Fig. 2: Example of AlphaGenome track predictions and detailed performance evaluations.

a, Observed and AlphaGenome-predicted genome tracks within a 1-Mb held-out region of human chr. 19 (0-based coordinates: 10587331–11635907) in the HepG2 cell line. The y-axis scales for each assay are defined in the Methods section. Strand-specific tracks are denoted as positive (+) or negative (−), whereas strand-agnostic tracks are shown without a strand symbol. Contact maps are pairwise interaction matrices; therefore, both x and y axes display genome coordinate positions. RNA-seq, ATAC-seq and DNase-seq track predictions are at 1-bp resolution; H3K27ac and CTCF ChIP-seq are at 128-bp resolution; and contact maps are at 2,048-bp resolution. b, Example predictions with splicing. Base-pair-resolution AlphaGenome predictions for a 50-kb region highlighting detailed splicing (donor/acceptor sites, splice site usage and splice junctions) and RNA-seq predictions around the LDLR gene. c, Track prediction performance evaluation across different modalities. Violin plots display the distribution of Pearson correlations between predicted and observed tracks evaluated on held-out test intervals. Each violin plot is grouped by modality and split by organism (human in red; mouse in blue). Filled circles with accompanying numerical values indicate the mean Pearson r per assay group and organism. Splice junction, RNA-seq, PRO-cap, CAGE and ChIP-seq tracks were log(1 + x) transformed, whereas the remainder were untransformed. d, Evaluation of RNA-seq gene log-expression prediction on held-out test intervals. The leftmost panel assesses the Pearson correlation between predicted and observed log-expression values across all genes within individual tracks. The middle and rightmost panels evaluate the prediction of tissue or cell-type specificity using quantile-normalized expression values (detailed in Methods); correlations are computed either across genes per track (middle) or across tracks per gene (right). e, Splice junction count prediction. Predicted versus observed splice junction read counts (log(1 + x) transformed; n = 1,344,738) and Pearson r between them in selected human tissues known for having distinct splicing patterns⁴⁹. Each hexagonal bin is coloured by the density of the data points in that bin, with warmer colours corresponding to higher density. The diagonal dotted line indicates perfect agreement (predicted = observed). More tissues are shown in Extended Data Fig. 2d. Obs., observed; Pred., predicted.