question about colors of alignments

[mocherry]

Dear all,

I have a short question about what the colors in alignments mean.

there are the grey read alignments and the greenish ones. What is the difference.

Help would be greatly appreciated.

Thanks and best,
Matthias

[jrobinso]

Please see the user documentation. I don't know what options you have chosen so can't answer the question directly, but you should find the answer in one of the sections on alignments, start here: https://igv.org/doc/desktop/#UserGuide/tracks/alignments/viewing_alignments_basics/