The phrase "alignment rate in" is correct and usable in written English.
It can be used in contexts where you are discussing the percentage or degree of alignment within a specific area or subject matter.
Example: "The alignment rate in our recent project was significantly higher than in previous ones, indicating improved collaboration among team members."
Alternatives: "degree of alignment in" or "alignment percentage in".
In these two simulated data sets, no matter whether the mismatch positions are designed to have high or low quality, all four aligners show a lower false alignment rate in the data set generated from 3000 exon regions (0.7-5%, see Table 9A, B) compared to the data set generated from 218 CpG islands that have more repetitive regions 14-177%, see Table 10A, B).
The comparatively low alignment rate especially in case of the L. braziliensis library is likely a result of incomplete assembly of the reference genome or the fact that we used a different L. braziliensis strain (a clinical isolate from the Peruvian Amazon region) than the strain used to generate the reference genome.
The effect of adapter sequences is also more serious, given the risk of incorporating adapter sequences into the final sequence assembly, compared with the mere reduction in the alignment rate typically seen in reference-based approaches.
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 mean alignment rate was 90.12% in males and 90.67% in females (Separate values for each family are given in Additional file 5).
Library sizes were of 32, 46, and 57 million unique reads, respectively, with alignment rate of 92% in each case.
According to the alignment rates shown in Figure 4a, all methods work with almost the same number of mapped reads when Bowtie2 is used.
However, descriptive statistics for alignment rate, such as those found in Table 2, should be interpreted with the fact that the test and control groups have significantly different initial LII scores.
Alignment of unmapped reads to a non-coding RNA database (RFAM) resulted in a 0.2% alignment rate, confirming that the bovine embryo libraries prepared using the Ovation V1 system did not contain large proportions of rRNA fractions.
In these tables, we report the very low alignment rate of Bowtie2, which is at most about 13%.
An overview of the data, including raw and post-QC read counts and alignment rates is given in Additional file 6.
