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The average recombination frequency in genes/cM was calculated by dividing the total number of genes (28,269) by the map length.
Dividing our genome size estimate (238 mb) by the map length yields an average estimated length of 160 kb/cM, which is slightly longer than the previous estimate of 141 kb/cM for D. magna and the 133 kb/cM for D. pulex.
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In the proximal region, the average RF for all marker pairs, weighted by the map lengths, was identical in the two sexes, but in the distal region it was nearly four times greater in females (3.6 1).
Assuming that the physical length of these genomic intervals is correctly predicted by the genome sequence, the map length divided by the segment size yields a recombination rate (cM/Mb) point estimate for each scaffold.
The EST-SSR marker ACMP00682, which mapped to the top portion of the A08 linkage group, increased the map length by 4.8 cM.
The map length estimated by the sum of recombination percentage between adjacent markers was 2750 cM and was slightly lower than the value obtained with the Kosambi distance as mapping function (2773 cM).
The map length covered by each LG varied from 71.57 cM (62 markers) in LG8 to 157.80 cM (162 markers) in LG4.
The observed genome length was obtained by summing up the map lengths of the 12 individual linkage groups.
Except for a few cases (marked by frames in Table S4), the map lengths for individual-set ordering and consensus ordering were identical or very similar.
The average resolution, calculated as the total physical size of the chromosome divided by the total map length, was 0.53 Mb cR-1 and a maximum of five-fold deviation from this value (0.1 and 1.8 Mb cR-1) along the chromosome was observed.
The female map with 202 markers covered an observed length of 1,814.5 cM with a mean distance between adjacent markers of 10.7 cM calculated as the arithmetic mean of the map distances between adjacent markers in each linkage group and not just simply by dividing the total map length by the number of markers.
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