Fig. 4

Comparison of the efficiency of SSLR on the simultaneous identification of DNA/RNA mock communities. SSLR was used to prepare and sequence four artificial virome containing different proportions of the DNA phage and RNA phage. A Effect of DMSO and heat treatment on the percentage of four phage genomes. These phage genome abundance values were calculated based on the quantity of DNA and RNA phages measured by NanoDrop. MD, Mock D with ratio of 90:10 for DNA and RNA; ME, Mock E with ratio of 50:50 for DNA and RNA; MF, Mock F with ratio of 10:90 for DNA and RNA. phi6 has 3 segments: large (6374 bp), medium (4063 bp), and small (2948 bp). B Heat treatment does not adversely affect sequencing error rates. The R package ShadowRegression estimates reference-free error rates (inset) based on a transform of the slope of read counts and their “shadows” (main plot line graphs). Shadows (y-axis) are a measure of the variation in read counts across different sequencing runs for the same sample. They are calculated by taking the logarithm of the ratio of read counts in one run to another run. A higher shadow value means a larger difference in read counts between the two runs. Tags (x-axis) are a measure of the abundance of reads for a given nucleotide position in a sample. They are calculated by taking the logarithm of the read count at that position. A higher tag value means a higher number of reads at that position. The figure shows the relationship between shadows and tags for different samples treated with or without heat/DMSO. The slope of this relationship is used to estimate the sequencing error rate for each sample, which is shown in the inset plots. The figures suggest that DMSO treatment does not affect the sequencing error rate significantly