If the IOZ determined by the final decision of the SISCOM read encompassed the location of surgical resection, the localization decision was considered correct.
The 454 pyrosequencing generated 242,261 reads, encompassing about 52.9 Mb of sequencing data.
They stated that these included shotgun reads encompassing STRs and SSRs, and sets of paired-end reads if one or both ends consist of STRs or SSRs.
We, therefore, conclude that the ChIP-seq reads encompassing the identified binding sites correspond to the active mtDNA rather than to NUMTs.
This was possible since trimmed 2 F reads encompass only part of exons 2 and 3, and all named alleles have complete exon 2 and 3 sequences.
In this case, it is possible to identify only those reads encompassing an insertion boundary as in case 1B from Fig. 1.
We observed that many chimeras found in the negative set by ChimeraScan were supported by reads encompassing the two exons of the genes involved in the fusion and were missing reads spanning over the fusion junction.
This produced a total of 605,027,558 sequence reads, encompassing 30,251 Mbases from all four cDNA libraries, embryos after 5 d (SE_5D), 10 d (SE_10D), 15 d (SE_15D) of in vitro culture and wild type (WT) leaf tissues (WT_L).
This revealed three sequence reads encompassing a cluster of three previously undetected nucleotide substitutions [c2244G >C + c2248T >C + c2250C >A] located in exon 23 of the CLCN7 gene encoding the anion transport protein ClC-7 (supplementary material Fig. S2).
However, some chimeric fusion features are common to all the fusion detection tool reports (e.g. genes involved in the fusion, genomic breakpoint coordinates, number of reads encompassing and spanning the fusion breakpoint, etc).. Thus, the internal database structure of Pegasus provides a unique point of access for all the information needed to fully describe a gene fusion candidate.
