TABLE 2.

Summary of read mapping to sample-specific reference sequences

Sample ID	Bowtie2		BWA-SW		GSNAP		NovoAlign
	Mean depth	Reads aligning	Mean depth	Reads aligning	Mean depth	Reads aligning	Mean depth	Reads aligning
TD024	28.53×	3,709	31.90×	3,988	27.69×	3,426	27.79×	3,463
TD031	62.33×	7,658	67.23×	8,044	60.33×	7,172	60.50×	7,267
TD062	50.01×	6,617	59.61×	7,468	45.92×	5,658	46.64×	5,751
CBL20	5,502×	539,906	4,734×	412,557	6,451×	618,464	5,156×	432,538
ROD	1,924×	165,506	1,794×	152,105	2,146×	176,885	1,862×	155,696