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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 WBIP384_HOUH_2013
Experiment 1Experiment 2matches to markers
between trials
WBIP384_HOUH_20132020_NDSU_Eurofins1
WBIP384_HOUH_20132018_CCRU_50K0
WBIP384_HOUH_20132019_GBS_WBDC0
WBIP384_HOUH_2013UMN_NSGC_GWAS0
WBIP384_HOUH_20132015GBS_MN0
WBIP384_HOUH_20132019N2YUMA0
WBIP384_HOUH_20132015iSelect_MN_plate11
WBIP384_HOUH_20132016GBS_WBDC0
WBIP384_HOUH_20132018_NDSU_Yuma_2R0
WBIP384_HOUH_20132017_NDSU_Yuma_2R1
WBIP384_HOUH_20132016_N2_PYTBC0
WBIP384_HOUH_20132016N2PYTA0
WBIP384_HOUH_20132016_HapMap_WEC0
WBIP384_HOUH_20132015N2PYT0
WBIP384_HOUH_2013WBIP384_HOUH_20130
WBIP384_HOUH_2013WBIP384_ABNAM_20120
WBIP384_HOUH_20132014_NDSU_9K1
WBIP384_HOUH_20132006BOPA1_UT_Plate61
WBIP384_HOUH_2013BOPA1_MN_WB_20111
WBIP384_HOUH_20139K_MN_GEN10_20131
WBIP384_HOUH_20139K_MN_CAP6_20131
WBIP384_HOUH_2013OWB_GBS_20120
WBIP384_HOUH_2013WBIP_9K_Parents1
WBIP384_HOUH_2013VC_MNWC4_2013_3840
WBIP384_HOUH_2013TCFW6_LTT_9K1
WBIP384_HOUH_2013Ethiopia_Eritrea_9K1
WBIP384_HOUH_2013VC_MNWC3_2013_3840
WBIP384_HOUH_2013MorexBarke_GBS_20120
WBIP384_HOUH_20132011BOPA1_MN_WC01
WBIP384_HOUH_2013VC_MNWC2_2012_3840
WBIP384_HOUH_2013VC_MNWC1_2011_3840
WBIP384_HOUH_2013VC_MNSC3_2012_3840
WBIP384_HOUH_2013VC_MNSC2_2011_3840
WBIP384_HOUH_20132010BOPA1_MN_GS_PARENTS1
WBIP384_HOUH_20132007BOPA1_MN_PRECAP1
WBIP384_HOUH_2013VC_FHB2010_3840
WBIP384_HOUH_2013CAPV2011_MN_9K1
WBIP384_HOUH_20132011_9K_NB_allplates1
WBIP384_HOUH_20132009BOPA2_AB_Plate50
WBIP384_HOUH_20132009BOPA2_WA_Plate40
WBIP384_HOUH_20132009BOPA2_VT_Plate10
WBIP384_HOUH_20132009BOPA2_UT_Plate60
WBIP384_HOUH_20132009BOPA2_OR_Plate20
WBIP384_HOUH_20132009BOPA2_N6_Plate90
WBIP384_HOUH_20132009BOPA2_N2_Plate80
WBIP384_HOUH_20132009BOPA2_MT_Plate100
WBIP384_HOUH_20132009BOPA2_MN_Plate30
WBIP384_HOUH_20132009BOPA2_BA_Plate70
WBIP384_HOUH_20132009BOPA1_WA_Plate41
WBIP384_HOUH_20132009BOPA1_VT_Plate11
WBIP384_HOUH_20132009BOPA1_UT_Plate61
WBIP384_HOUH_20132009BOPA1_OR_Plate21
WBIP384_HOUH_20132009BOPA1_N6_Plate91
WBIP384_HOUH_20132009BOPA1_N2_Plate81
WBIP384_HOUH_20132009BOPA1_MT_Plate101
WBIP384_HOUH_20132009BOPA1_MN_Plate31
WBIP384_HOUH_20132009BOPA1_BA_Plate71
WBIP384_HOUH_20132009BOPA1_AB_Plate51
WBIP384_HOUH_20132006BOPA2_UT_Plate60
WBIP384_HOUH_2013POPA1_Steptoe_Morex_Mapping1
WBIP384_HOUH_2013POPA1_Oregon_Wolf_Barley_Mapping1
WBIP384_HOUH_2013POPA1_Morex-Barke_Mapping1
WBIP384_HOUH_2013POPA1-2_CAPcore1
WBIP384_HOUH_20132008BOPA2_MT_Plate100
