Fig. 1: Example of a read recruitment plot.

This figure showcases the result of processing a Blastn search of metagenomic short reads (each matching read is represented by a dot in main panel 1) against a reference MAG sequence recovered from the same metagenome (x-axis). 1 Main panel representing the reads recruited (mapped), placed by location (x-axis) and identity (y-axis) across the reference sequence. 2 Sequencing depth (or coverage) across the reference, i.e., how many reads map at each base pair position, in logarithmic scale. Bars lower than the average represent regions with fewer mapped reads, which denote gene content differences. 3 Identity histogram of mapped reads per unit of identity (light gray) and smoothed spline (black), in logarithmic scale. 4 Sequencing depth histogram. Peaks based on the sequencing depth revealed in panel 2 are automatically identified as skewed normal distributions (in red). The background of panels 1 and 3, and the line colors in panels 2 and 4, correspond to matches with identity above (dark blue) and below (light blue) a user-defined cutoff. By default, the identity cutoff is set to 95%. Note the area of sequence discontinuity denoted by a decrease, by more than one order of magnitude (x-axis, panel 3), in the number of reads mapping around 95% identity (red arrow) relative to reads mapping at >98% identity. ANIr is estimated based on reads in the dark blue area only and represents the average nucleotide identity of reads to the reference sequence. The MAG represents an uncultivated member of the Actinobacteria phylum that shows about 45% average amino acid (AAI) to Ilumatobacter coccineus, its closest related named species with available genome representative(s). The metagenome was obtained from a planktonic sample from 1000 m in the Gulf of Mexico.