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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 2009BOPA1_MN_Plate3
Experiment 1Experiment 2matches to markers
between trials
2009BOPA1_MN_Plate32020_NDSU_Eurofins5
2009BOPA1_MN_Plate32018_CCRU_50K18
2009BOPA1_MN_Plate32019_GBS_WBDC0
2009BOPA1_MN_Plate3UMN_NSGC_GWAS11
2009BOPA1_MN_Plate32015GBS_MN0
2009BOPA1_MN_Plate32019N2YUMA3
2009BOPA1_MN_Plate32015iSelect_MN_plate120
2009BOPA1_MN_Plate32016GBS_WBDC0
2009BOPA1_MN_Plate32018_NDSU_Yuma_2R3
2009BOPA1_MN_Plate32017_NDSU_Yuma_2R5
2009BOPA1_MN_Plate32016_N2_PYTBC3
2009BOPA1_MN_Plate32016N2PYTA2
2009BOPA1_MN_Plate32016_HapMap_WEC0
2009BOPA1_MN_Plate32015N2PYT3
2009BOPA1_MN_Plate3WBIP384_HOUH_20131
2009BOPA1_MN_Plate3WBIP384_ABNAM_20121
2009BOPA1_MN_Plate32014_NDSU_9K17
2009BOPA1_MN_Plate32006BOPA1_UT_Plate615
2009BOPA1_MN_Plate3BOPA1_MN_WB_201115
2009BOPA1_MN_Plate39K_MN_GEN10_201323
2009BOPA1_MN_Plate39K_MN_CAP6_201323
2009BOPA1_MN_Plate3OWB_GBS_20120
2009BOPA1_MN_Plate3WBIP_9K_Parents20
2009BOPA1_MN_Plate3VC_MNWC4_2013_3843
2009BOPA1_MN_Plate3TCFW6_LTT_9K20
2009BOPA1_MN_Plate3Ethiopia_Eritrea_9K21
2009BOPA1_MN_Plate3VC_MNWC3_2013_3843
2009BOPA1_MN_Plate3MorexBarke_GBS_20120
2009BOPA1_MN_Plate32011BOPA1_MN_WC015
2009BOPA1_MN_Plate3VC_MNWC2_2012_3843
2009BOPA1_MN_Plate3VC_MNWC1_2011_3843
2009BOPA1_MN_Plate3VC_MNSC3_2012_3840
2009BOPA1_MN_Plate3VC_MNSC2_2011_3840
2009BOPA1_MN_Plate32010BOPA1_MN_GS_PARENTS15
2009BOPA1_MN_Plate32007BOPA1_MN_PRECAP15
2009BOPA1_MN_Plate3VC_FHB2010_3840
2009BOPA1_MN_Plate3CAPV2011_MN_9K19
2009BOPA1_MN_Plate32011_9K_NB_allplates20
2009BOPA1_MN_Plate32009BOPA2_AB_Plate56
2009BOPA1_MN_Plate32009BOPA2_WA_Plate46
2009BOPA1_MN_Plate32009BOPA2_VT_Plate16
2009BOPA1_MN_Plate32009BOPA2_UT_Plate66
2009BOPA1_MN_Plate32009BOPA2_OR_Plate20
2009BOPA1_MN_Plate32009BOPA2_N6_Plate96
2009BOPA1_MN_Plate32009BOPA2_N2_Plate86
2009BOPA1_MN_Plate32009BOPA2_MT_Plate106
2009BOPA1_MN_Plate32009BOPA2_MN_Plate30
2009BOPA1_MN_Plate32009BOPA2_BA_Plate76
2009BOPA1_MN_Plate32009BOPA1_WA_Plate415
2009BOPA1_MN_Plate32009BOPA1_VT_Plate115
2009BOPA1_MN_Plate32009BOPA1_UT_Plate615
2009BOPA1_MN_Plate32009BOPA1_OR_Plate221
2009BOPA1_MN_Plate32009BOPA1_N6_Plate915
2009BOPA1_MN_Plate32009BOPA1_N2_Plate815
2009BOPA1_MN_Plate32009BOPA1_MT_Plate1015
2009BOPA1_MN_Plate32009BOPA1_MN_Plate321
2009BOPA1_MN_Plate32009BOPA1_BA_Plate715
2009BOPA1_MN_Plate32009BOPA1_AB_Plate515
2009BOPA1_MN_Plate32006BOPA2_UT_Plate66
2009BOPA1_MN_Plate3POPA1_Steptoe_Morex_Mapping11
2009BOPA1_MN_Plate3POPA1_Oregon_Wolf_Barley_Mapping11
2009BOPA1_MN_Plate3POPA1_Morex-Barke_Mapping11
2009BOPA1_MN_Plate3POPA1-2_CAPcore11
2009BOPA1_MN_Plate32008BOPA2_MT_Plate106
