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Fig. 4 | Genome Biology

Fig. 4

From: Meiotic crossovers are associated with open chromatin and enriched with Stowaway transposons in potato

Fig. 4

Genomic features associated with meiotic crossovers. a An example of the expected versus observed distributions of crossover counts for chromosome 1 of potato. b Frequencies of the two W4M6 haplotypes, blue and orange, overlaid with − log10 transformed P values from a chi-squared test for distorted segregation (black dots). The red dashed line across the plot represents the − log10 transformed significance threshold of P < 0.01. c Overlap analysis of crossovers with various genomic features (orange). Matched “cold regions” were also compared against different genomic features (blue), in addition to simulations of random regions (purple). Error bars represent the standard deviation of 10,000 simulations. If an interval overlapped more than one genomic feature, the interval was counted towards each overlapping feature. d Aggregated plot of crossover frequency relative to all potato genes. Genes were split into 50 windows and up- and downstream regions were split into 25-bp windows. Counts of crossovers were averaged across genes for each window. Orange, crossovers; blue, cold regions; gray, random regions. e Heatmap of gene ontology (GO) terms associated with crossover-overlapped, cold, and random genes. No terms were significant in either random or cold data sets, and thus the only GO terms shown are those that were significantly enriched for crossover-associated genes. P values are expressed as Benjamini–Hochberg corrected P values

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