Alignments
An alignment maps one of your sequencing reads against a reference genome and reports the matched region. This guide explains the alignment information shown in Genome Detail and Cancer Candidate Detail.
What is an alignment?
When your DNA is processed, each accepted read is compared against reference sequences. If a clear match is found, GENOTURK records the aligned range on the reference genome together with the confidence of the match and the supporting samples.
Alignments are produced automatically by the background analysis pipeline once processing completes.
Alignment ranges
Each alignment row reports the following:
- Chromosome - the chromosome of the reference genome
- Accession - the identifier of the reference sequence
- Position - the start and end coordinate of the aligned region
- Samples - which reads supported this alignment
Confidence
Every alignment has a confidence score from 0 to 100%, colour coded on the page:
90%+ high confidence70-90% medium confidencebelow 70% low confidence
Comments
You can discuss each alignment with your team by attaching comments. The comment system supports threaded replies, so conversations stay organised:
- Reply directly to any comment to build a thread
- Comments on an alignment are shown both on the Genome Detail page and on the aligned Cancer Candidate page
Where to find alignments
Open a genome to see all of its alignments in the Alignments section. The Cancer Candidate Detail page also lists the new and old alignments that produced the candidate, with the same per-alignment comments.