AGP file

AGP files are used to describe the assembly of a sequences from smaller fragments. This document contains the differences between AGP versions 1.1 and 2.0 and their mappings to the INSDC feature table format.

Full information about the AGP format is available from NCBI.


AGP 1.1 AGP 2.0 assembly_gap feature
Gap type Linkage Gap type Linkage Linkage evidence /gap_type /linkage_evidence
clone no contig no   between scaffolds  
contig no contig no   between scaffolds  
repeat no repeat no   repeat between scaffolds  
centromere no centromere no   centromere  
telomere no telomere no   telomere  
short_arm no short_arm no   short_arm  
heterochromatin no heterochromatin no   heterochromatin  
fragment no scaffold yes *1 within scaffold *1
fragment yes scaffold yes *1 within scaffold *1
clone yes scaffold yes *1 within scaffold *1
repeat yes repeat yes *1 repeat within scaffold *1

*1: For AGP 1.1 submissions the corresponding AGP 2.0 linkage evidence and the /linkage_evidence qualifier value is 'unspecified'. The full list of AGP 2.0 linkage evidence values and their mappings to the linkage_evidence qualifier values is:

AGP 2.0
Linkage evidence
assembly_gap feature
paired-ends paired-ends
align_genus align genus
align_xgenus align xgenus
align_trnscpt align trnscpt
within_clone within clone
clone_contig clone contig
map map
strobe strobe
unspecified unspecified