This is application dependent. In Virtuoso, SPARQL and SQL share the same query execution engine, query optimizer, and cost model. If data is highly regular (i.e., a good fit for relational representation), and if queries typically access most of the row, then SQL will be more efficient. If queries are unpredictable, data is ragged, schema changes frequent, or inference is needed, then RDF will do relatively better.

The recent Berlin SPARQL Benchmark shows some figures comparing Virtuoso SQL and SPARQL and SPARQL in front of relational representation. However, the test workload is heavily biased in favor of relational. See also BSBM: MySQL vs Virtuoso.

With the TPC-H workload, relationally stored data, and SPARQL mapped to SQL, we find that with about half the queries there is no significant cost to SPARQL. With some queries there is additional overhead because the mapping does not produce a SQL query identical to that specified in the benchmark.