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4. GS De Novo Assembler and GS Reference Mapper Appendices : 4.16 Types of Structural Rearrangements : 4.16.9 Exon Splice
4.16.9
Exon Splice
Exon splices are essentially deletions, but they occur only in projects mapping cDNA reads to a genomic reference, and only if both ends of the deletion are within the same gene. They are supported by chimeric shotgun reads. We do not currently use Paired End reads for cDNA projects.
Example Output:
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EXON SPLICE
SubjAccno      SubjPos1    RegionName1    SubjPos2     RegionName2  Length  Confidence
chr10   276051  ZMYND11 276833  ZMYND11 782     High
 
 
Consensus: chr10                    276011+ 
CTGACATTGCGAGGATGCTATATAAAGACACATGTCATGAGGTACTATTCATTGCCCAATAGTTATACTCTTTCTATAAC 276090
                                        *
# supporting shotgun reads, pos 276051: 3
# non-supporting shotgun reads, pos 276051: 0
 
Consensus: chr10                    276793+ ATATTTTATGTAGGCTAAAGTAGTTTCTTTTCTTTTTCAGCTGGATGAACTGCAGCTTTGCAAGAATTGCTTTTACTTG 276871
                                        *
 
# supporting shotgun reads, pos 276833: 3
# non-supporting shotgun reads, pos 276833: 0
 
 
Individual Variation IDs: 7
 
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