Table 2.

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

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

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