Table 5. Computer Simulation of SNP Accrual in the Setting of a Transition Bias Leads to Enhancement of Conservative Mutations.

Imposed Substitution Bias	Sequence	No. Runs	Muts/Run	Resulting Ncon∶Con	P-Value vs. Corresponding unbiased substitution
Unbiased	Artificial Sequence	10	50	2.95	----
	CFTR	10	50	1.93	----
	CFTR GC-RICH	10	10	1.75	----
CFTR Mutation Database Derived Transition Bias (See Table 2)	Artificial Sequence	10	50	2.8	2.46 E-15
	CFTR	10	50	2.04	----
	CFTR GC-RICH	10	10	1.56	2.89 E-19
Exon Derived Transition Bias (See Table 1)	Artificial Sequence	10	50	2.52	5.96 E-58
	CFTR	10	50	1.53	4.31 E-85
	CFTR GC-RICH	10	10	1.57	3.45 E-29
Intron Derived Transition Bias (See Table 1)	Artificial Sequence	10	50	2.25	8.40 E-32
	CFTR	10	50	1.99	----
	CFTR GC-RICH	10	10	1.17	6.49 E-18

SNPs were stochastically placed in 1) an artificial, assembled gene containing 1480 codons arranged randomly (i.e. random codons were used to generate a 4440 bp sequence), 2) the CFTR coding sequence (1480 codons), or 3) a GC-rich region of CFTR. The computer-generated positions to be mutated were selected randomly, and the choice of base replacement (e.g. with or without a particular transition bias) derived as above, according to the CFTR mutation database (Table 2), or rates observed for exonic or intronic SNPs (Table 1). The ratios for non-conservative (Ncon) to conservative (Con) SNPs are shown. Table 5 is the result of 10 simulation runs per sequence, indicating significant differences even after small numbers of SNP incorporation.