Table 3. Summary of alignment and variation calling using SOAP3-dp and BWA with different parameters and datasets.

	Running time				SNP						Indels
Program/Type	(h)		Reads aligned	Properly Paired	w/o			w/			w/o	w/
	Aln.	GATK			Total	dbSNP	Homozygous	Total	dbSNP	Homozygous	Total	Total
BWA (Default, PE100)	99	32	93.30%	92.10%	3,996,730	3,926,590	1,620,269	3,922,841	3,876,262	1,609,899	370,231	383,347
BWA (-o 1 -e 50 -L, PE100)	3,363	36	96.74%	94.80%	4,040,813	3,955,380	1,609,729	3,946,627	3,896,737	1,601,049	385,216	417,832
SOAP3-dp (Default, PE100)	6	35	98.03%	96.98%	4,120,165	4,028,414	1,615,376	4,015,725	3,956,371	1,604,106	407,533	406,845
BWA (Default, PE150)	266	46	90.30%	89.17%	3,963,085	3,897,866	1,621,742	3,911,386	3,862,977	1,616,767	350,201	384,684
SOAP3-dp (Default, PE150)	14	92	97.66%	96.54%	4,139,625	4,055,314	1,612,213	4,067,552	4,002,750	1,612,351	409,925	422,427

PE100 and PE150 represent the 100 bp and 150 bp paired-end reads of YH sample. ‘w/’ and ‘w/o’ indicates whether the alignments were processed with and without GATK's local realignment respectively. ‘dbSNP’ is the number of detected SNPs found in dbSNP v135. The running times were rounded to hour.