Table 1.

The alignment rate and precision of each alignment method on single-end simulated data with different read length.

	50-bp		75-bp		100-bp
	Align.Rate(%)	Prec(%)	Align.Rate(%)	Prec(%)	Align.Rate(%)	Prec(%)
BWA	79.4737	99.7359	73.7762	99.7975	30.3573	99.7208
BWA(mem)	-	-	82.8545	99.8912	83.0971	99.8004
RAUR(BWA)	83.5165	99.3132	86.5413	99.1875	87.8022	99.1834
Bowtie2	74.8779	99.6313	77.8351	99.7501	71.4820	99.8918
Bowtie2(local)	-	-	85.206	95.8658	82.3958	95.5368
RAUR(Bowtie2)	83.0495	98.2984	85.3716	98.3442	86.8258	98.2009

There are 7,740,912 simulated single-end reads with length 50-bp, 5,156,962 with length 75-bp, and 3,868,843 with length 100-bp.