skip to main content
Roche logo
4. GS De Novo Assembler and GS Reference Mapper Appendices : 4.16 Types of Structural Rearrangements : 4.16.1 Deletion
4.16.1
Deletion
Deletions involve only one subject, with two positions for the beginning and end. They can be supported by chimeric shotgun reads or stretched mate pairs.
Example output:
======================================================================
DELETION
SubjAccno      SubjPos1   RegionName1     SubjPos2  RegionName2     Length  Confidence
gi|6322016|ref|NC_001141.1|     107240          117741          10501   High
 
 
Consensus: gi|6322016|ref|          107205+ 
AATCACAATAGGCAACTCTAAATCATCGTCCAATGTCACAGGAATGGTGTCGGTTGGTTCTGGTGCAAGCAACGT 107279
                                   *
# supporting shotgun reads, pos 107240: 33
# non-supporting shotgun reads, pos 107240: 0
 
Consensus: gi|6322016|ref|          117701+ 
GCTGAACAACAGGCGAAAGTGGATGCTGAGAAACTGCTGGTTGGGTTATTGGATCTGAACATAAAACAACCATAGTCT 117778
                                        *
 
# supporting shotgun reads, pos 117741: 36
# non-supporting shotgun reads, pos 117741: 0
 
 
17 mate pairs forward, 5' to 3', coverage = 17, frequency = 100.00
From position 107193 to position 118269
+9930   2
+10198  0
+10466  3
+10734  2
+11002  5
+11270  1
+11538  1
+11806  1
+12074  1
+12342  1
 
 
Individual Variation IDs: 241, 242
 
======================================================================