Fig. 3

a The number of discovered REF– Alu elements in individual NA12877 depending on the depth of coverage. Various depth coverage levels were generated by randomly selecting a subset of reads from the FASTQ file. b The frequency of false-negative Alu elements found in simulations. FN1 denotes false negatives that could not be detected because they are inserted in nonunique regions of the genome. FN2 denotes false-negative findings that were undetectable because they are inserted within unsequenced regions of the genome (N-rich regions). Error bars indicate 95% confidence intervals from 20 replicates