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A Survey of Genomic Traces Reveals a Common Sequencing Error, RNA Editing, and DNA Editing

Figure 3

DNA editing in human HERVL-A1.

Trace 1735626615 aligns uniquely to chromosome 2 where the known retrotransposon HERVL-A1 is located (chr2: 100697697–100700125). A cluster of 15 G-to-A mismatches (worst mismatch phred 35; best mismatch phred 49) suggests that the trace originates from an edited version of the element. Support for the APOBEC source of the editing comes from the preferred GG-to-AG motif (11 out of the 15 cases) and GA-to-AA (remaining 4 cases) which is the dinucleotide context (in the same order) in an HIV hypermutated genome, and is the sequence motif of APOBEC3G and APOBEC3F [31].

Figure 3