Quantum key distribution (QKD) gradually has become a crucial element of practical secure communication. In different scenarios, the security analysis of genuine QKD systems is complicated. A universal secret key rate calculation method, used for realistic factors such as multiple degrees of freedom encoding, asymmetric protocol structures, equipment flaws, environmental noise, and so on, is still lacking. Based on the correlations of statistical data, we propose a security analysis method without restriction on encoding schemes. This method makes a trade-off between applicability and accuracy, which can effectively analyze various existing QKD systems. We illustrate its ability by analyzing source flaws and a high-dimensional asymmetric protocol. Results imply that our method can give tighter bounds than the Gottesman-Lo-Lutkenhaus-Preskill (GLLP) analysis and is beneficial to analyze protocols with complex encoding structures. Our work has the potential to become a reference standard for the security analysis of practical QKD.
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