Figure 3

Comparison of RNA-seq-derived gene models with Histoplasma ab initio gene predictions. The accuracy of the RNA-seq-derived and ab initio gene models for G186A were measured as the frequency of mRNA reads that match the modeled gene structures (A), the percentage of exon structures with mRNA experimental support (B), and direct sequencing of mRNAs (C-E). (A) Percentages indicate the number of cDNA library reads that match to exons (blue), introns (red), intergenic regions (green), or spanning multiple regions (yellow) in the RNA-seq-derived or ab initio gene set models. (B) Accuracy of the exon definition is indicated by the percentage of exons with perfect support (blue; at least 99% of the exon length is covered by mRNA reads), fair support (red; 70% to 99% of the exon length is covered by mRNA reads), or poor support (green; less than 70% of the exon length is covered by mRNA reads). (C-E) Schematics of gene structures are shown as exons (horizontal boxes below the x-axis) for RNA-seq-derived models (red) and the ab initio predictions (blue). The horizontal represents the genome sequence in that interval. Vertical histogram (grey bars) depicts the frequency of mRNA reads that match that particular region of the genome sequence. Models are depicted for the MFS5 gene (C) that encodes an MFS-family transporter, the HYP12 gene (D) and the HYP13 gene (E), two genes encoding factors of unknown function.