Questions about 'NOTAL'

[ChuanzhengWei]

Hi, In the manual, you define 'NOTAL' as 'Un-aligned region', but when I use igv to visualize these regions, I found that it is not completely unaligned, but there are a large number of SNPs, and this situation is very common. Some screenshots are placed below for display. I want to know if this is normal? Or are there any ways to improve this situation? This is my code.

refgenome=HYZ.TCJ.fasta
qrygenome=353.chr.fasta
minimap2 -ax asm5 -t 32 --eqx ${refgenome} ${qrygenome}> HYZ_353.sam

syri -c HYZ_353.sam -r ${refgenome} -q ${qrygenome} -F S --prefix HYZ_353

Chr02 18345492 18384552 - - - - - NOTAL129 - NOTAL -

Chr09 43760031 44558535 - - - - - NOTAL954 - NOTAL -

Chr07 39308549 39722542 - - - - - NOTAL726 - NOTAL -

Please give me some suggestions, thanks!

[mnshgl0110]

By default, syri filters out small alignments or alignment with low alignment identity. As a result, these alignments would be filtered out resulting in NOTAL. Using -f makes syri use the full list of alignments (without any filtering).

[ChuanzhengWei]

Thank you!