Table 2.

Raw resequencing data for F. tularensis LVS and F. tularensis SCHU S4 samples

Expt. No.	Array	Bases/array	Bases called	Call rate (%)	SNPs	% SNPs of called bases
Raw Data for F. tularensis LVS
007	A	301 470	298 283	98.943	30	0.010
	B	302 018	298 072	98.693	30	0.010
	C	301 394	297 350	98.658	35	0.012
	D	296 905	292 333	98.460	43	0.015
	E	290 100	283 408	97.693	21	0.007
	F	273 824	230 750	84.269	1087	0.471
	Total	1 765 711	1 700 196	96.290	1246	0.073
013	A	301 470	297 426	98.659	30	0.010
	B	302 018	297 614	98.542	28	0.009
	C	301 394	297 381	98.669	38	0.013
	D	296 905	291 534	98.191	45	0.015
	E	290 100	285 828	98.527	27	0.009
	F	273 824	234 169	85.518	1688	0.721
	Total	1 765 711	1 703 952	96.502	1856	0.109
Raw data for F. tularensis SCHU S4
008	A	301 470	288171	95.589	1331	0.462
	B	302 018	291499	96.517	1293	0.444
	C	301 394	291 988	96.879	1571	0.538
	D	296 905	282 940	95.296	1545	0.546
	E	290 100	280 992	96.860	1306	0.465
	F	273 824	258 411	94.371	1326	0.513
	Total	1 765 711	1 694 001	95.939	8372	0.494
014	A	301 470	292 313	96.963	1383	0.473
	B	302 018	290 452	96.170	1298	0.447
	C	301 394	290 080	96.246	1532	0.528
	D	296 905	282 768	95.239	1539	0.544
	E	290 100	280 557	96.710	1293	0.461
	F	273 824	256 803	93.784	1259	0.490
	Total	1 765 711	1 692 973	95.881	8304	0.490

For these results, a quality score threshold of 12 and a call rate cutoff of zero were used, as explained in the text. All base positions on the chip set were considered (LVS, SCHU S4 and plasmid reference sequences). This accounts for the much higher SNP count from chip F in the LVS experiments.