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  T3 Barley Sandbox

Marker Synonyms Report

BLAST Analysis: This analysis uses BLAST to find markers within the Triticeae Toolbox database that have similar sequence. A marker is identified as a match if either
1. the sequence homology is > 99% and alignment length is > 95% of the query sequence.
2. there is only one mismatch and the alignment length is > 95% of the query sequence.
The analysis uses blastn v2.2.28+ with the following arguments "-outfmt 6 -dust no -word_size 16 -task megablast -evalue 1e-08". The top level page gives a summary of the matching markers for each experiment. Select the experiment link to give the second level of a detailed comparison for one experiment. Select the "match to other markers" to get the list of individual BLAST results. Reference: BLAST Help

Included Data: GBS markers that are already anchored to the reference genome (labeled as WCSS1) where not analyzed. The BLAST database included all markers loaded in T3 as or April 26, 2015.

Interpretation: The blast hits between a marker and itself have been removed. When an experiment is compared to itself you will still see a small number of matches because the markers may match within the experiment. Before 2013 the markers were checked for sequence matches when imported and if a match was found a synonym was created. For the large GBS experiments the marker sequence was not checked for sequence matches to the existing database of markers.

BLAST matches for experiment 2006BOPA1_AB_Plate5
Experiment 1Experiment 2matches to markers
between trials
2006BOPA1_AB_Plate52020_NDSU_Eurofins0
2006BOPA1_AB_Plate52018_CCRU_50K1
2006BOPA1_AB_Plate52019_GBS_WBDC0
2006BOPA1_AB_Plate5UMN_NSGC_GWAS1
2006BOPA1_AB_Plate52015GBS_MN0
2006BOPA1_AB_Plate52019N2YUMA0
2006BOPA1_AB_Plate52015iSelect_MN_plate11
2006BOPA1_AB_Plate52016GBS_WBDC0
2006BOPA1_AB_Plate52018_NDSU_Yuma_2R0
2006BOPA1_AB_Plate52017_NDSU_Yuma_2R0
2006BOPA1_AB_Plate52016_N2_PYTBC0
2006BOPA1_AB_Plate52016N2PYTA0
2006BOPA1_AB_Plate52016_HapMap_WEC0
2006BOPA1_AB_Plate52015N2PYT0
2006BOPA1_AB_Plate5WBIP384_HOUH_20130
2006BOPA1_AB_Plate5WBIP384_ABNAM_20120
2006BOPA1_AB_Plate52014_NDSU_9K1
2006BOPA1_AB_Plate52006BOPA1_UT_Plate62
2006BOPA1_AB_Plate5BOPA1_MN_WB_20112
2006BOPA1_AB_Plate59K_MN_GEN10_20132
2006BOPA1_AB_Plate59K_MN_CAP6_20132
2006BOPA1_AB_Plate5OWB_GBS_20120
2006BOPA1_AB_Plate5WBIP_9K_Parents1
2006BOPA1_AB_Plate5VC_MNWC4_2013_3840
2006BOPA1_AB_Plate5TCFW6_LTT_9K1
2006BOPA1_AB_Plate5Ethiopia_Eritrea_9K1
2006BOPA1_AB_Plate5VC_MNWC3_2013_3840
2006BOPA1_AB_Plate5MorexBarke_GBS_20120
2006BOPA1_AB_Plate52011BOPA1_MN_WC02
2006BOPA1_AB_Plate5VC_MNWC2_2012_3840
2006BOPA1_AB_Plate5VC_MNWC1_2011_3840
2006BOPA1_AB_Plate5VC_MNSC3_2012_3840
2006BOPA1_AB_Plate5VC_MNSC2_2011_3840
2006BOPA1_AB_Plate52010BOPA1_MN_GS_PARENTS2
2006BOPA1_AB_Plate52007BOPA1_MN_PRECAP2
2006BOPA1_AB_Plate5VC_FHB2010_3840
2006BOPA1_AB_Plate5CAPV2011_MN_9K1
2006BOPA1_AB_Plate52011_9K_NB_allplates1
2006BOPA1_AB_Plate52009BOPA2_AB_Plate50
2006BOPA1_AB_Plate52009BOPA2_WA_Plate40
2006BOPA1_AB_Plate52009BOPA2_VT_Plate10
2006BOPA1_AB_Plate52009BOPA2_UT_Plate60
2006BOPA1_AB_Plate52009BOPA2_OR_Plate20
2006BOPA1_AB_Plate52009BOPA2_N6_Plate90
2006BOPA1_AB_Plate52009BOPA2_N2_Plate80
2006BOPA1_AB_Plate52009BOPA2_MT_Plate100
2006BOPA1_AB_Plate52009BOPA2_MN_Plate30
2006BOPA1_AB_Plate52009BOPA2_BA_Plate70
2006BOPA1_AB_Plate52009BOPA1_WA_Plate42
2006BOPA1_AB_Plate52009BOPA1_VT_Plate12
2006BOPA1_AB_Plate52009BOPA1_UT_Plate62
2006BOPA1_AB_Plate52009BOPA1_OR_Plate22
