Bacterial Contamination

At PlantGDB, efforts are undertaken to identify and remove all contaminant DNA so that a clean dataset is made available to researchers. Here, we use the Vmatch program (with options -d -p -l 50 -exdrop 1 -identity 90) to screen EST sequences against E. coli genomes for bacterial sequences contaminations. The table below summarizes the total count of "contamination".

To view a list of sequences flagged as contaminated, click on the number in the "Sequence Count" column.

Organism Contamination_Type Sequence Count
Spirogyra_pratensisBacteria25
Striga_hermonthicaBacteria76
Suaeda_glaucaBacteria1
Suaeda_salsaBacteria34
Syntrichia_ruralisBacteria22
Taiwania_cryptomerioidesBacteria2
Tamarix_androssowiiBacteria157
Tamarix_hispidaBacteria146
Taraxacum_kok_saghyzBacteria7
Taraxacum_officinaleBacteria4
Taxus_cuspidataBacteria3
Theobroma_cacaoBacteria383
Trifolium_pratenseBacteria99
Triphysaria_pusillaBacteria1
Triphysaria_versicolorBacteria2
Triticum_aestivumBacteria1363
Triticum_dicoccoidesBacteria338
Triticum_durumBacteria67
Triticum_monococcumBacteria13
Tropaeolum_majusBacteria8


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