The primary structures containing data and analysis products are peptidereads_fig2.mat (for figure 2) and peptiderereads_fig3.mat (for figure 3). The main analysis scripts for these data structures are callvariants_fig2.m and reread_analysis_fig3.m respectively. Data for figures S6 (S6_reread_data.dat) and S8 (S8_hetero_data.dat), and the analysis script used to produce figure S6 (S6_reread_analysis.m) are also included. Other files are dependencies of these main scripts. The fields in peptidereads_fig2 are as follows: folder, eventnum, reducedStart, reducedEnd, suspicious, hasreread: notes for internal use variant: the true identity of the single-amino-acid substitution variant data: the ion current data for each read downsampled to 5 kHz. omit: whether the read was omitted from analysis due to length relativeDNAend: the index in the data where the DNA portion of the read ends. relativeLinkerEnd: the index in the data where the linker portion of the read ends. DNAlevels, Peplevels, Alllevels: extracted ion current levels for the DNA region, the peptide region, and everything. cal: the multiplicative and additive constants applied to calibrate the read caldata: the data with calibration constants applied cons0D, cons0W, cons0G, cons0DNA: initial guesses for consensuses based on hand curation of data. pepDcons0, pepWcons0, pepGcons0: the portion of the handmade consensus with the variant levels. pepDcons, pepWcons, pepGcons: the portion of the iterated consensus with the variant levels. inhandconsensus: whether the read was used in generation of the inital guess consensuses. inconsensus: whether the read was used in generation of either the initial guess or iterated consensuses. confidence: the relative likelihood of each variant assigned to the read incalls: whether the data was used in variant calling (i.e., not used in consensus generation) params: the analysis parameters used