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The average physical length between the recombination bin markers was 137.68 kb, and the average annotated gene loci among the markers ranged from 15.34 for Chr04 to 22.09 for Chr01 (Table 2).
This technique enables us to measure length based on not only wavelength (e.g., [6 9]) but also the adjacent pulse repetition interval length (APRIL) (e.g., [10 20]), where APRIL denotes the physical length between two adjacent pulses.
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In spite of a nearly six-fold increase in genome coverage compared to a previous study in rice (0.31/0.05), some regions in Syn10 still exhibited longer physical lengths between bin markers, especially in the regions near the centromeres of chromosomes 1, 4, 6, 7, 9, 10, with ten larger bins that ranged from 11.2 Mb to 18.8 Mb.
However, the correlation between the number of markers and number of deletions (r = 0.97, P < 0.001) was much higher as compared to the correlations between physical length of the chromosome and number of deletions (r = 0.46, P = 0.14).
Tight correlation was not found between the physical length for each chromosome and the number of BES-SSR markers mapped for each linkage group in our study or the genetic length of the linkage group, meaning that the largest chromosomes did not have more SSRs or longer length as a genetic map.
Scatter plots between rMHH and physical length of block (Fig. S4) show their inverse correlation but suggest that the elongated block length alone is not adequate for efficient detection of rapid fixations caused by selective sweeps.
Considering scaffolds with physical length >500kb, we find no correlation between recombination rate and gene density.
The relationship between variance explained and physical length of the chromosome was expressed as the coefficient of determination (r) from the regression of variance explained on physical length.
The RI is obtained by taking the ratio between the optical pathlength and the physical length.
In A03, the correlation between the genetic length and the physical length appeared to be almost linear across the entire chromosome.
The discrepancy between the genome length and the physical length of all contigs might be generated by the potential redundancy of contigs, which could be detected and merged with more evidences.
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