Implementation of two high through-put techniques in a novel application: detecting point mutations in large EMS mutated plant populations

Table 1 ProDH screen results

	M2 4x (a)	M2 8x (b)	M3 8x (c)
Total # lines screened (N)	8025	8025	6692
# of positive pools after Screen 1 (on pools) (P1)	87	33	23
# of positive individuals after Screen 2 (on individuals from positive pools) (P2)	47	32	27
# of confirmed mutations after sequencing (P3)	12	4	8
# detected as % of # of followed up after Screen 1 (D1)	13.80%	12.10%	34.80%
# of false negatives (no mutant detected while present) (F1)	1	9	No data
False negative rate (fraction) (F1-f)	0.25	0.75	No data
Mutation detection frequency (mutations per 1000 kb amplicon length) MD1	1.9	0.63	1.5
True mutation frequency (mutations per 1000 kb amplicon length) M1	2.53	2.53	No data

Explanations of variable names: in the description the general variable name is given (e.g. P1). To indicate the value in the table, indices a, b and c have been used to indicated the column. Calculation details: P1, P2, P3, F1 were direct results. D1 = P3/P1 (expressed as %), e.g. D1a = P3a/P1a = 12/87 = 13.8%. F1a-f = F1a/P1b (expressed as fraction = 1/4 = 0.25; F1b-f = F1b/P1a (expressed as fraction = 9/12 = 0.75. MD1 = P3/(N*amplicon length) = (12/(8025 * 788)) * 1,000,000 = 1.9 per 1,000 kb; M1a = MD1a/(1-F1a-f) = 1.9/(1-0.25) = 1.9/(0.75) = 4 * 1.9/3 = 2.53; M1b - MD1b/(1-F1b-f) = 0.64/(1-0.75) = 0.63/(0.25) = 4 * 0.63/1 = 2.53

ISSN: 1746-4811