Table 6.

Different Random Sets

Set	Ctgs	F−	F+	Qs	Order	Order/no Qsa
1	42 + 1	102 − 59	59	112 (13)	(2770, 3400, 9)	(186, 220, 0)
2	43 + 2	95 − 50	108	48 (12)	(2861, 3414, 1)	(395, 475, 0)
3	38 + 1	88 − 49	91	145 (14)	(3024, 3634, 25)	(414, 458, 1)
4	44 + 4	92 − 44	123	243 (16)	(2871, 3416, 10)	(391, 458, 1)
4b	27 + 0	35 − 9	236	8 (1)	(111, 16, 0)	(84, 11, 0)
4c	6 + 0	7 − 2	312	22 (1)	(508, 422, 1)	(4, 1, 0)

(Ctgs) contigs; (F−) false-negative; (F+) false-positive; (Qs) questionable. 

Each of the first four sets is a different random selection of 16,692 clones from the same pool, a 25× coverage with clone lengths of 130–190 kb, and one marker per 45 kb, and there is one chimeric contig. The error includes end fragments, 4% F+, 4% F, and the tolerance distribution of (16, 20, 18, 15, 12, 9, 6, 4). All the data sets were assembled with a 7 tolerance, 1e-10 cutoff with cutoff plus marker table (1 1e-08, 2, 1e-07, 3 1e-06). On the average, 17% of the clones are buried. The data sets assembled without markers resulted in 143, 155, 137, and 138 contigs, respectively. 

^aThe second order triplet is for the contigs with no Q clones. 

^bThe data set is the same as the previous one but without error. The set with error has 28 F+ clones with an average of 7 F+ overlaps per clone, whereas the set without error has 32 F+ clones with an average of 13 F+ overlaps per clone. 

^cThe data set is the same as the previous one that has no error but is assembled with a tolerance of 0 and a cutoff of 1e-12. The largest contig with no F+'s has 4738 clones and two out-of-order pairs.