Hi
I have studied genetic variation and something ambiguous terms confused me.
The below paragraphs contains the words that make me confused.
I search for those word on the Internet but I didn't get the potential meaning of them. Particular, flanking sequence is very hard concept for me. I often saw that term in fusion-concept. but I cannot fully understand.
Could you explain those two term easily to me?
Genetic variants that are mapped to segmental duplications are most likely sequence alignment errors and should be treated with extreme caution. Sometimes they manifest as SNPs with high fold coverage and probably high confidence score, but they may actually represent two non-polymorphic sites in the genomes that happen to have the same flanking sequence. To identify variants in these regions, use the command below.
Are you aware what segmetal duplications are? The are just like genomic repeats, except with much, much less copies per genome. And just as you can't be sure about variants in repeats, you can't be sure about variants in segmental duplications ("should be treated with extreme caution.").
"Flanking sequence" - sequences downstream/upstream from your site/variant.