According to IGV visualization settings, IGV displays a specified number of randomly sampled alignments configured by the downsampling parameters instead of keeping all of them in memory: You can check your IGV alignment display settings using Preferences window, click

• View>Preferences>Alignments.

Check the link for further clarification: https://software.broadinstitute.org/software/igv/Preferences

Check under the Alignments tab.

Hope this help.