Figure 3 shows the relationship between the mapping ratio and the species classification.
In summary, SCRS data amplified by MDA or MALBAC had a lower duplication ratio, a higher mapping ratio, and a higher genome recovery than that from DOP-PCR.
Therefore, increasing the numbers of mismatches and gaps will contribute to increasing the mapping ratio and subsequent biological analyses, even if the method is probabilistic.
Even with this improvement, various limitations and problems remain unsolved, which include reduced mapping ratios, shifts in read mappings and the selection of which variants to include to remove biases.
Ultimately, it was found that there were no discernible differences in KO ID assignment and mapping ratios of KO assigned CDSs to the KEGG modules when comparing between Sanger and Illumina reads using contigs longer than 500 bp for analysis.
To test the applicability of the interspecies mapping approach, we examined the relationship between species classification and mapping ratios.
The percent coefficient of variation (%CV) of total bases and mapping ratios among the 12 samples was small (Table 1), indicating that the quality of the sequence reaction was comparable among the samples.
The number of clean reads and mapping ratio are presented in the supplemental material (Additional file 3: Table S3), and the mapping ratios were all more than 90%, which suggests that sequencing was sufficient.
A total of 40.2 M and 37.9 M clean reads were obtained from RNA-seq in autotrophic and heterotrophic samples, with 80.7% and 81.2% mapping ratios to the genome, respectively (Additional file 1 Table S9).
