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4. GS De Novo Assembler and GS Reference Mapper Appendices : 4.16 Types of Structural Rearrangements : 4.16.3 Substitution
4.16.3
Substitution
Substitutions involve only one subject, with two positions for the beginning and end. They are a combination of a deletion and an insertion, such that X subject bases are replaced by Y sample bases. Substitutions are supported only by shotgun reads.
Example output:
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SUBSTITUTION
SubjAccno	SubjPos1	RegionName1	SubjPos2	RegionName2	Length	Confidence
M_genitalium	174010		174128		117	High
 
 
Consensus:                   173975+ 
TGTTAGGTGGGCAGTTTGACTGGGGCGGTCGCCTCCTAAAAGGTAACGGAGGCGCACAAAGGTACCTTCA 174044
                                   *
# supporting shotgun reads, pos 174010: 5
# non-supporting shotgun reads, pos 174010: 15
 
Consensus:                   174088+ CTTGACTGTGAGACTTACAGGTCGAACAGGTGAGAAATCAGGTCATAGTGATCCGGTGGTTCAGTATGGAATGGC 174162
                                     ****
 
# supporting shotgun reads, pos 174128: 11
# non-supporting shotgun reads, pos 174128: 7
 
 
Individual Variation IDs: 1, 2, 3
 
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