Question about white strands

[Nancy De Nève]

Hi,

I have questions about the low quality reads that appear coloured in white.

Does it mean that the sequencing is of bad quality? Or instead is it a problem of quality of alignment? For example for a region highly homologous?

Can I be confident for a mutation only found in that kind of white strands?

Thanks

[igv-help]

The hollow/white alignments have a mapping quality (MAPQ) value of zero in the BAM file. The exact interpretation depends on the mapping aligner so you should check the documentation of the aligner used. It commonly means that the read mapped here and equally well to another locus or loci.  If you want to see where else a read maps, right click on the read and select "BLAT read sequence". See https://igv.org/doc/desktop/#UserGuide/tools/blat/ for more information about using the BLAT tool.