Figure 2. The distribution of qualities of the sequencing reads for the two analyzed samples.

A. The sequencing quality of III:2. B. The sequencing quality of V:1. The X-axis represents the position along each sequence read. In this study we performed 80 bp sequencing, so the label of X-axis is from 0 to 80. The Y-axis is the Phred quality score of each base along sequence reads. The higher the score, the more accurate a base call. The quality scores of 20, 30 and 40 represent 99%, 99.9% and 99.99% accuracy of a base call. The intensity of the blue dot refers to the quantity of sequences with the same quality score. The darker the blue, the more bases/sequences at the dot. The quality scores of first 50 bp of most reads for both samples are higher than those of the last 30 bp, thus the darker blue dots accumulate around Q30 (Phred score of 30) from 0 to 30 bp along reads, while Q5 is observed between 60∼80 bp along reads. In order to get more accurate base calling, we filtered these low quality reads during the data analysis.