Development and application of Potential SNP Scores (PSS) to filter out previously unannotated genome variations. (A) The distribution of mismatch ratios of all non-gSNPs mismatches and (B) known gSNPs in H9 cells. PSS was given to test the possibility of a mismatch for either genomic variation (PSS = −1, with mismatch ratio ≥ 95% or between 40% ~ 60% in grey shadow) or editing (PSS = +1, with mismatches ratios between 5% ~ 40% or between 60% ~ 95%) in H9 cells. (C) Application of PSS to filter out previously unannotated genome variations. Over 97% of known genomic SNPs were filtered out with PSS cutoff at 3 (red dashed line). (D) Validation of previously unannotated genome variations predicted with PSS cutoff. Three examples with Sanger sequencing results were shown with their genomic locations, types of conversion and PSSs (full validation list is available in Additional file 6).