a, Distribution of sequence coverage of reference genome by 454-reads is random. Coverage, calculated in consecutive 5-kb windows, exhibited a Poisson distribution with a mean of 7.4-fold across all chromosomes except the X. Shoulder at 3.7X represents coverage of the X chromosome. b, Coverage is a key factor in detection of both alleles at heterozygous positions. For 31,709 markers heterozygous by microarray, but which exhibited only a single allele by DNA sequencing, the coverage was lower (red line, mean 5.7X) than the overall coverage for all SNPs (blue line, mean 7.8X). c, Size distribution of deletions. Deletions were readily observed in alignments of 454-reads to the reference genome. Note the peak in the size range at 300–350 bases owing to polymorphic Alu transposon insertion sites.