AGP files

AGP files describe the assembly of a genome from smaller sequences.  For full information about these files, please visit NCBI. Below are the differences between the AGP versions 1.1 and 2.0.


The table below shows mappings between AGP 1.1 and AGP 2.0:

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
/linkage_evidence
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

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18 Aug 2014: Changes to SRA XML 1.5
Small changes to Experiment XML, Analysis XML, EGA Dataset XML, EGA DAC XMLs were deployed on 11th of August 2014.

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From 16th June 2014, the date format used in the advanced search will be changed to ISO format (YYYY-MM-DD).

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From 10th of June 2014 the ENA SAMPLE checklist XML will be updated and the older version will be deprecated.