High-throughput marker discovery in melon using a self-designed oligo microarray

BMC Genomics

Table 1 Sequence validation of putative SFPs

SFP per UniGene	No. of genes	FP	TP	PPV*	Proportion of genes by SFP on array	Proportion of genes by SFP number in sequence validation
1	118	21	97	0.82	0.68	0.55
2	62	17	60	0.78	0.19	0.29
3	21	9	20	0.69	0.07	0.10
>3	12	8	13	0.62	0.06	0.06
Total	213	55	190	*0.79	1	1

Summary of bioinformatics analysis of 245 SFPs sequenced from the two different DNA pools of PI and 'Dulce'. The sequence data were compared to the database data. TP-True positive. FP-False positive. PPV-Positive predictive value.
*Total PPV was recalculated by taking into account the actual representation of the different SFPs per UniGene group in the population. PPV = TP/[TP+FP] for each number of SFPs per gene category. The calculations were performed to adjust the validated SFP results with the proportions discovered by bioinformatics analysis.

ISSN: 1471-2164