ALT Mapping-by-sequencing of the lcd1 mutant of rice. Several statistics have been evaluated across all chromosomes, and the results are presented as Manhattan plots. Each dot corresponds to an individual biallelic marker segregating in the population. Weighted moving averages (continuous lines) have been calculated for each statistic using a sliding window containing 3 adjacent markers. (a) SNP-index (allele frequency) in the D bulk. (b) SNP-index in the R bulk. (c) Δ(SNP-index), calculated as the difference between the SNP-index of the D bulk and the SNP-index of the R bulk. The shaded area is delimited by the moving averages of the lower and upper bounds of 95% confidence intervals, using the Bonferroni correction for multiple testing (with n = 151 tests). (d) Euclidean distance. (e) G-statistic, calculated as described by Magwene et al. (2011). (f) -log(p-value) of two-tailed Fisher’s exact tests. The dashed line marks the Bonferroni-corrected 5% significance threshold, calculated cons

ALT Mapping-by-sequencing in different species using MAPtools. The dots in each Manhattan plot correspond to the -log(p-value) of two-tailed Fisher’s exact tests performed for individual biallelic markers segregating in the mapping population, as determined using data from the R and D bulks. The lines correspond to the weighted moving averages calculated for a sliding window containing n adjacent markers. The dashed line marks the significance threshold calculated using the Bonferroni correction. (a) Mapping of the lcd1 mutation of rice; n = 3. (b) Mapping of a suppressor of the xantha mutant of rice; n = 2. (c) Mapping of an ascorbate-enriched mutant of tomato; n = 20. (d) Mapping of the green petiole-1 mutant of strawberry; n = 20. (e) Mapping of a white fruit mutant of strawberry; n = 100. (f) Mapping of a glossy mutant of Chinese cabbage; n = 100. (g) Mapping QTL for a rice blast disease; n = 100