Table 2.

Metrics considered in calling SNPs by each of the four algorithms

	SOAPsnp	Atlas-SNP2	SAMtools	GATK-UGT
Quality score	Recalibrated	Raw	Recalibrated	Recalibrated
Machine cycle	Yes	Yes	No	Yes
Allele type	Yes	No	No	Yes
Duplication level	Penalty in quality score	No	No	No
Swap-base	No	Yes	No	No
MNP events	No	Yes	No	No
NQS	No	Yes	No	No
Coverage variation	No	Yes	No	No
Base dependency	Yes	No	Yes	No
Strand independency	No	NO	Yes	No