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Most contigs contained one to six ESTs.
Most contigs contained 2 4 ESTs, and the largest contig was formed by 854 ESTs.
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Here, it can be noted that the left-most contigs tend to contain genes whose expression peaks at earlier developmental stages, whereas the right-most contigs contain genes whose expression peaks in the late postnatal or adult lilbraries (Figure 3B).
Scaffolds are identified by accession numbers, with sequence identity shown for the 5'-most contig and the 3'-most contig contained in that scaffold.
Nine most abundant contigs contained more than 100 ESTs each, suggesting a high transcript level of the corresponding genes.
The analysis of the structure of the BAC contigs revealed a high proportion of 'stacked' contigs, that is, contigs containing regions of depth that exceeded by far the estimated coverage of the library used (5.7×); in fact, most of the contigs contained BACs sharing one border, a feature most probably explained by the unequal use of BamHI restriction sites during library construction.
Most of the contigs contained sequences found in one to three libraries, with the largest category being contigs represented by clones from two libraries (393 clones).
Our analysis indicated, that in most cases contigs containing forward and reverse assembled reads despite unidirectional read orientation (FR contigs) were assemblies of transcripts from overlapping genes.
The number of ESTs per contig ranged from 2 (1016 contigs) to 78 (one contig, corresponding to a lectin-related protein), while most contigs (83%) contained 4 or fewer ESTs, and only 15 contigs (0.8% of total) included more than 20 EST sequences (Additional File 2B).
The majority of sequences (62% on average) could not be incorporated into assemblies, and most of the assembled contigs contained only two reads.
Most (91.7%) of these contigs contained only one SSR; the greatest number of SSRs detected in a single contig was seven.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com