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  • MeliBio
    Junior Member
    • Feb 2025
    • 4
    #1

    Black Reads in IGV - Long Read Sequencing Analysis

    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!
    ​
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