Mapping of reads to genomes - (Item I)

Additional Information to Figure 4: Coverage of bacterial i) reference genomes and ii) isolates by metagenomic reads from vitreous of endophthalmitis patients. For each individual patient, the metagenomic shotgun reads for the most abundant microbial organism were extracted and mapped to the respective reference genome sequence in the database. For patients C1 and I7 a microbial organism could not be assigned confidently, and these patients are regarded as “sterile” endophthalmitis cases.
In the two cases where metagenomics analysis and culture results from the hospital were not identical (patients C5 and I3), we examined the reads for all organisms detected in the metagenomics analysis.
For the patients for which isolates were obtained and WGS generated, we mapped the respective metagenomic shotgun reads to these assemblies.
The most outer circle displays the genome sequence (including scaffolds and contigs). The orange and blue inner circles display the depth of mapped reads originating from the samples that were extracted with the QIA and UCP DNA extraction methods, respectively.

Reference

Kirstahler P, Bjerrum SS, Friis-Møller A, la Cour M, Aarestrup FM, Westh H., and Pamp SJ. (2018) Genomics-Based Identification of Microorganisms in Human Ocular Body Fluid. Scientific Reports, doi:10.1038/s41598-018-22416-4.