A method for simultaneous quantification of homology directed repair and non-homologous end joining (NHEJ) genome editing products in a sample of cells, wherein said sample of cells comprises cells that have been contacted with a site-specific genome editing reagent configured to cleave or nick DNA in a target genomic region and an HDR template nucleic acid, the method comprising: a) forming a plurality of mixture partitions having an average volume, wherein the mixture partitions comprise: i) the target genomic region; ii) a DNA-dependent DNA polymerase; iii) a forward and a reverse oligonucleotide amplification primer, wherein the forward and reverse primers hybridize to opposite strands of, and flank, the target genomic region, and wherein the primers are configured to amplify the target genomic region in the presence of the polymerase; iv) a detectably labeled oligonucleotide reference probe, wherein the reference probe hybridizes to a wild-type target genomic region, a target genomic region containing an HDR mutation introduced by homology directed repair of DNA damage from the site specific genome editing reagent, and a target genomic region containing an NHEJ mutation introduced by NHEJ repair of DNA damage from the site specific genome editing reagent; v) a detectably labeled oligonucleotide HDR probe, wherein the HDR probe hybridizes to the target genomic region containing the HDR mutation; and vi) a detectably labeled oligonucleotide NHEJ drop-off probe, wherein the NHEJ drop-off probe hybridizes to the wild-type target genomic region, and wherein the NHEJ drop-off probe does not hybridize to the target genomic region containing the NHEJ mutation; b) amplifying the target genomic region in the plurality of mixture partitions; and c) determining a quantity of wild-type target genomic regions, a quantity of target genomic regions containing an HDR mutation, and a quantity of target genomic regions containing an NHEJ mutation by detecting hybridization of the labeled probes to the target genomic regions in the plurality of mixture partitions. a) forming a plurality of mixture partitions having an average volume, wherein the mixture partitions comprise: i) the target genomic region; ii) a DNA-dependent DNA polymerase; iii) a forward and a reverse oligonucleotide amplification primer, wherein the forward and reverse primers hybridize to opposite strands of, and flank, the target genomic region, and wherein the primers are configured to amplify the target genomic region in the presence of the polymerase; iv) a detectably labeled oligonucleotide reference probe, wherein the reference probe hybridizes to a wild-type target genomic region, a target genomic region containing an HDR mutation introduced by homology directed repair of DNA damage from the site specific genome editing reagent, and a target genomic region containing an NHEJ mutation introduced by NHEJ repair of DNA damage from the site specific genome editing reagent; v) a detectably labeled oligonucleotide HDR probe, wherein the HDR probe hybridizes to the target genomic region containing the HDR mutation; and vi) a detectably labeled oligonucleotide NHEJ drop-off probe, wherein the NHEJ drop-off probe hybridizes to the wild-type target genomic region, and wherein the NHEJ drop-off probe does not hybridize to the target genomic region containing the NHEJ mutation; i) the target genomic region; ii) a DNA-dependent DNA polymerase; iii) a forward and a reverse oligonucleotide amplification primer, wherein the forward and reverse primers hybridize to opposite strands of, and flank, the target genomic region, and wherein the primers are configured to amplify the target genomic region in the presence of the polymerase; iv) a detectably labeled oligonucleotide reference probe, wherein the reference probe hybridizes to a wild-type target genomic region, a target genomic region containing an HDR mutation introduced by homology directed repair of DNA damage from the site specific genome editing reagent, and a target genomic region containing an NHEJ mutation introduced by NHEJ repair of DNA damage from the site specific genome editing reagent; v) a detectably labeled oligonucleotide HDR probe, wherein the HDR probe hybridizes to the target genomic region containing the HDR mutation; and vi) a detectably labeled oligonucleotide NHEJ drop-off probe, wherein the NHEJ drop-off probe hybridizes to the wild-type target genomic region, and wherein the NHEJ drop-off probe does not hybridize to the target genomic region containing the NHEJ mutation; b) amplifying the target genomic region in the plurality of mixture partitions; and c) determining a quantity of wild-type target genomic regions, a quantity of target genomic regions containing an HDR mutation, and a quantity of target genomic regions containing an NHEJ mutation by detecting hybridization of the labeled probes to the target genomic regions in the plurality of mixture partitions.