Under settings that permit the higher fraction of correct placement of reads with BFAST, the false mapping rate is also lower than other methods, with the exception being the case of insertions, where SHRiMP has a lower false mapping rate (with much decreased sensitivity).
The average mapping rate was 77.7%.
For each tissue type, the mapping rate was similar between RefGene and UCSC.
The highest total mapping rates were observed for P. banksiana and P. contorta, while the lowest mapping rate was obtained for P. lambertiana, as expected from their phylogenetic relationship and previous studies [ 8].
The reads mapping rate is the ratio of reads that are aligned to the annotated transcripts sequences.
The mean reads mapping rate was 70.8 ± 4.2% (Additional file 2: Table S1), of which 66.1 ± 0.6% mapped uniquely against the predicted gene set [ 15].
The overall mapping rate was only 1.67% in the control sample, while in the experimental sample, the rate was higher (9.42%) (a ratio of 5.6 between two datasets).
Assembly quality was assessed by aligning the transcripts onto the scaffolds, and 97.5% mapping rate was observed (Additional file 1: Table S2).
This reads mapping rate is considerably higher than those reported by other authors working with Malus (35.8% of uniquely mapped reads according to [ 18]; 65% of total reads according to [ 19]).
Although the second sequencing produced about 3 × more data than the first, its mapping rate was about 3 × lower, and overall, the mappable reads were almost the same (Additional file 3: Table S3).
