A method for quantitating a rate of on-target genome editing in a genome of a cell, the method comprising: a) providing genomic nucleic acid from the cell, wherein the genomic nucleic acid has an exogenous donor polynucleotide, or a portion thereof, inserted into double stranded break points in the cell; b) fragmenting the genomic nucleic acid to generate a plurality of genomic nucleic acid fragments, wherein at least one of the genomic nucleic acid fragments contains the inserted donor polynucleotide or the portion thereof; c) generating a plurality of mixture partitions containing circular genomic nucleic acid fragments and a pair of amplification primers, wherein the circular genomic acid fragments are generated by circularizing the genomic nucleic acid fragments either prior to or after the partitions are generated, wherein the pair of amplification primers are complementary to opposite strands of the donor polynucleotide or portion thereof, and wherein the pair of amplification primers are oriented such that the 5' ends are proximal to each other and the 3' ends are distal to each other when hybridized to a genomic nucleic acid fragment containing the inserted donor polynucleotide or portion thereof before circularization; d) amplifying the genomic nucleic acid fragments with the pair of amplification primers to selectively generate amplicons in mixture partitions that contain one or more genomic fragments containing the inserted donor polynucleotide or portion thereof; e) detecting the amplicon in the mixture partitions and detecting a sequence proximal to an on-target genome-editing reagent cleavage site; and f) counting the number of mixture partitions containing amplicons and counting either or both of (i) the number of mixture partitions containing the amplicons and the sequence proximal to the on-target genome-editing reagent cleavage site and (ii) the number of mixture partitions containing the amplicons and not containing the sequence proximal to the on-target genome-editing reagent cleavage site, thereby quantitating a rate of on-target genome editing in the genome of the cell. a) providing genomic nucleic acid from the cell, wherein the genomic nucleic acid has an exogenous donor polynucleotide, or a portion thereof, inserted into double stranded break points in the cell; b) fragmenting the genomic nucleic acid to generate a plurality of genomic nucleic acid fragments, wherein at least one of the genomic nucleic acid fragments contains the inserted donor polynucleotide or the portion thereof; c) generating a plurality of mixture partitions containing circular genomic nucleic acid fragments and a pair of amplification primers, wherein the circular genomic acid fragments are generated by circularizing the genomic nucleic acid fragments either prior to or after the partitions are generated, wherein the pair of amplification primers are complementary to opposite strands of the donor polynucleotide or portion thereof, and wherein the pair of amplification primers are oriented such that the 5' ends are proximal to each other and the 3' ends are distal to each other when hybridized to a genomic nucleic acid fragment containing the inserted donor polynucleotide or portion thereof before circularization; d) amplifying the genomic nucleic acid fragments with the pair of amplification primers to selectively generate amplicons in mixture partitions that contain one or more genomic fragments containing the inserted donor polynucleotide or portion thereof; e) detecting the amplicon in the mixture partitions and detecting a sequence proximal to an on-target genome-editing reagent cleavage site; and f) counting the number of mixture partitions containing amplicons and counting either or both of (i) the number of mixture partitions containing the amplicons and the sequence proximal to the on-target genome-editing reagent cleavage site and (ii) the number of mixture partitions containing the amplicons and not containing the sequence proximal to the on-target genome-editing reagent cleavage site, thereby quantitating a rate of on-target genome editing in the genome of the cell.