Fig. 6.

—SNP loci replicate early in zebrafish. (A) SNPs show a shift toward earlier replication at 28hpf when compared with genomic regions in general (excluding exonic and regulatory regions). This trend is consistent in all three independent data sets: NHGRI-1 (LaFave et al. 2014), SNPFisher (Butler et al. 2015), and Zebrafish Strain DB (Bowen et al. 2012). The replication timing profiles in 10-Mb regions surrounding all SNP sites were aggregated and averaged as described in figure 2A. In parallel, 20 sets of randomly permuted, chromosome-matched SNP locations were analyzed in a similar manner, also excluding exonic and regulatory regions. (B) SNPs replicate early in zebrafish and may possibly even shift to earlier replication along development. Same as (A) for all developmental time points, with the average permutation profile for each time point subtracted from the average SNP profile. (C) SNPs are enriched in late-to-early and constant replicating regions across all data sets, whereas being consistently depleted in early-to-late replicating regions. Replicating regions were classified according to HMM classification (Siefert et al. 2017). Chi-square P ≪ 10⁻³⁰⁰ for all categories.