<sequencingResult>

This element defines the results of a sequencing assay. It is used to report the results of sequencingAssays and pcrAssays.

PCR assay results
When reporting the results of a pcrAssay, the genotype of the sample at positions at which no variants are reported is considered to be the same as the reference sequence. If the entire amplicon could not be sequenced, the interrogatedRange element should be used to define the regions that were successfully sequenced so that the sample's genotype in the regions that could not be sequenced will be correctly marked as unknown.

Sequencing assay results
When reporting the results of a sequencingAssay, the genotype of the sample at positions at which no variants are reported is dependent on the value of the assay's referenceSequenceIsDefault subelement. If referenceSequenceIsDefault is true, then the genotype of the sample at positions at which no variants are reported is calculated in the same way as those of a pcrAssay as described above. Otherwise, the genotype at any position other than those reported are considered to be unknown.

This element must be defined for all samples on which a sequencing assay was performed on even if no results or no variants are found so that it is possible to distinguish between samples that have no variants and samples for which no results could be obtained.

Examples:

To report the result of a sequencing assay that failed:

<sequencingResult>
  <assayXref resource="local">SEQUENCING_ASSAY_1</assayXref>
  <sequencedBothStrands>true</sequencedBothStrands>
  <noResult />
</sequencingResult>

To report the result of a PCR assay that discovered no variants:

<sequencingResult>
  <assayXref resource="local">PCR_ASSAY_1</assayXref>
  <sequencedBothStrands>true</sequencedBothStrands>
</sequencingResult>

To report the result of a PCR assay that discovered variants:

<sequencingResult>
  <assayXref resource="local">PCR_ASSAY_1</assayXref>
  <sequencedBothStrands>true</sequencedBothStrands>
  <variant>
    ...
  </variant>
  <variant>
    ...
  </variant>
</sequencingResult>

Attributes

pharmgkbId	A unique identifier assigned by the PharmGKB (the PharmGKB Accession Id). This attribute is used to refer to data that is already in the PharmGKB and is only supplied when editing or adding to such data. See the FAQ for details.
localId	A unique identifier for this element assigned by the submitter. The only rule it must follow is that no two XML elements can be assigned the same localId within a single XML document. See the FAQ for details.

note	A note.
submitter	This element's submitter.
assayXref	A cross-reference to the sequencing assay that produced this result, which must be defined under the parent experiment element.
interrogatedRange	The range of confidently assayed nucleotides. If none is specified, it is assumed that the entire amplicon was read accurately. The only situation in which multiple interrogatedRanges must be specified is in the rare case where the assay could not sequence through the entire amplicon. For example, if there is a series of repeats in the middle of the amplicon that cannot be sequenced, two interrogated ranges can be defined to indicate the bases on either side of the series of repeats were sequenced.
sequencedBothStrands	Flags whether both strands were sequenced: true false This element is optional and defaults to false if the noResult subelement is present. This element maps to dbSNP's SEQ_BOTH_STRANDS tag.
noResult	Flags that the assay produced no result.
- or -
variant	A variant found by the assay.

Validation Rules

Content validation performed on this element:

• The assayXref must cross-reference a sequencing assay.
• The assayXref must cross-reference an assay that is defined under the same experiment as the one this result is under.
• The start and stop positions of all interrogatedRanges must lie on both the reference sequence and the assay's amplicon (if the assay performed was a PCR assay) or analyzedRegion (if the assay performed was a sequencing assay).

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