WBIP384_HOUH_20132008BOPA1_MT_Plate101
WBIP384_HOUH_20132008BOPA2_WA_Plate40
WBIP384_HOUH_20132008BOPA1_WA_Plate41
WBIP384_HOUH_20132008BOPA2_VT_Plate10
WBIP384_HOUH_20132008BOPA1_VT_Plate11
WBIP384_HOUH_20132008BOPA2_UT_Plate60
WBIP384_HOUH_20132008BOPA1_UT_Plate61
WBIP384_HOUH_20132008BOPA2_OR_Plate20
WBIP384_HOUH_20132008BOPA1_OR_Plate21
WBIP384_HOUH_20132008BOPA2_N6_Plate90
WBIP384_HOUH_20132008BOPA1_N6_Plate91
WBIP384_HOUH_20132008BOPA2_N2_Plate80
WBIP384_HOUH_20132008BOPA1_N2_Plate81
WBIP384_HOUH_20132008BOPA2_MN_Plate30
WBIP384_HOUH_20132008BOPA1_MN_Plate31
WBIP384_HOUH_20132008BOPA2_BA_Plate70
WBIP384_HOUH_20132008BOPA1_BA_Plate71
WBIP384_HOUH_20132008BOPA2_AB_Plate50
WBIP384_HOUH_20132008BOPA1_AB_Plate51
WBIP384_HOUH_2013POPA2_Steptoe-Morex_Mapping0
WBIP384_HOUH_2013POPA2_OWB_Mapping0
WBIP384_HOUH_2013POPA2_CAPcore0
WBIP384_HOUH_2013POPA2_Morex-Barke_Mapping0
WBIP384_HOUH_2013POPA3_Morex-Barke_Mapping0
WBIP384_HOUH_2013POPA3_Steptoe-Morex_Mapping0
WBIP384_HOUH_2013POPA3_OWB_Mapping0
WBIP384_HOUH_2013POPA3_CAPcore0
WBIP384_HOUH_20132006BOPA2_OR_Plate20
WBIP384_HOUH_20132007BOPA2_WA_Plate40
WBIP384_HOUH_20132007BOPA2_VT_Plate10
WBIP384_HOUH_20132007BOPA2_OR_Plate20
WBIP384_HOUH_20132007BOPA2_N6_Plate90
WBIP384_HOUH_20132007BOPA2_N2_Plate80
WBIP384_HOUH_20132007BOPA2_MT_Plate100
WBIP384_HOUH_20132007BOPA2_MN_Plate30
WBIP384_HOUH_20132007BOPA2_BA_Plate70
WBIP384_HOUH_20132007BOPA2_UT_Plate60
WBIP384_HOUH_20132007BOPA2_AB_Plate50
WBIP384_HOUH_20132007BOPA1_WA_Plate41
WBIP384_HOUH_20132007BOPA1_VT_Plate11
WBIP384_HOUH_20132007BOPA1_OR_Plate21
WBIP384_HOUH_20132007BOPA1_N6_Plate91
WBIP384_HOUH_20132007BOPA1_N2_Plate81
WBIP384_HOUH_20132007BOPA1_MT_Plate101
WBIP384_HOUH_20132007BOPA1_MN_Plate31
WBIP384_HOUH_20132007BOPA1_BA_Plate71
WBIP384_HOUH_20132007BOPA1_UT_Plate61
WBIP384_HOUH_20132007BOPA1_AB_Plate51
WBIP384_HOUH_20132006BOPA2_WA_Plate40
WBIP384_HOUH_20132006BOPA2_VT_Plate10
WBIP384_HOUH_20132006BOPA2_N6_Plate90
WBIP384_HOUH_20132006BOPA2_N2_Plate80
WBIP384_HOUH_20132006BOPA2_MT_Plate100
WBIP384_HOUH_20132006BOPA2_MN_Plate30
WBIP384_HOUH_20132006BOPA2_BA_Plate70
WBIP384_HOUH_20132006BOPA2_AB_Plate50
WBIP384_HOUH_20132006BOPA1_WA_Plate41
WBIP384_HOUH_20132006BOPA1_VT_Plate11
WBIP384_HOUH_20132006BOPA1_OR_Plate21
WBIP384_HOUH_20132006BOPA1_N6_Plate91
WBIP384_HOUH_20132006BOPA1_N2_Plate81
WBIP384_HOUH_20132006BOPA1_MT_Plate101
WBIP384_HOUH_20132006BOPA1_MN_Plate31
WBIP384_HOUH_20132006BOPA1_BA_Plate71
WBIP384_HOUH_20132006BOPA1_AB_Plate51

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.