(a) Real mosaic SNVs detected by different tools from three individuals (1465, 4638, 4643) with 250× WGS data, validated by multiple single cells as well as targeted sequencing. MosaicForecast detected more mosaic SNVs with lower allele fractions (AF≤0.05) than GATK HaplotypeCallers and MosaicHunter. (b) Of the candidate mosaics called by MosaicForecast, PCR-based samples have a lot more G>T mutations, which are known to be correlated with oxidative DNA damage, especially sites in haploid chromosomes (chrX/Y in male). Haploid chromosomes have 50% lower amount of DNA for library preparation and sequencing, which is likely to be correlated with the bias. (c) Of the IonTorrent validated mosaics detected by MosaicForecast, MosaicHunter or GATK HaplotypeCallers were only able to detect <65%, and a large fraction of low-allele fraction mosaics (AF≤0.05) were missed by these tools.