These QTLs had low phenotypic variance (<12 %) for all the nine traits namely plant height, primary branching, SPAD chlorophyll meter reading, percentage of sound mature kernels, 100 kernel weight, shelling percentage, HI, HYLD and PYLD.
We also found that there was a strong correlation between viral-read percentages and day 4 body weight loss (Spearman correlation coefficient = −0.73) and that viral-read percentages were strongly predictive of weight loss at day 4 (p-value <1.34×10−10).
After sequencing, we observed low variation in read percentages (0.2% to 1.55%) among the 96 demultiplexed samples.
Total viral read counts and viral read percentages varied greatly among founders, and with different viruses and at different time points.
The scatter plot of viral-read percentages and day 4 weight loss is shown in Figure S14, in which a clear linear relation can be observed.
Moreover, as in the case of L. lactis, the OV control libraries had lower rRNA read percentages than the SMART and TS libraries.
Our results identify four SNPs that universally appeared with M/E read percentages of 100% in all of the four samples used or with less than 100% M/E reads percentages in some of the samples used, suggesting inherited or somatic mutations respectively.
To better compare viral reads, viral read counts were normalized to host read counts, which varied as a result of sequencing technology and our sequencing depth requirement, to yield viral read percentages.
Of note, none of the five pathogenic mutations showed any evidence of mosaicism, either by the mutation read percentages in the next generation sequencing data or the Sanger sequencing traces (Supplementary Material, Fig. S2).
There was no correlation between viral-read percentages and day 2 weight loss, probably because it was too early in the course of infection for body weight to be impacted by infection.
