Good's coverage, abundance-based coverage estimator (ACE), Chao1 richness estimator, Shannon index, and Simpson index were calculated based on the OTU data.
Note that these maps do not reflect organism abundances, although very small areas can indicate genomes that were partially sampled due to low sequence coverage (for abundance information see Supplementary file 3 and Figure 8 figure supplement 1).
Our study suggested that geographical, social and economic factors were closely related with each other in urban ecological systems, and have important impacts on urban forest coverage and abundance.
Finally, the protein coverage and abundance of key chloroplast pathways and processes is discussed.
These measurements were used to estimate percent coverage, relative abundance, population density, and geometric diameter, with the mathematical assumption that colonies are circular.
Genes within an operon were defined based on continuous read coverage, transcript abundance and detection of pair-end reads among these genes in all of the triplicates.
All of the Solexa reads were mapped against the 44 oral reference genomes in Human Microbiome Project [ 26] to assess the coverage and abundance of these sequenced isolates or their close neighbours in saliva microbiota.
Each transcript with an alternative 3 ′UTR is associated to its assembled transcript id (e.g. TCONS_0000X, for Cufflinks transcriptome assembly files), and through it, to all the corresponding analysis results, so that useful information (read coverage, expression abundance, etc).
This may in part be attributed to the lack of vegetation coverage and abundance of dry, exposed soil, and construction sites in the city of Beijing and its surrounding areas, especially during the winter seasons.
HUMAnN was configured to generate KO abundances from BLAST hits of enzymes as well as coverage and abundances for KEGG pathways and modules.
To determine if the NORA metagenome encodes unique functions compared to healthy subjects, we applied HUMAnN (Abubucker et al., 2012) to quantitate the coverage and abundances of KEGG (Kanehisa and Goto, 2000) modules (small sets of genes in well-defined metabolic pathways) in healthy controls (n = 5) and a representative set of NORA subjects (n = 14) with and without Prevotella.
