Additional file 4: of Assembly of chloroplast genomes with long- and short-read data: a comparison of approaches using Eucalyptus pauciflora as a test case

Figure S3. The summary of short-read-only and hybrid assemblies with SPAdes short-read correction. Long and Short indicate the coverage of this assembly. A. The total coverage of the chloroplast genome across all contigs output by the assembler. The number is the number of contigs of each assembly, whereas the heatmap is the genome coverage (it could be over 100% if some duplications exist). Numbers marked with red contained a single contig covering the whole chloroplast genome. The heatmap color is reversed compared to the Fig. 1 to make the color in all figure panel A show consistence. B. The assembly length of different assemblies after manual curation (e.g. removing duplicate regions). Numbers marked with red denote assemblies with the expected length, in the range 155,938 bp–155,945 bp. C. The mapping rate of validation reads to the assemblies after manual curation. Assemblies with highest mapping rate (99.43%) are marked with red. D. The average per-base error rate of validation reads mapped to each manually-curated genome assembly. Assemblies with the lowest error rate (0.0007) are marked with red. (PNG 1550 kb