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All markers were assigned to linkage groups, and the maximum intermarker distance was 10.3 cM.
The maximum intermarker distance (13.2) is on chromosome 8, flanking a previously discovered inversion (Lowry and Willis 2010; Lowry et al. 2012).
We were able to construct a linkage map with an average intermarker distance of 1.8 cM, and a maximum intermarker distance of 10.3 cM.
Linkage distance and marker order were calculated by two-point analysis using mapmaker/exp 3.0b for Unix (http://www.nslij-genetics.org/soft/mapmaker), the Kosambi mapping function, a maximum intermarker distance of 36 cM, and a minimum LOD score of 4.0.
The parameters were set as follows: maximum intermarker distance for LD comparisons (maxdistance) to 1000, output to pairwise LD text table format (dprime), minimum minor allele frequency (minMAF) to 0.1, and minimum Hardy-Weinberg P-value (hwcutoff) to 0.001.
On the basis of a maximum intermarker distance of 36 cM, the presence of 13 singletons together with three more LGs than the number of N. furzeri chromosomes, we estimated that at least 576 cM (36 × 16) were not accounted for in this map.
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The average intermarker distance was 1.81 cM, and the maximum distance between adjacent markers was 10.3 cM.
The sex-average linkage map spans 1192 centiMorgans (cM) with an average intermarker distance of 11.4 cM and 1648 cM when the ends of the linkage groups and the autosomal unlinked markers are added.
We present two new AI-RIL populations of Arabidopsis thaliana genotyped with an average intermarker distance of 600 kb.
The map for this population has an average intermarker distance of 3.2 cM, so many of the intervals are quite narrow.
To calculate the total length of each chromosome, we added two times the average intermarker distance for that chromosome to account for chromosome ends [69].
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