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Table 3
Predicted probe set deletions using various combinations of log₂ratio and proportion (probes flagged/total probes) or adjacent probes including TPR and FPR rates as described in Table 1 and Additional file 2.
Mutant line	Count of probe sets predicted to be deleted for different proportion (Prop) and log ratio (LR) combinations				Count of probe sets predicted to be deleted for different run length (RL)^aand log ratio (LR) combinations

	LR = -0.6 Prop = 0.5	LR = -0.8 Prop = 0.5	LR = -1.0 Prop = 0.3	LR = -1.0 Prop = 0.4	LR = -0.8 RL = 3	LR = -1 RL = 2	LR = -1 RL = 3

d1	168	45	50	39	63	66	39
D256	2	0	0	0	1	11	0
D2943	2	0	0	0	2	2	1
G282	359	89	139	69	333	560	109
G650	123	46	29	19	55	45	23
G6485	24	0	0	0	0	2	0
G6489	35	5	5	1	7	7	2
G6603	163	0	0	0	54	30	3
G6686	15	5	9	8	10	14	5
G6728	24	0	0	0	4	15	1
G7534	41	2	2	2	46	35	5
G9799	29	25	28	24	34	55	24
N1856	40	36	40	33	36	41	30
N2045	50	17	22	19	26	37	21
WT check	10	0	1	0	16	88	3

TPR	0.800	0.767	0.833	0.800	0.800	0.833	0.800
FPR1	0	0	0	0	0	0	0
FPR2	0.0002	< 0.0001	< 0.0001	< 0.0001	0.0008	0.004	0.0002

^aRun length is group of adjacent probes within a probe set that meet a defined log ratio cutoff.
Bruce et al. BMC Genomics 2009 10:129 doi:10.1186/1471-2164-10-129

Table 3