Figure 2

Validation of 5’-SIMPLE using known full length L1 elements. (A) CLC Genomics Workbench window view of a representative fixed full length L1 element detected by SIMPLE. L1PA4 represents a known full length L1 element on chromosome 1. Small green lines at bottom are forward SIMPLE reads, reading into the 5’ end of the L1PA4 element. (B) Frequency distribution of the number of reference full length L1 elements detected by SIMPLE versus the number of independent SIMPLE hits detected for that element. On average, a reference full length L1 was assayed by nine independent SIMPLE reads, with the vast majority of reference full length L1 elements assayed by at least two independent reads. (C) CLC Genomics Workbench window view of a representative non-reference full length L1 element detected by SIMPLE. As in (A), green bars represent forward SIMPLE reads, however in this case, there is no reference full length L1 at the expected site in the genome. (D) Frequency distribution of the number of non-reference, known polymorphic full length L1 elements detected by SIMPLE versus the number of independent SIMPLE hits detected for that element. On average, a non-reference full length L1 was assayed by seven independent SIMPLE reads, with the vast majority of reference full length L1 elements assayed by at least two independent reads.