Table 1.

Raw resequencing results for F. tularensis LVS query against F. tularensis LVS reference

Expt. No.	Array	Bases/array	Bases called	Call cate (%)	SNPs	% SNPs of called bases	True–positive SNPs (expected/detected)
007	A	301 470	300 490	99.675	49	0.016	0/0
	B	302 018	297 231	98.415	23	0.008	0/0
	C	301 394	296 530	98.386	27	0.009	0/0
	D	296 905	291 127	98.054	33	0.011	0/0
	E	290 100	282 102	97.243	18	0.006	1/1
	F	234 779	227 722	96.994	17	0.007	2/2
	Total	1 726 666	1 695 202	98.178	167	0.010	3/3
013	A	301 470	300 267	99.601	54	0.018	0/0
	B	302 018	296 718	98.245	25	0.008	0/0
	C	301 394	296 372	98.334	29	0.010	0/0
	D	296 905	290 472	97.833	32	0.011	0/0
	E	290 100	284 220	97.973	20	0.007	1/1
	F	234 779	229 583	97.787	17	0.007	2/2
	Total	1 726 666	1 697 632	98.318	177	0.010	3/3

The results shown are for the LVS sample, using the Affymetrix-recommended batch analysis parameters, including a quality score threshold of 12 and a call rate cutoff of 0.5. Those portions of chip F that represent the SCHU S4 reference and the plasmids were excluded from this analysis. Therefore, this represents the performance of the system under ideal circumstances: the chips are challenged with a sample that is essentially identical to the chip reference.