The Lake Malawi cichlid SV landscape. (A) Heatmap showing length difference of alleles for each nonreference sample versus the A. calliptera backbone across 5000 random bubbles, shown as columns. A positive value (green) represents an insertion, and a negative value (brown) represents a deletion, with darker colors indicating larger SVs/indels. (B) Number of SV alleles by type. (C) Length deviations of nonreference alleles across different sample frequencies. Dashed line denotes 50 bp.