Schema for Augustus Genes (BUSCO) - Augustus Gene Predictions with BUSCO Training Set
  Database: DereCAF1    Primary Table: augustusBUSCO    Row Count: 12,717   Data last updated: 2022-10-20
fieldexampleSQL type info
bin 585smallint(5) unsigned range
name scaffold_1230.g19.t1varchar(255) values
chrom scaffold_1230varchar(255) values
strand -char(1) values
txStart 0int(10) unsigned range
txEnd 638int(10) unsigned range
cdsStart 0int(10) unsigned range
cdsEnd 638int(10) unsigned range
exonCount 3int(10) unsigned range
exonStarts 0,250,423,longblob  
exonEnds 193,367,638,longblob  
score 0int(11) range
name2 scaffold_1230.g19varchar(255) values
cdsStartStat unkenum('none', 'unk', 'incmpl', 'cmpl') values
cdsEndStat unkenum('none', 'unk', 'incmpl', 'cmpl') values
exonFrames 2,2,0,longblob  

Sample Rows
 
binnamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEndsscorename2cdsStartStatcdsEndStatexonFrames
585scaffold_1230.g19.t1scaffold_1230-0638063830,250,423,193,367,638,0scaffold_1230.g19unkunk2,2,0,
585scaffold_1240.g18.t1scaffold_1240-396141239614121396,1412,0scaffold_1240.g18unkunk2,
585scaffold_1246.g25.t1scaffold_1246+330111333011131330,1113,0scaffold_1246.g25unkunk0,
585scaffold_1247.g8.t1scaffold_1247-012330123320,325,275,1233,0scaffold_1247.g8unkunk0,1,
585scaffold_1251.g28.t1scaffold_1251+758147575814752758,1217,1136,1475,0scaffold_1251.g28unkunk0,0,
585scaffold_1255.g6.t1scaffold_1255+1159001159002115,411,322,900,0scaffold_1255.g6unkunk0,0,
585scaffold_1259.g10.t1scaffold_1259-012990129920,993,220,1299,0scaffold_1259.g10unkunk2,2,
585scaffold_1260.g7.t1scaffold_1260+010550105510,1055,0scaffold_1260.g7unkunk2,
585scaffold_1264.g31.t1scaffold_1264+153308215330822153,2608,936,3082,0scaffold_1264.g31unkunk0,0,
585scaffold_1286.g2.t1scaffold_1286+0759075920,522,467,759,0scaffold_1286.g2unkunk1,0,

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

Augustus Genes (BUSCO) (augustusBUSCO) Track Description
 

Description

This track shows the gene models from the Augustus gene predictor using the species-specific parameters estimated from a training set produced by BUSCO.

Methods

The training set used to estimate the species-specific parameters for the Augustus analysis was produced by BUSCO using the arthropoda_odb9 dataset.

Transposons remnants identified by RepeatMasker were provided as hints to the Augustus gene predictor. The following additional parameters were used with the Augustus gene predictor:

  --strand=both
  --noInFrameStop=true
  --gff3=on
  --uniqueGeneId=true
  --protein=off
  --codingseq=off
  --introns=off
  --stop=off
  --cds=on
  --singlestrand=false
  --UTR=off
  --genemodel=partial

References

Stanke M, Waack S. Gene prediction with a hidden Markov model and a new intron submodel. Bioinformatics. 2003 Oct;19 Suppl 2:ii215-25.

Simão FA, Waterhouse RM, Ioannidis P, Kriventseva EV, Zdobnov EM. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics. 2015 Oct 1;31(19):3210-2.