NGSengine

<Loci>

Inside the <Sample/> tag the <Loci> tag can be found. This tag contains a <Locus> tag, which in the case for our TARR export example is only present once. 

<Loci>

<Locus>

….

< Locus/>

< Loci/ >

The <Locus/> tag contains the result information for the locus and additional information that is required to reconstruct the entire analysis. First there is some locus information:

<Name>HLA-A</Name>

          <SampleName>E00921-multiplex-514-706</SampleName>

          <User Name="reviewer1" DateTime="2019-06-26T08:28:35.3513429Z" Level="First reviewer" />

          <Mappability AcceptedReads="10938" UsedReads="11002" TotalReads="11002" PercentageUsed="99.4" />

          <ReadLength Minimum="1" Maximum="151" Median="-1" Mean="134" />

          <ReadDepth Minimum="391" Maximum="1193" Median="964" Mean="-1" />

          <QuestionMarkPositions>2966</QuestionMarkPositions>

          <PhasingRegions>1</PhasingRegions>

          <NumberOfGenotypes>10</NumberOfGenotypes>

…..

<SampleName> : this is a repeat of the information available above, the sample the locus corresponds to.

<User>: this tag contains the name of the reviewer, the date the review was performed and their level.

<Mappability>: these are the mappability statistics for the locus. 

<ReadLength>: readlength statistics for the locus. 

<ReadDepth>: readdepth statistics for the locus. 

<QuestionMarkPositions>: the position of a nucleotide in the analysis which NGSengine was not able to resolve appropriately.

<PhasingRegions>: the number of different regions that were constructed during the phasing section of the analysis. 

<NumberOfGenotypes>: the number of alternative genotypes combinations that would fit the locus analysis result.