Extended Data Fig. 5: Gene and repetitive element distribution along chromosomes for Smic1.1N.

a, Relative abundance of genes (blue), LINE repeats (red), and mapped RNA–Seq reads (gray) for chromosomes 4, 26, and 59. b, Gene number along regions 2.5 Mb from telomeric ends, averaged for chromosomes of sizes of at least 5 Mb and measured in 100 kb windows. Gene number is observed to decrease as distance to telomeres increases. c, Directionality of genes in the genome. A similar number of genes is found in both strands. d, Frequencies of changes in gene orientation. Gene orientation changes defined as the occurrences of neighboring genes located in opposite strands and measured in sliding windows of 10 genes. Observed (blue) and assuming an equal and independent probability of gene orientation (red). e, Distribution of genes in blocks of co-oriented genes. f, Cumulative distribution of genes in blocks of co-oriented genes. 50% of the genes are found in blocks of 9 or more co-oriented genes (red). g, LINEs number along regions 2.5 Mb from telomeric ends, averaged for chromosomes of sizes of at least 5 Mb and measured in 100 kb windows. LINEs number is observed to increase as distance to telomeres increases. h, Correlations between Gene number, GC content, RNA–Seq data, and Repeat types: LINE, DNA transposons, Simple, and Unclassified. Correlation coefficients are displayed as a color and size gradient between positive (blue) and negative (red) values. Correlations were done at 100 kb windows.