Supplementary Figure 1: Construction of ssLPPs and cLPP. The protocol of producing singlestranded LPPs involved six principle steps 1,2, while double-stranded LPPs can be constructed in two steps directly from the double-stranded probe precursor by enzymatic end trimming and 5’ phosphorylation. cLPP construction is greatly simplified and easy to control. Time effort for constructing ssLPP is ~8 hrs and ~4 hrs for cLPP. Supplementary Figure 2: Reagent cost estimate for cLPP target capture. The expenses are the total reagent cost per sample for cLPP construction including oligonucleotide primers ($7.70 per probe), target capture reagents ($2), library preparation including multiplex PCR ($2), PCR quantification using Agilent Bioanalyzer ($2) and size selection using Sage Science Pippin Prep ($3) assuming four barcoded sample libraries per MiSeq run. The cost estimate does not include technician labor cost, machine purchase and operating costs, computation and analysis costs. The total cost for target capture and library preparation (“sequencing-ready”) are increasingly economical with <$1 per gene and sample when studying 10 or more genes in at least 1,000 samples, or 40 or more genes in at least 100 samples. Supplementary Figure 3: Read 1 and read 2 base qualities (Q scores) for 175/150 P
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