Figure 4

True positive (TP) clones associated with a molecular marker in a contig map. Several scenarios were encountered when clones were screened by PCR[9]. (A) All TP clones associated with a marker shared a DNA fragment and had therefore a spanning or inclusion relations. (B) No common DNA fragment was observed in all TP clones associated with a marker but two or more contiguous clones had fingerprint overlaps. (C), (D), and (E) All TP clones associated with a marker were grouped to more than one contig (D), or a contig and singleton (C), or all TP clones were singletons (E). In scenarios C, D, and E, some of the TP clones were usually located at the end of one contig and the rest were located at the end of another contig, or were singletons. The cause of these scenarios was the high stringency used in contig assembly that resulted in two separated contigs or in a contig and a singleton.