2009BOPA1_MN_Plate32008BOPA1_MT_Plate1015
2009BOPA1_MN_Plate32008BOPA2_WA_Plate46
2009BOPA1_MN_Plate32008BOPA1_WA_Plate415
2009BOPA1_MN_Plate32008BOPA2_VT_Plate16
2009BOPA1_MN_Plate32008BOPA1_VT_Plate115
2009BOPA1_MN_Plate32008BOPA2_UT_Plate66
2009BOPA1_MN_Plate32008BOPA1_UT_Plate615
2009BOPA1_MN_Plate32008BOPA2_OR_Plate26
2009BOPA1_MN_Plate32008BOPA1_OR_Plate215
2009BOPA1_MN_Plate32008BOPA2_N6_Plate96
2009BOPA1_MN_Plate32008BOPA1_N6_Plate915
2009BOPA1_MN_Plate32008BOPA2_N2_Plate86
2009BOPA1_MN_Plate32008BOPA1_N2_Plate815
2009BOPA1_MN_Plate32008BOPA2_MN_Plate36
2009BOPA1_MN_Plate32008BOPA1_MN_Plate315
2009BOPA1_MN_Plate32008BOPA2_BA_Plate76
2009BOPA1_MN_Plate32008BOPA1_BA_Plate715
2009BOPA1_MN_Plate32008BOPA2_AB_Plate56
2009BOPA1_MN_Plate32008BOPA1_AB_Plate515
2009BOPA1_MN_Plate3POPA2_Steptoe-Morex_Mapping9
2009BOPA1_MN_Plate3POPA2_OWB_Mapping9
2009BOPA1_MN_Plate3POPA2_CAPcore9
2009BOPA1_MN_Plate3POPA2_Morex-Barke_Mapping9
2009BOPA1_MN_Plate3POPA3_Morex-Barke_Mapping1
2009BOPA1_MN_Plate3POPA3_Steptoe-Morex_Mapping1
2009BOPA1_MN_Plate3POPA3_OWB_Mapping1
2009BOPA1_MN_Plate3POPA3_CAPcore1
2009BOPA1_MN_Plate32006BOPA2_OR_Plate26
2009BOPA1_MN_Plate32007BOPA2_WA_Plate46
2009BOPA1_MN_Plate32007BOPA2_VT_Plate16
2009BOPA1_MN_Plate32007BOPA2_OR_Plate26
2009BOPA1_MN_Plate32007BOPA2_N6_Plate96
2009BOPA1_MN_Plate32007BOPA2_N2_Plate86
2009BOPA1_MN_Plate32007BOPA2_MT_Plate106
2009BOPA1_MN_Plate32007BOPA2_MN_Plate36
2009BOPA1_MN_Plate32007BOPA2_BA_Plate76
2009BOPA1_MN_Plate32007BOPA2_UT_Plate66
2009BOPA1_MN_Plate32007BOPA2_AB_Plate56
2009BOPA1_MN_Plate32007BOPA1_WA_Plate415
2009BOPA1_MN_Plate32007BOPA1_VT_Plate115
2009BOPA1_MN_Plate32007BOPA1_OR_Plate215
2009BOPA1_MN_Plate32007BOPA1_N6_Plate915
2009BOPA1_MN_Plate32007BOPA1_N2_Plate815
2009BOPA1_MN_Plate32007BOPA1_MT_Plate1015
2009BOPA1_MN_Plate32007BOPA1_MN_Plate315
2009BOPA1_MN_Plate32007BOPA1_BA_Plate715
2009BOPA1_MN_Plate32007BOPA1_UT_Plate615
2009BOPA1_MN_Plate32007BOPA1_AB_Plate515
2009BOPA1_MN_Plate32006BOPA2_WA_Plate46
2009BOPA1_MN_Plate32006BOPA2_VT_Plate16
2009BOPA1_MN_Plate32006BOPA2_N6_Plate96
2009BOPA1_MN_Plate32006BOPA2_N2_Plate86
2009BOPA1_MN_Plate32006BOPA2_MT_Plate106
2009BOPA1_MN_Plate32006BOPA2_MN_Plate36
2009BOPA1_MN_Plate32006BOPA2_BA_Plate76
2009BOPA1_MN_Plate32006BOPA2_AB_Plate56
2009BOPA1_MN_Plate32006BOPA1_WA_Plate415
2009BOPA1_MN_Plate32006BOPA1_VT_Plate115
2009BOPA1_MN_Plate32006BOPA1_OR_Plate215
2009BOPA1_MN_Plate32006BOPA1_N6_Plate915
2009BOPA1_MN_Plate32006BOPA1_N2_Plate815
2009BOPA1_MN_Plate32006BOPA1_MT_Plate1015
2009BOPA1_MN_Plate32006BOPA1_MN_Plate315
2009BOPA1_MN_Plate32006BOPA1_BA_Plate715
2009BOPA1_MN_Plate32006BOPA1_AB_Plate515

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.