{% extends "sharedTemplates/base.html" %} {% block title %}Help annotation report{% endblock %} {% block body %}
Each annotation report (Known or Novel) contains the following columns with detailed information about the identified segments:
Column | Explanation | Example |
---|---|---|
Sample | The name of the sample. | Sample_001 |
Haplotype | The haplotype ID (maternal or paternal). | 1 |
Region | The annotated region. | IGHV |
Segment | The gene segment type. | V |
Start coord | The start coordinate on the annotated contig. | 12345 |
End coord | The end coordinate on the annotated contig. | 12789 |
Strand | Segment orientation: + for 5' to 3', - for 3' to 5'. | + |
Library name | The closest reference gene segment name associated with the identified segment. | IGHV3-23*01 |
Target name | The name assigned to the novel gene segment, based on the closest reference, with -like appended. | IGHV3-23-like |
Short name | The gene name, according to IMGT nomenclature. | IGHV3*01 |
Similar references | Other reference gene segments sharing the same coordinates; the best match is chosen based on mutation count and name. | IGHV3-33*02 |
Target sequence | The nucleotide sequence of the novel gene segment. | ATGGTGCAAGC... |
Library sequence | The nucleotide sequence of the closest reference segment. | ATGGTGCAAAC... |
Mismatches | Total mismatches between novel and reference segment. | 3 |
% Mismatches of total alignment | Percentage of mismatches over the full alignment length. | 1.5% |
% identity | Percentage of identical bases across the alignment. | 98.5% |
BTOP | BLAST traceback string showing exact mutations (substitutions, insertions, deletions). | 10A5G3T |
SNPs | Number of single nucleotide polymorphisms (SNPs) detected. | 2 |
Insertions | Number of insertions relative to the reference. | 1 |
Deletions | Number of deletions relative to the reference. | 0 |
Mapping tool | The tool used for segment mapping. | Minimap2 |
Function | The segment's classification: Functional, ORF, or Pseudogene. | Functional |
Status | Indicates if the segment is Known or Novel. | Novel |
Message | Annotation notes, e.g., presence of stop codons. | The STOP-CODON at the 3' end of the V-REGION can be deleted by rearrangement |
Population | Population group associated with the sample (if available). | Dutch |