File S1 - Direct Amplification, Sequencing and Profiling of Chlamydia trachomatis Strains in Single and Mixed Infection Clinical Samples

This file contains text with detailed descriptions of the experiments, MAP binstrain and coverage plots and tables with additional information about synthetic data files. File S1 also contains the following figures and tables: Figure S1, Map of The C. trachomatis D/UW3/CX genome. Figure S2, binstrain β estimates for the single strain/uni-mixture entire (whole) genome simulated samples and binstrain beta estimates for the single strain/uni-mixture 100 kb targetedsimulated samples. Figure S3, binstrain β estimates for the 10 bi-mixture entire (whole) genome simulated samples and binstrain beta estimates for the 10 bi-mixture 100 kb targeted simulated samples. Figure S4, MAP plots for the whole genome simulated 10 bi-mixture samples and100 kb targeted simulated 10 bi-mixture samples. Figure S5, binstrain β estimates for the 4 tri mixture entire (whole) genome simulated samples and binstrain β estimates for the 4 tri mixture 100 kb targeted simulated samples. Figure S6, MAP plots for the whole genome simulated 4 tri-mixture samples and 100 kb targeted simulated 10 tri-mixture samples. Figure S7, binstrain β estimates for 6 simulated recombinant strains. Figure S8, MAP plots for the whole genome simulated recombinant samples. Figure S9, binstrain β estimates for experimental Set 1. Figure S10, MAP plots for the 100 kb regions of Set1. Figure S11, binstrain β estimates for clinical sample Set 2. Figure S12, MAP plots for the real 100 kb regions of Set 2. Figure S13, binstrain β estimates for clinical sample Set 3. Figure S14, MAP plots for the 100 kb targeted genome clinical samples of Set 3. Figure S15, Distribution of the Normalized Average Coverage across the entire 100 kb targeted region in Set 1. Figure S16, Normalized standard deviation of coverage in Set 1. Figure S17, Box plots representing the distribution of the normalized coverage in bins of 10 kB regions across the entire 100 kb region targeted in sample set 1. Figure S18, Distribution of the Normalized Average Coverage across the entire 100 kb targeted region of the clinical samples in Set 2. Figure S19, Normalized standard deviation of coverage of sample Set 3. Figure S20, Box plots representing the distribution of the normalized coverage in bins of 10 kB regions across the entire 100 kb region targeted in sample set 2. Figure S21, Distribution of the Normalized Average Coverage across the entire 100 kb targeted region of the clinical samples in Set 3. Figure S22, Normalized standard deviation of coverage of samples in Set 3. Figure S23, Box plots representing the distribution of the normalized coverage in bins of 10 kB regions across the entire 100 kb region targeted in sample set 3. Figure S24, Breakdown of binstrain results for sample 3.18. Figure S25, Breakdown of binstrain results for sample 3.19. Table S1, List of C. trachomatis genomes used for primer design, ancestral sequence regeneration and whole genome MAUVE alignment to generate the SNP pattern file used in this study. Table S2, List of the C. trachomatis genomes used for simulating uni, bi and tri artificial mixed infected samples and their binstrain beta estimates. (PDF)