a continuous read, false if not continuous. - expected-copy-number: (optional) Integer for how many copies of the sequence block were expected (0 to n). - description: (optional) Text description of the targeted region, like "HLA-A exon 3" - xs:anyAttribute: Custom use attribute for additional sequence information. (optional)</xs:documentation> </xs:annotation> <xs:complexType> <xs:sequence> <xs:element ref="hmlns:sequence" minOccurs="1" maxOccurs="1"/> <xs:element ref="hmlns:variant" minOccurs="0" maxOccurs="unbounded"/> <xs:element ref="hmlns:sequence-quality" minOccurs="0" maxOccurs="unbounded"/> </xs:sequence> <xs:attribute name="reference-sequence-id" type="xs:IDREF" use="required"/> <xs:attribute name="start" type="hmlns:position-type" use="optional"/> <xs:attribute name="end" type="hmlns:position-type" use="optional"/> <xs:attribute name="strand" use="optional"> <xs:simpleType> <xs:restriction base="xs:string"> <xs:enumeration value="-1"/> <xs:enumeration value="1"/> <xs:enumeration value="+"/> <xs:enumeration value="-"/> </xs:restriction> </xs:simpleType> </xs:attribute> <xs:attribute name="phasing-group" type="xs:string" use="optional"/> <!-- DEPRECATED: Use phase-set --> <xs:attribute name="phase-set" type="xs:string" use="optional"/> <xs:attribute name="continuity" type="xs:boolean" use="optional"/> <xs:attribute name="expected-copy-number" use="optional"> <xs:simpleType> <xs:restriction base="xs:int"> <xs:minInclusive value="0"/> </xs:restriction> </xs:simpleType> </xs:attribute> <xs:attribute name="description" use="optional"> <xs:simpleType> <xs:restriction base="xs:string"> <xs:minLength value="1"/> </xs:restriction> </xs:simpleType> </xs:attribute> <!-- Custom use attribute for additional information (optional) --> <xs:anyAttribute/> </xs:complexType> </xs:element> |