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Are you sure you have looked into the HiFiasm output files (fasta and GFA) in detail and excluded non-primary contigs, hap1, hap2 and other…
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You can use seqtk to find gaps in a fasta
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see also : https://www.biostars.org/p/9537698/ ; https://www.biostars.org/p/9464312/ ; https://www.biostars.org/p/417123/
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what's the gray section ? it's the read you want ? do you only want the reads that end at the splice event (single point location) ?
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