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The average alignment rate was 0.89 (s.d. 0.02) and 0.86 (s.d. 0.03) for human and mouse, respectively.
The mean alignment rate was 90.12% in males and 90.67% in females (Separate values for each family are given in Additional file 5).
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This relatively low alignment rate is an intrinsic characteristic of SOLiD 4 System sequencing [ 20].
Table 4 shows execution times of all three versions tested on a small subset of 1000 reads of PacBio datasets, which alignment rate is shown in Figure 3 (Human-Ref19-1 and Human-Ref19-2).
The test group's mean alignment rates were 0.99 compared to a control rate of 0.44, with a comparison group of 23 control arches and 111 treatment arches.
Overall read alignment rates were above 90%% for all libraries.
An overview of the data, including raw and post-QC read counts and alignment rates is given in Additional file 6.
Thus, even though our alignment rates were somewhat lower than we might have expected, we think that our datasets are valid and large enough to draw meaningful conclusions about the exosomal RNA content.
For quality control assurances, we confirmed that cfDNA-fragment sizes were near equal between samples pre- and post-fragmentation, and the DNA library yields and percent-alignment rates were nearly equal for the three sample pools (Additional file 3: Figure S2).
For shorter alignments, this rate was adjusted to account for slight variations along the sequence (this resulted in rates varying from 0.0085 to 0.0121).
For every position of each protein alignment, a substitution rate was assigned using a discrete-gamma distribution.
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