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4. GS De Novo Assembler and GS Reference Mapper Appendices : 4.16 Types of Structural Rearrangements : 4.16.5 Duplication, Tandem (May or May Not Be Inverted)
4.16.5
Duplication, Tandem (May or May Not Be Inverted)
Tandem duplications are only on one subject. The reference, start, and end of the duplicated segment are given, along with the length.
Example output:
DUPLICATION, TANDEM, INVERTED
SubjAccno     SubjPos1      RegionName1   SubjPos2    RegionName2   Length  Confidence
gi|85666114|ref|NC_001136.7|    1406931         1427860         20929   High
 
Consensus: gi|85666114|ref         1406891+ 
GTCTTGTTTCGTGGACCTTGCACTTCGTAGATTCATCATGTTCTATACGTTTTTCATTTCCGCATTCTAAACCCAAAAGA 1406970
                                        *
# supporting shotgun reads, pos 1406931: 7
# non-supporting shotgun reads, pos 1406931: 10
 
Consensus: gi|85666114|ref         1427820+ 
GGGCTTGCGTCATGGACCAGGATTGAGAATCTAAAGAATCCTTCATATTTTCTAACTGTTTACGTTTATTTAAAATCTTC 1427899
                                        *
 
# supporting shotgun reads, pos 1427860: 7
# non-supporting shotgun reads, pos 1427860: 0
 
 
7 mate pairs reverse, 3' to 5', coverage = 7, frequency = 70.00
From position 1407092 to position 1427633
+16255
+16563
+16594
+16672
+16722
+16736
+16880
 
8 mate pairs inverted, 3' to 3', coverage = 8, frequency = 88.89
From position 1407295 to position 1427939
+16618
+17518
+17782
+18954
+19048
+19092
+19102
+20346
 
Individual Variation IDs: 328, 329, 330, 332
 
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