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

BMC Bioinformatics

Table 2 Number of true-positives, false-positives, true-negatives, and false-negatives in SNP verification by Sanger sequencing for no quality control vs. trimming vs. masking

Aligners	No quality control				Trimming				Masking
Aligners	TP	FP	TN	FN	TP	FP	TN	FN	TP	FP	TN	FN
BWA	35	2 (2.3%)	84	2	35	2 (2.3%)	84	2	35	0 (0%)	86	2
BOWTIE2	35	6 (7.0%)	80	2	35	2 (2.3%)	84	2	35	0 (0%)	86	2

TP: True-Positive, FP: False-Positive, TN: True-Negative, FN: False-Negative. The value with parenthesis in the FP cell denotes the false-positive rate in percent.

ISSN: 1471-2105