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Table 2 Rare SNPs identified using the PELE-Seq, ORP, and standard DNA-Seq methods, at various read depths

From: High-specificity detection of rare alleles with Paired-End Low Error Sequencing (PELE-Seq)

Average read depth per barcode PELE positives PELE false positives ORP positives ORP false positives Standard positives Standard false positives
1000 13 0 6 0 6 2
5000 19 0 18 0 24 7
10000 42 0 37 0 36 12
15000 36 0 32 0 35 13
18000 40 0 35 0 41 42
  1. A control spike-in library containing 64 expected rare alleles present at 0.42 % frequency was sequenced with the PELE-Seq, ORP, and Standard DNA-Seq methods at various read depths. The read depths listed are for the overlapping paired-end (OPE) reads per barcode of the PELE-Seq libraries. The methods are compared using the same number of raw reads, such that the standard DNA-Seq bam files have a read depth that is 2.4× that of the PELE-Seq bam files (2400–43,000× per barcode), to account for the loss associated with merging overlapped reads to create ORPs