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Fig. 4 | BMC Genomics

Fig. 4

From: Accurate recombination estimation from pooled genotyping and sequencing: a case study on barley

Fig. 4

Assessment of recombination rate; A The recombination rate’s RMSE between HGM and the consensus map and nPGM and the consensus map regarding marker count in windows. B Average correlation coefficient of the nPGM and HGM recombination rate compared to the consensus map in 50 MB windows regarding variant genotyping depths. C Deviation of the cM/MB recombination rate, assessed by nPGM, from the consensus map. Value depends on the physical position (x-axis), the genotyping density (color), and the population (shape). The genome is divided by chromosomes (gray blocks on top) D Observed recombination fraction (square rooted for better visualization purpose; cM/MB) for nPGM (gold), Haldane genetic map (turquoise), and the consensus map (gray). 42.077 variants and a genotyping depth of 2000 were used to simulate the population. For this set, the recombination rate in 50 MB windows was calculated. E Estimated genetic map position (y-axis) in relation to the physical position (x-axis) for the same sample as illustrated in D. The genetic map position is the result of aggregating the single marker recombination rate along the chromosomes. Color scheme identical to subfigure D

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