Vector 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 UniVec for vector contaminations . The table below summarizes the total count of "vector contamination".
To view a list of sequences flagged as contaminated, click on the number in the "Sequence Count" column.
| Organism | Contamination_Type | Sequence Count |
|---|---|---|
| Eucalyptus_globulus | Vector | 16 |
| Eucalyptus_globulus_subsp__bicostata | Vector | 118 |
| Eucalyptus_grandis | Vector | 213 |
| Eucalyptus_gunnii | Vector | 967 |
| Eucalyptus_tereticornis | Vector | 3 |
| Eulaliopsis_binata | Vector | 4 |
| Euonymus_alatus | Vector | 94 |
| Euphorbia_esula | Vector | 266 |
| Euphorbia_lagascae | Vector | 3 |
| Euphorbia_tirucalli | Vector | 1 |
| Eutrema_halophilum | Vector | 331 |
| Eutrema_salsugineum | Vector | 86 |
| Fagopyrum_tataricum | Vector | 1 |
| Fagus_sylvatica | Vector | 229 |
| Festuca_arundinacea | Vector | 646 |
| Festuca_pratensis | Vector | 2695 |
| Festuca_rubra_subsp__commutata | Vector | 2 |
| Ficus_elastica | Vector | 453 |
| Fragaria_chiloensis | Vector | 1 |
| Fragaria_vesca | Vector | 92 |
| Fragaria_vesca_subsp__vesca | Vector | 87 |
| Fragaria_x_ananassa | Vector | 40 |
| Fraxinus_excelsior | Vector | 6 |
| Fritillaria_cirrhosa | Vector | 5 |
| Garcinia_mangostana | Vector | 4 |
| Geranium_dissectum | Vector | 2 |
| Gerbera_hybrid_cultivar | Vector | 354 |
| Gevuina_avellana | Vector | 1 |
| Ginkgo_biloba | Vector | 1023 |
| Glycine_clandestina | Vector | 1 |
| Glycine_max | Vector | 9446 |
| Glycine_soja | Vector | 97 |
| Glycyrrhiza_uralensis | Vector | 7 |
| Gnetum_gnemon | Vector | 77 |
| Gossypium_arboreum | Vector | 452 |
| Gossypium_barbadense | Vector | 335 |
| Gossypium_hirsutum | Vector | 5050 |
| Gossypium_raimondii | Vector | 333 |
| Guizotia_abyssinica | Vector | 11 |
| Gypsophila_perfoliata | Vector | 3 |
| Haberlea_rhodopensis | Vector | 2 |
| Haematococcus_pluvialis | Vector | 1 |
| Hedera_helix | Vector | 22 |
| Hedyotis_terminalis | Vector | 283 |
| Helianthus_annuus | Vector | 141 |
| Helianthus_argophyllus | Vector | 2 |
| Helianthus_ciliaris | Vector | 3 |
| Helianthus_exilis | Vector | 2 |
| Helianthus_maximiliani | Vector | 1 |
| Helianthus_paradoxus | Vector | 1 |
| Helianthus_petiolaris | Vector | 4 |
| Helianthus_tuberosus | Vector | 5 |
| Helicosporidium_sp__ex_Simulium_jonesi | Vector | 33 |
| Hevea_brasiliensis | Vector | 756 |
| Hieracium_piloselloides | Vector | 1 |
| Hordeum_vulgare | Vector | 445 |
| Hordeum_vulgare_subsp__vulgare | Vector | 2917 |
| Humulus_lupulus | Vector | 34 |
| Huperzia_serrata | Vector | 6 |
| Hydrilla_verticillata | Vector | 2 |
| Hypericum_hookerianum | Vector | 3 |
| Ipomoea_batatas | Vector | 1292 |
| Ipomoea_nil | Vector | 7 |
| Ipomoea_trifida | Vector | 12 |
| Ipomopsis_aggregata | Vector | 140 |
| Iris_brevicaulis | Vector | 56 |
| Iris_fulva | Vector | 26 |
| Iris_x_hollandica | Vector | 2 |
| Jatropha_curcas | Vector | 142 |
| Juglans_hindsii_x_Juglans_regia | Vector | 579 |
| Juglans_regia | Vector | 117 |
| Kadua_centranthoides | Vector | 413 |
| Kalanchoe_x_houghtonii | Vector | 54 |
| Kalidium_foliatum | Vector | 1 |
| Karelinia_caspia | Vector | 1 |
| Klebsormidium_subtile | Vector | 150 |
| Knorringia_sibirica | Vector | 16 |
| Lablab_purpureus | Vector | 2 |
| Lactuca_perennis | Vector | 4 |
| Lactuca_saligna | Vector | 4 |
| Lactuca_sativa | Vector | 19 |
| Lactuca_serriola | Vector | 9 |
| Lactuca_virosa | Vector | 4 |
| Larix_kaempferi | Vector | 1 |
| Lathyrus_odoratus | Vector | 12 |
| Lathyrus_sativus | Vector | 36 |
| Lens_culinaris | Vector | 7 |
| Lepidium_latifolium | Vector | 2 |
| Lepidium_sativum | Vector | 1 |
| Leucaena_leucocephala | Vector | 1 |
| Leymus_chinensis | Vector | 26 |
| Leymus_cinereus_x_Leymus_triticoides | Vector | 47 |
| Leymus_mollis | Vector | 3 |
| Lilium_davidii_var__willmottiae | Vector | 1 |
| Lilium_formosanum | Vector | 58 |
| Lilium_hybrid_division_VII | Vector | 3 |
| Lilium_longiflorum | Vector | 4 |
| Lilium_regale | Vector | 1 |
| Limnanthes_alba | Vector | 1254 |
| Limonium_bicolor | Vector | 1056 |