2006BOPA1_AB_Plate52009BOPA1_N6_Plate92
2006BOPA1_AB_Plate52009BOPA1_N2_Plate82
2006BOPA1_AB_Plate52009BOPA1_MT_Plate102
2006BOPA1_AB_Plate52009BOPA1_MN_Plate32
2006BOPA1_AB_Plate52009BOPA1_BA_Plate72
2006BOPA1_AB_Plate52009BOPA1_AB_Plate52
2006BOPA1_AB_Plate52006BOPA2_UT_Plate60
2006BOPA1_AB_Plate5POPA1_Steptoe_Morex_Mapping1
2006BOPA1_AB_Plate5POPA1_Oregon_Wolf_Barley_Mapping1
2006BOPA1_AB_Plate5POPA1_Morex-Barke_Mapping1
2006BOPA1_AB_Plate5POPA1-2_CAPcore1
2006BOPA1_AB_Plate52008BOPA2_MT_Plate100
2006BOPA1_AB_Plate52008BOPA1_MT_Plate102
2006BOPA1_AB_Plate52008BOPA2_WA_Plate40
2006BOPA1_AB_Plate52008BOPA1_WA_Plate42
2006BOPA1_AB_Plate52008BOPA2_VT_Plate10
2006BOPA1_AB_Plate52008BOPA1_VT_Plate12
2006BOPA1_AB_Plate52008BOPA2_UT_Plate60
2006BOPA1_AB_Plate52008BOPA1_UT_Plate62
2006BOPA1_AB_Plate52008BOPA2_OR_Plate20
2006BOPA1_AB_Plate52008BOPA1_OR_Plate22
2006BOPA1_AB_Plate52008BOPA2_N6_Plate90
2006BOPA1_AB_Plate52008BOPA1_N6_Plate92
2006BOPA1_AB_Plate52008BOPA2_N2_Plate80
2006BOPA1_AB_Plate52008BOPA1_N2_Plate82
2006BOPA1_AB_Plate52008BOPA2_MN_Plate30
2006BOPA1_AB_Plate52008BOPA1_MN_Plate32
2006BOPA1_AB_Plate52008BOPA2_BA_Plate70
2006BOPA1_AB_Plate52008BOPA1_BA_Plate72
2006BOPA1_AB_Plate52008BOPA2_AB_Plate50
2006BOPA1_AB_Plate52008BOPA1_AB_Plate52
2006BOPA1_AB_Plate5POPA2_Steptoe-Morex_Mapping1
2006BOPA1_AB_Plate5POPA2_OWB_Mapping1
2006BOPA1_AB_Plate5POPA2_CAPcore1
2006BOPA1_AB_Plate5POPA2_Morex-Barke_Mapping1
2006BOPA1_AB_Plate5POPA3_Morex-Barke_Mapping0
2006BOPA1_AB_Plate5POPA3_Steptoe-Morex_Mapping0
2006BOPA1_AB_Plate5POPA3_OWB_Mapping0
2006BOPA1_AB_Plate5POPA3_CAPcore0
2006BOPA1_AB_Plate52006BOPA2_OR_Plate20
2006BOPA1_AB_Plate52007BOPA2_WA_Plate40
2006BOPA1_AB_Plate52007BOPA2_VT_Plate10
2006BOPA1_AB_Plate52007BOPA2_OR_Plate20
2006BOPA1_AB_Plate52007BOPA2_N6_Plate90
2006BOPA1_AB_Plate52007BOPA2_N2_Plate80
2006BOPA1_AB_Plate52007BOPA2_MT_Plate100
2006BOPA1_AB_Plate52007BOPA2_MN_Plate30
2006BOPA1_AB_Plate52007BOPA2_BA_Plate70
2006BOPA1_AB_Plate52007BOPA2_UT_Plate60
2006BOPA1_AB_Plate52007BOPA2_AB_Plate50
2006BOPA1_AB_Plate52007BOPA1_WA_Plate42
2006BOPA1_AB_Plate52007BOPA1_VT_Plate12
2006BOPA1_AB_Plate52007BOPA1_OR_Plate22
2006BOPA1_AB_Plate52007BOPA1_N6_Plate92
2006BOPA1_AB_Plate52007BOPA1_N2_Plate82
2006BOPA1_AB_Plate52007BOPA1_MT_Plate102
2006BOPA1_AB_Plate52007BOPA1_MN_Plate32
2006BOPA1_AB_Plate52007BOPA1_BA_Plate72
2006BOPA1_AB_Plate52007BOPA1_UT_Plate62
2006BOPA1_AB_Plate52007BOPA1_AB_Plate52
2006BOPA1_AB_Plate52006BOPA2_WA_Plate40
2006BOPA1_AB_Plate52006BOPA2_VT_Plate10
2006BOPA1_AB_Plate52006BOPA2_N6_Plate90
2006BOPA1_AB_Plate52006BOPA2_N2_Plate80
2006BOPA1_AB_Plate52006BOPA2_MT_Plate100
2006BOPA1_AB_Plate52006BOPA2_MN_Plate30
2006BOPA1_AB_Plate52006BOPA2_BA_Plate70
2006BOPA1_AB_Plate52006BOPA2_AB_Plate50
2006BOPA1_AB_Plate52006BOPA1_WA_Plate42
2006BOPA1_AB_Plate52006BOPA1_VT_Plate12
2006BOPA1_AB_Plate52006BOPA1_OR_Plate22
2006BOPA1_AB_Plate52006BOPA1_N6_Plate92
2006BOPA1_AB_Plate52006BOPA1_N2_Plate82
2006BOPA1_AB_Plate52006BOPA1_MT_Plate102
2006BOPA1_AB_Plate52006BOPA1_MN_Plate32
2006BOPA1_AB_Plate52006BOPA1_BA_Plate72
2006BOPA1_AB_Plate52006BOPA1_AB_Plate52

In 2009 the Toronto International Data Release Workshop agreed on a policy statement about prepublication data sharing. Accordingly, the data producers are making many of the datasets in T3 available prior to publication of a global analysis. Guidelines for appropriate sharing of these data are given in the excerpt from the Toronto Statement

I agree to the Data Usage Policy as specified in Toronto Statement.