Black Reads in IGV - Long Read Sequencing Analysis

[MeliBio]

Hi everyone,

I'm currently analyzing a long-read sequencing dataset and have encountered an issue in IGV. Some of my reads appear completely black (see attached image). I’m not sure what this means—could it indicate poor mapping quality, low confidence alignments, or something else?

Does anyone know what black-colored reads represent in IGV for long-read sequencing data? Any insights would be greatly appreciated!

Thanks in advance!

[jrobinso]

I don't know! It is not low mapping quality. Is it possible these reads have "YC" tags? If you right click one of the reads and select "copy read details" there might be some useful information. If you are able to post that here I will look.

[MeliBio]

I don't know! It is not low mapping quality. Is it possible these reads have "YC" tags? If you right click one of the reads and select "copy read details" there might be some useful information. If you are able to post that here I will look.

Thank you for your response! I looked further into it and found that these reads were actually soft-clipped. That explains why they appeared this way in IGV. I appreciate your help!