NAME

       show-diff - show diff information (part of mummer package)

SYNOPSIS

       show-diff [options]<deltafile>

DESCRIPTION

       -f            Output diff information as AMOS features

       -h            Display help information

       -H            Do not show header

       -q            Show diff information for queries

       -r            Show diff information for references (default)

       Outputs  a  list  of  structural differences for each sequence in the reference and query,
       sorted by position. For a reference  sequence  R,  and  its  matching  query  sequence  Q,
       differences  are  categorized as GAP (gap between two mutually consistent alignments), DUP
       (inserted  duplication),  BRK  (other  inserted  sequence),   JMP   (rearrangement),   INV
       (rearrangement  with inversion), SEQ (rearrangement with another sequence). The first five
       columns of the output are seq ID, feature type, feature start, feature  end,  and  feature
       length.  Additional  columns  are  added  depending  on the feature type. Negative feature
       lengths indicate overlapping adjacent alignment blocks.

       IDR GAP gap-start gap-end gap-length-R gap-length-Q gap-diff

       IDR DUP dup-start dup-end dup-length

       IDR BRK gap-start gap-end gap-length

       IDR JMP gap-start gap-end gap-length

       IDR INV gap-start gap-end gap-length

       IDR SEQ gap-start gap-end gap-length prev-sequence next-sequence

       Positions always reference the sequence with the given ID. The sum  of  the  fifth  column
       (ignoring  negative  values)  is  the total amount of inserted sequence. Summing the fifth
       column after removing DUP features is total unique inserted sequence. Note that  unaligned
       sequence  are  not  counted,  and  could  represent  additional  "unique"  sequences.  See
       documentation for tips on how to interpret these alignment break features.