A, Evaluated with all of high-quality markers with genome alignments (28,267) (left), with a set of markers (16,077) which was aligned to unique positions of A, B and C genomes (ABC-markers, middle), and markers (12,781) which were uniquely aligned to B (8278) and C (4503) genomes right), respectively.
After the alignment to the cassava genome [ 41], 1,185,928 tags (54.6%) were aligned to unique positions while 229,629 tags (10.6%) were aligned to multiple positions and the remaining 757,678 tags (34.9%) could not be aligned.
The reads that perfectly matched S. japonicum genome were aligned to unique consensus sequences of TEs using the program SOAP[ 29].
A, Evaluated with a set of markers (16,077) which was aligned to unique positions of A, B and C genomes (ABC-markers).
In contrast, reads from MeDIP samples that were aligned to unique positions in the reference genome covered 26%-56%-56%the genome, while an additional 14%-19 14%-19e genome was covered by distributed k-mer repeats (Additional file 7A).
Those reads that can be aligned to a unique position in the genome and also to a unique position in the junctions are also considered multi-maps, and are, in many cases, indicators of the presence of a pseudogene or processed copy of a gene in the genome.
Previous studies have applied various rules for sequence selection: sequences must start with a restriction motif [ 8], sequences must be aligned to a unique location in the genome [ 9], and sequences must have a minimum average sequence quality (SQ) score of 20 [ 8, 9].
Amongst the 30 most significant novel miRNAs identified in P. alecto (Table 1), 15 were homologous to known vertebrate miRNAs but contained unique differences, while the remaining 15 could not be aligned to existing miRNAs and may represent unique or highly divergent bat miRNAs.
Each aligned read was assigned a mapping quality that indicates whether the read has a unique alignment or can be aligned to multiple positions in the genome [ 22].
These reads were aligned to nine unique PRAMEY sequences identified through BlastClust [48] with 100% similarity and 100% coverage as the criteria.
