The phrase "alignment rate" is correct and usable in written English.
It can be used in contexts where you are discussing the degree to which two or more elements are aligned or correspond with each other, often in data analysis or performance metrics.
Example: "The alignment rate of our marketing strategy with customer preferences has significantly improved this quarter."
Alternatives: "correspondence rate" or "congruence rate".
Unfortunately, despite these steps, the alignment rate of each aligner was significantly lower than expected, so to offset this, the fastx toolkit was used to filter out low quality reads (Table 1).
Sequencing performance QC (Step 3) is performed during the alignment process, by estimating specific statistical metrics (that is total number of reads, % of unpaired reads, % of reads aligned 0 times, % reads aligned exactly once, % of reads aligned more than once, and overall alignment rate) for each sequenced sample.
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).
BLASR performed better on alignment rate with the whole dataset successfully aligned while BWA-MEM outperformed in processing time (sequential executions: 766 seconds for BWA-MEM, 7,668 seconds for bt-FF, 12,532 for BLASR, and 13,845 for bt-2.2.1).
Using Bowtie 2 (Langmead and Salzberg 2012), reads were aligned to the reference genome sequence UMD 3.1 with an average alignment rate of 97.6%, that covered 99.23% of the genome (supplementary table S1, Supplementary Material online).
Alignment of spliced reads is more difficult than for unspliced reads and leads to lower proportions of the starting libraries being aligned, but this alone is unlikely to account for the relatively low alignment rate.
The libraries were aligned with the mango transcriptome at alignment rates (mapped reads/total reads) of 90.84, 90.02, 89.48, 89.77, 90.70, 90.11, 90.25 and 90.35% for samples 1 to 8, respectively.
However, Novoalign exhibits higher false alignment rates compared to the other three aligners.
Of the surviving reads, ~60 % aligned to the reference genome (Microcystis aeruginosa NIES-843) with the highest alignment rates occurring on day 2 (87 %; Additional file 1: Table S1).
Finally, we noticed that a few treatment group records displayed remarkable alignment rates (>3 mm/week).
One notable change is that the second treatment center displays significantly worse alignment rates.
