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.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.46.4.
.TH SHOW-DIFF "1" "April 2015" "mummer 3.23" "User Commands"
.SH NAME
show-diff \- show diff information (part of mummer package)
.SH SYNOPSIS
.B show\-diff
.RI [options] <deltafile>
.SH DESCRIPTION
.TP
\fB\-f\fR Output diff information as AMOS features
.TP
\fB\-h\fR Display help information
.TP
\fB\-H\fR Do not show header
.TP
\fB\-q\fR Show diff information for queries
.TP
\fB\-r\fR Show diff information for references (default)
.PP
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.
.TP
IDR GAP gap\-start gap\-end gap\-length\-R gap\-length\-Q gap\-diff
.TP
IDR DUP dup\-start dup\-end dup\-length
.TP
IDR BRK gap\-start gap\-end gap\-length
.TP
IDR JMP gap\-start gap\-end gap\-length
.TP
IDR INV gap\-start gap\-end gap\-length
.TP
IDR SEQ gap\-start gap\-end gap\-length prev\-sequence next\-sequence
.PP
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.
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