Table 3.

The number of TP (true positive), and FP (false positive) in the re-aligned reads from single-end simulated datasets.

	50-bp			75-bp			100-bp
	#RA	#TP	#FP	#RA	#TP	#FP	#RA	#TP	#FP
RAUR(BWA)	312,949	284,796	28,153	658,289	629,733	28,556	2,222,453	2,197,995	24,458
RAUR(Bowtie2)	632,552	519,586	112,966	388,654	293,101	95,553	593,629	532,641	60,988

#RA is the number of confidently re-aligned reads with mapping quality not less than 10, #TP is the number of confidently and correctly re-aligned reads, and #FP is the number of confidently but incorrectly re-aligned reads.