Table 3

Computer simulations of the effects of haplotype polymorphism on contig assembly using FPC.

% different fingerprint bands

% average sequence divergence

Consensus band units for entire region

Map coverage of the region

Number of contigs

% Questionable clones


0

0

1,172.5 ± 39.9

1.0 ± 0.0

1.1 ± 0.3

0.0 ± 0.0


25

2.5

1,252.4 ± 89.0

1.1 ± 0.1

1.2 ± 0.4

6.0 ± 4.9


42*

4.2

1,681.6 ± 129.4

1.4 ± 0.1

2.2 ± 1.0

18.8 ± 8.5


50

5.0

1,717.7 ± 206.5

1.4 ± 0.2

2.2 ± 0.9

24.7 ± 9.2


For each level of sequence divergence average and standard deviation values were computed for each of the parameters out of ten replicates. Coverage values are the ratio between the CB map length of the simulated contig and the CB map length of the original region (1,192 CB units).

* The average of 42% difference in fingerprint bands results from two areas without differences (containing 100 bands each, simulating small regions of identity by descent) and 50% difference in the rest of the region. In the other two cases differences were randomly distributed across the region.

Scalabrin et al. BMC Genomics 2010 11:204   doi:10.1186/1471-2164-11-204

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