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Table 4 The number of Hawaiian SNPs and the false-negative rate

From: Masking as an effective quality control method for next-generation sequencing data analysis

Aligners No quality control Trimming Masking
BWA 104,858 (6.4%) 105,355 (6.0%) 104,775 (6.5%)
BOWTIE2 104,422 (6.8%) 104,470 (6.8%) 104,297 (6.9%)