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.

mummer 3.23                                        April 2015                                       SHOW-DIFF(1)