The mean sequence sizes for Control shmiR and CGGBP1 shmiR LINE-1 PCR products are 394.3 ± 75.27 and 401.0 ± 69.01 bps respectively.
A total of 4,058,656 raw reads were obtained from the 16 different tissue libraries, with a mean sequenced size length of 355 bp (Additional file 1: Table S1, Additional file 1: Table S2, Additional file 1: Table S3).
There were 55 intra scaffold gaps in P. alba cp genome with a mean sequence gap size of 1252 bp.
The mean library insert sequence size was 272 bp and both ends of the library were sequenced to generate 100 bp raw paired end reads.
The CSF distribution has a strong right asymmetry with standard deviation and mean variance with sequence sizing (Fig. 2).
Based on the number of BESs matching at least one A. thaliana sequence in the Swissprot database (1,591), the mean sequence length of the BES (599 bp), the size of the oak genome (740 Mb), the total size of the BESs (9,535 kb) and the mean size of a gene (2 kb - [ 19]), we estimated a number of 29,340 genes.
5′ and 3′ UTRs and deep intronic sequences were not targeted to avoid increasing the sequence target size that would have strongly decreased the mean sequence coverage.
After quality checks, trimming of adapters and size selection using custom scripts (see Methods) 14,563,748 Illumina GAIIx reads (6,913,826 read pairs, insert size ~250-300 bands, and 736,096 single reads; mean sequence length 107.8 bases) and 1,495,941 GS FLX sequences (mean sequence length 363.2 bases), i.e. 16,059,689 reads in total, were used as input to the sequencing assembly pipeline.
The primer sequences, sequence size and sequence position in Onc.
These reads were assembled into 52,535 distinct sequences (mean size: 466 bp) and 16,596 sequences were annotated with an E-value above 10-5.
