This simulation compares different coverages and error. It also compares HICF and agarose. The results show that HICF is better than agarose even with error. The results also show the benefit of reducing your error.

Type   Set   Cutoff	Coverage	Error	#Ctgs	Score	#Qs (#ctgs w/Qs)
HICF     1   1e-40
	10x	6%	24	0.892	0(0)
	10x	12.5%	46	0.802	39(11)
	20x	6%	2	0.874	0(0)
	20x	12.5%	8	0.710	328(7)
HICF     2    1e-50
	10x	6%	43	0.886	0
	10x	12.5%	79	0.797	13(9)
	20x	6%	9	0.874	1(1)
	20x	12.5%	17	0.724	106(10)
Agarose  2  1e-12
	10x	6%	163	0.959	0(0)
	10x	12.5%	211	0.921	8(8)
	20x	6%	67	0.928	0(0)
	20x	12.5%	147	0.872	55(33)

The same set of clones were used for a given set, except the 20x has an additional 10x clones. So the same clones are used for the HICF Set2 and Agarose Set2. Though the number of contigs for the 20x/12.5% error is less than for the 10x/6% error, the number of Qs is much higher, implying an increase in the problem within the map. These problems will lead to more time for manually editing the map and increased difficulty in selecting a MTP (see MTP simulation). The take home message from this simulation is that if you reduce your error, you can reduce your coverage. Moreover, the amount of overlap between clones (i.e. the endpoint coordiantes) will be closer to correct. Note, they can never be exact since there in not enough information in the bands, but the less error in the fingerprints, the less error in the overlap. Reduce your error!!

For HICF, we typically get 12.5% error per clone. For Agarose, it really depends on how good the band-calling is. We had exceptionally good band-callers for the maize agarose fingerprints and had an average <6% error per clone. To test your error, do the following: (1) refingerprint a plate of clones, (2) for the second plate, give the clones the same name but a different gel name, and add them to your fpc database (Update .cor)  (3) On the Project Window, select Search, then select "Find clones with mult gels > cutoff". Iit will list all the clones where the two gels do not match below the given cutoff. At the end of the output, the final statistics will be displayed as the following example: