Homo- and heterozygous deletions in SJK genome detected by anomalously spaced read pairs. (A) Homozygous 2.3-kb genomic deletion; (B) heterozygous 5-kb genomic deletion. Pink and blue bars, large deletions detected by anomalously spaced read pairs; green bars, regularly spaced read pairs mapped by the ungapped alignment algorithm in MAQ; gray bars, regularly spaced read pairs mapped by Smith-Waterman gapped alignment algorithm in MAQ; and red bars, singletons (reads without mate pairs).