When fully zoomed in, the selected reads are highlighted by a red rectangle.
Composite alignments of the selected reads from the 23 plants with the unigene set were evaluated based on different parameters in SAMtools (see methods for details).
Finally, the selected reads were aligned to the reference regions with CLUSTALW (Thompson et al., 1994) to confirm the presence of variants in the AM356-8 chloreadasetread set.
Second, the selected reads were mapped to the B73 reference genome and only reads mapped to a unique location in the genome were retained.
Among the selected reads, 12,754,484 sequences from P. notoginseng roots mapped perfectly to the transcriptome, amounting to 18.98 %, of the total reads (Table 2).
Alignment of all the selected reads from 23 plants with the unigenes revealed a total of 359,769 variants including 96.74 % SNPs and 3.26 % INDELs.
The reference genomes obtained from NCBI library enabled the calculation of the sequencing depth of the selected reads, and the determination of the percentage of reads left over compared to the original sequence data.
Contigs assembled from the selected reads were merged to generate the maxicircle assembly covering the coding region, from which other contigs were added progressively based on mate pair information and identity to extend the assembly into the non-coding region.
Among the selected reads, 9,619,834 sequences from the mature ovary and 11,019,895 sequences from the immature ovary mapped perfectly to the chicken genome (Additional file 1: Table S1), amounting to 66.14 and 74.59% of the total reads, respectively; and 5,834,400 reads in mature and 3,919,973 reads in immature ovaries were found to be similar to miRNAs.
By the simultaneous aligning of these selected reads to the host genome and the transgenic cassette, the identification approach allows determining precisely the localization of the transgenic cassette and the sequence of its flanking regions.
