A method for analysing nucleic acids in a sample, the nucleic acids containing a first target nucleic acid segment and a second target nucleic acid segment, the method comprising: (a)performing a pre-amplification to generate first template molecules from the first target nucleic acid segment and generate second template molecules from the second target nucleic acid segment, wherein each of the first template molecules comprises sequences generated from a first universal primer sequence, a second universal sequence, and a first identity sequence tag, and each of the second template molecules comprises sequences generated from the first universal primer sequence, the second universal sequence, and a second identity sequence tag; (b) dispersing the sample to a substrate in a flow cell for random distribution of the first template molecules and the second template molecules among respective reaction wells of the substrate, wherein the number of the first template molecules and the second template molecules in each of the reaction wells is less than 1 on average; (c) in situ performing nucleic acid amplification reaction to generate a plurality of first amplicons from the first template molecules and a plurality of second amplicons from the second template molecules, wherein the first amplicons and the second amplicons are fixed on respective inner surfaces within the respective reaction wells of the substrate in the flow cell; (d) in situ identifying the first identity sequence tag of the first template molecules of the first amplicons and the second identity tag of the second template molecules of the second amplicons on the respective inner surfaces within the respective reaction wells of the substrate in the flow cell, wherein a signal of the first identity sequence tag represents a positive identification of the first target nucleic acid segment, and a signal of the second identity sequence tag represents a positive identification of the second target nucleic acid segment; and (e) performing statistical calculation for quantifying the first target nucleic acid segment and the second target nucleic acid segment through the number of the reaction wells, the number of the positive identification of the first target nucleic acid segment, and the number of the positive identification of the second target nucleic acid segments. (a)performing a pre-amplification to generate first template molecules from the first target nucleic acid segment and generate second template molecules from the second target nucleic acid segment, wherein each of the first template molecules comprises sequences generated from a first universal primer sequence, a second universal sequence, and a first identity sequence tag, and each of the second template molecules comprises sequences generated from the first universal primer sequence, the second universal sequence, and a second identity sequence tag; (b) dispersing the sample to a substrate in a flow cell for random distribution of the first template molecules and the second template molecules among respective reaction wells of the substrate, wherein the number of the first template molecules and the second template molecules in each of the reaction wells is less than 1 on average; (c) in situ performing nucleic acid amplification reaction to generate a plurality of first amplicons from the first template molecules and a plurality of second amplicons from the second template molecules, wherein the first amplicons and the second amplicons are fixed on respective inner surfaces within the respective reaction wells of the substrate in the flow cell; (d) in situ identifying the first identity sequence tag of the first template molecules of the first amplicons and the second identity tag of the second template molecules of the second amplicons on the respective inner surfaces within the respective reaction wells of the substrate in the flow cell, wherein a signal of the first identity sequence tag represents a positive identification of the first target nucleic acid segment, and a signal of the second identity sequence tag represents a positive identification of the second target nucleic acid segment; and (e) performing statistical calculation for quantifying the first target nucleic acid segment and the second target nucleic acid segment through the number of the reaction wells, the number of the positive identification of the first target nucleic acid segment, and the number of the positive identification of the second target nucleic acid segments.