(a) Workflow for estimating the fraction of input haploid genome equivalents (hGEs) recovered post-capture but prior to sequencing using the mark and recapture method to estimate population size. (b) Comparison of observed total hGEs (left) and duplex hGEs (right) with estimations of their respective numbers in the post-capture library. The robustness of mark-recapture estimation was assessed over a wide range of sequencing depths by (i) using two lanes with ~2 fold difference in sequencing reads and (ii) down-sampling Lane 1 to 1/2 and 1/10 the original number of reads. Notably, when Lane 1 was down-sampled to approximately the same number of reads as Lane 2, the quantities of observed hGEs were comparable between the two lanes (see green square and red triangle), validating the results. Additional details are provided in Supplementary Note.