Figure 30: Variation in features along human chromosome 22.
From: Initial sequencing and comparative analysis of the mouse genome
a, Variation in tAR (red) and t4D (blue) in 5-Mb windows, overlapping by 4-Mb, along human chromosome 22. Only windows with at least 800 aligned fourfold degenerate sites and 800 aligned ancestral repeat sites are shown. The position of the window is plotted at the midpoint. Horizontal dotted lines indicate the genome-wide estimates of tAR and t4D. Confidence intervals were computed on the basis of the number of ancestral repeat and fourfold degenerate sites aligning in each window; points where the confidence interval does not overlap the genome-wide estimate indicate windows with significant differences in evolutionary rate. b, Similar to a, but with t*AR and t*4D, the normalized rates obtained taking residuals of tAR and t4D from the quadratic functions of (G+C) content shown in Fig. 31. c, Fraction of DNA (blue) that is not in lineage-specific repeats identified by RepeatMasker and does not align to mouse, NAanc, and the fraction of DNA (green) contained in human lineage-specific LTR repeats identified by RepeatMasker, along with t*AR (red), calculated in overlapping 5-Mb windows as in b. d, SNP density (blue) in each overlapping 5-Mb window (average number of SNPs per 10 kb) calculated using SNPs from random reads (The SNP Consortium website; data were collected in July 2002, http://snp.cshl.org). The average recombination rate (black) in each 5-Mb window, in cM per Mb, estimated from the deCode genetic map269 is shown, as well as t*AR (red), calculated in overlapping 5-Mb windows as in b.
