Additional file 2: Figure S1. of Genome-wide SNP discovery and population structure analysis in pepper (Capsicum annuum) using genotyping by sequencing
Creators: name: F. Taranto
name: N. D’Agostino
name: B. Greco
name: T. Cardi
name: P. Tripodi
Publisher: name: Figshare
Year: 2016
Subjects: subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Biotechnology
subject: Ecology
subject: 69999 Biological Sciences not elsewhere classified
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: FOS: Mathematics
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: FOS: Health sciences
subject: 60506 Virology

description: Bar charts illustrating the distribution of master tag coverage at each position, along the 12 pepper chromosomes. The peri-centromeric region for each chromosome is indicated in grey and has been identified using the markers listed in the Additional file 1: Table S3. Figure S2. Bar chart describing the distribution of the 32,950 SNPs on the 12 pepper chromosomes. Figure S3. Bar chart describing the distribution of SNP types divided according to nucleotide substitution as transitions (black) and transvertions (grey). Figure S4. Scatter plot of linkage disequilibrium decay (r2) against the genetic distance for linked SNP throughout the CM334 pepper reference genome. Figure S5. Evaluation of the best grouping number (K) of the Bayesian clustering analysis using the Evanno’s method. a) Plot of mean likelihood L(K) and variance for 10 independent runs for each value of K for K = 2–15. b) Evanno’s plot generated by STRUCTURE HARVESTER for the detection of the true number of clusters (the most likely value of K). The highest value was at K = 3, indicating that the 222 accessions likely form 3 sub-populations. Figure S6. Gap statistic plots for the dataset including 222 pepper accessions. The number of inferred Ks ranging from 1 to 15 are shown in the graph. a) The blue and red curves are the estimated expectation of log (Wk) and the observed log (Wk), respectively. b) The x-axis represents different possible Ks (K3 is the best value) and y-axis represent the gap value. Figure S7. Hierarchical clustering (K = 3) of 222 C. annuum accessions and derived subgroups obtained at minimum variance cluster &lt;0.1, using the AWclust software. Figure S8. Evaluation of the best grouping number (K) of the Bayesian clustering analysis performed on 191 C. annuum accessions using the Evanno’s method. a) Plot of mean likelihood L(K) and variance for 10 independent runs for each value of K for K = 1–15. b) Evanno’s plot generated by STRUCTURE HARVESTER for the detection of the true number of clusters (the most likely value of K). The highest value was at K = 3, indicating that the 191 accessions included in cluster I (Fig. 2) likely form 3 sub-populations. Figure S9. Gap statistic plots for the dataset including the 191 pepper accessions belonging to cluster I (Fig. 2). The number of inferred Ks ranging from 1 to 15 are shown in the graph. a) The blue and red curves are the estimated expectation of log (Wk) and the observed log (Wk), respectively. b) The x-axis represents different possible Ks (K2 is the best value) and y-axis represent the gap value. (PDF 3470 kb)