Small polymorphisms are a source of ancestral bias in structural variant breakpoint placement.

To examine whether sequencing error in phased assemblies affects SV locations, we compared breakpoints in 21 CLR genomes with 11 HiFi genomes and find a marginally significant enrichment for differences in insertions (4.40% vs. 4.29%, P = 0.025, Student's t -test) but no enrichment for deletions (1.75% vs. 1.77%, P = 0.52, Student's t -test), which we confirmed with permutation tests ( P = 0.012 insertions, P = 0.74 deletions, 100,000 permutations).

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A large increase in distance for deletions failed to reach significance (741.9 bp vs. 12.8 bp, P = 0.19, Welch's t -test, Cohen's d = 2.23) ( Fig. 2 C).

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