Structural variations (SVs) in repetitive sequences could only be detected within a broad region due to imprecise breakpoints, leading to classification errors and inaccurate trait analysis. Through manual inspection at 4532 variant regions identified by integrating 14 detection pipelines between two tomato genomes, we generated an SV benchmark at base-pair resolution. Evaluation of all pipelines yielded F1-scores below 53.77% with this benchmark, underscoring the urgent need for advanced detection algorithms in plant genomics. Analyzing the alignment features of the repetitive sequences in each region, we summarized four patterns of SV breakpoints and revealed that deviations in breakpoint identification were primarily due to copy misalignment. According to the similarities among copies, we identified 1635 bona fide SVs with precise breakpoints, including substitutions (223), which should be taken as a fundamental SV type, alongside insertions (780), deletions (619), and inversions (13), all showing preferences for SV occurrence within AT-repeat regions of regulatory loci. This precise resolution of complex SVs will foster genome analysis and crop improvement.