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Table 6 Joint probabilities of SCOs on chromosomes from B. coprophila and P. hygida as an example

From: Chromosome-scale scaffolds of the fungus gnat genome reveal multi-Mb-scale chromosome-folding interactions, centromeric enrichments of retrotransposons, and candidate telomere sequences

 

P. hygida chromosomes

 

X

C

B

A

Marginal B. cop

B. coprophila chromosomes

X

0.253

0.002

0.002

0.003

0.261

II

0.000

0.166

0.001

0.003

0.170

III

0.002

0.001

0.241

0.004

0.248

IV

0.002

0.002

0.002

0.315

0.321

 

Marginal P. hyg

0.258

0.170

0.247

0.325

 
  1. This is an example, showcasing the two fungus gnats, of the input used for computing the raw entropy score before min–max normalization (see Methods), including the observed marginal probabilities of finding a single copy ortholog (SCO) on a given chromosome from a given species and the observed joint probabilities of finding a SCO on a given pair of chromosomes between the species. B. coprophila and P. hygida chromosomes are ordered by corresponding chromosomes as defined in Table 5, such that the highest joint probabilities are along the diagonal (left-to-right, top-to-bottom). The joint probabilities correspond to the proportions of SCOs that appear on (or the probabilities that any given SCO will appear on) each pair of inter-species chromosomes. Marginal probabilities (italicized) are obtained by summing the non-rounded values in the rows for B. coprophila and the columns for P. hygida (summed values rounded to 3 digits)*. The raw entropy score is computed on the observed joint probabilities. To get the minimum possible entropy the joint probabilities between these species could take given their SCO distributions, entropy is computed on each set of marginal probabilities separately, then averaged. To get the maximum entropy, entropy is computed on the set of joint probabilities expected at random, which are defined as the products of each inter-species pair of marginal probabilities. Min–max normalized entropy (MMNE) scores are then computed as: (observed entropy – minimum entropy)/(maximum entropy – minimum entropy). See the Methods for further details
  2. * Note that joint probabilities were rounded to 3 digits for simplifying this table, but not for computing the entropy. This results in a difference between the sum of rounded joint probabilities in a column or row and the reported marginal probability computed from summing non-rounded joint probabilities, then rounding the sum. The difference is only in the third position after the decimal
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BMC Genomics

ISSN: 1471-2164

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