SYNOPSIS

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.