sequence-quality 

Defines the quality for a range within the consensus sequence block.

        Attribute:
        ---------  
        - start:         (required) Sequence start position for quality - inclusive
        - end:           (required) Sequence end position for quality - not inclusive
        - quality-score: (required) Value indicating the quality of the consensus sequence.

Element Information

Model

Attributes

QName Type Fixed Default Use Inheritable Annotation
quality-score quality required
sequence-end position-type required
sequence-start position-type required

Used By

Element consensus-sequence-block

Source 

<xs:element name="sequence-quality">
  <xs:annotation>
    <xs:documentation>Defines the quality for a range within the consensus sequence block. Attribute: --------- - start: (required) Sequence start position for quality - inclusive - end: (required) Sequence end position for quality - not inclusive - quality-score: (required) Value indicating the quality of the consensus sequence.</xs:documentation>
  </xs:annotation>
  <xs:complexType>
    <xs:attribute name="sequence-start" type="hmlns:position-type" use="required"/>
    <xs:attribute name="sequence-end" type="hmlns:position-type" use="required"/>
    <xs:attribute name="quality-score" type="hmlns:quality" use="required"/>
  </xs:complexType>
</xs:element>

Sample

< consensus-sequence-block xmlns = "http://schemas.nmdp.org/spec/hml/1.0" reference-sequence-id = "ref1" start = "29942124" end = "29944020" strand = "1" phase-set = "1" continuity = "true" expected-copy-number = "1" description = "HLA-A exon 1" >

< sequence>

TTTCTTGGAGCAGGTTAAACATGAGTGTCATTTCTTCAACGGGACGGAGCGGGTGCGGTTCCTGGACA GATACTTCTATCACCAAGAGGAGTACGTGCGCTTCGACAGCGACGTGGGGGAGTACCGGGCGGTGACG GAGCTGGGGCGGCCTAGCGCCGAGTACTGGAACAGCCAGAAGGACCTCCTGGAGCAGAGGCGGGCCGA GGTGGACACCTACTGCAGACACAACTACGGGGTTGTGGAGAGCTTCACA

</ sequence>

< variant reference-bases = "T" alternate-bases = "C" start = "29942937" end = "29943001" >

< variant-effect term = "missense_variant" />

</ variant>

< variant reference-bases = "CG" alternate-bases = "C" start = "29942999" end = "29943025" >

< variant-effect term = "frameshift_variant" />

</ variant>

< variant reference-bases = "A" alternate-bases = "AT" start = "29942760" end = "29942852" >

< variant-effect term = "stop_gained" />

</ variant>

< sequence-quality sequence-start = "29942937" sequence-end = "29943001" quality-score = "1.0" />

< sequence-quality sequence-start = "29942955" sequence-end = "29943020" quality-score = "1.0" />

</ consensus-sequence-block>