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Annotation Report Columns

Each annotation report (Known or Novel) contains the following columns with detailed information about the identified segments:

Column Explanation Example
SampleThe name of the sample.Sample_001
HaplotypeThe haplotype ID (maternal or paternal).1
RegionThe annotated region.IGHV
SegmentThe gene segment type.V
Start coordThe start coordinate on the annotated contig.12345
End coordThe end coordinate on the annotated contig.12789
StrandSegment orientation: + for 5' to 3', - for 3' to 5'.+
Library nameThe closest reference gene segment name associated with the identified segment.IGHV3-23*01
Target nameThe name assigned to the novel gene segment, based on the closest reference, with -like appended.IGHV3-23-like
Short nameThe gene name, according to IMGT nomenclature.IGHV3*01
Similar referencesOther reference gene segments sharing the same coordinates; the best match is chosen based on mutation count and name.IGHV3-33*02
Target sequenceThe nucleotide sequence of the novel gene segment.ATGGTGCAAGC...
Library sequenceThe nucleotide sequence of the closest reference segment.ATGGTGCAAAC...
MismatchesTotal mismatches between novel and reference segment.3
% Mismatches of total alignmentPercentage of mismatches over the full alignment length.1.5%
% identityPercentage of identical bases across the alignment.98.5%
BTOPBLAST traceback string showing exact mutations (substitutions, insertions, deletions).10A5G3T
SNPsNumber of single nucleotide polymorphisms (SNPs) detected.2
InsertionsNumber of insertions relative to the reference.1
DeletionsNumber of deletions relative to the reference.0
Mapping toolThe tool used for segment mapping.Minimap2
FunctionThe segment's classification: Functional, ORF, or Pseudogene.Functional
StatusIndicates if the segment is Known or Novel.Novel
MessageAnnotation notes, e.g., presence of stop codons.The STOP-CODON at the 3' end of the V-REGION can be deleted by rearrangement
PopulationPopulation group associated with the sample (if available).Dutch
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