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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 2015N2PYT
Experiment 1Experiment 2matches to markers
between trials
2015N2PYT2020_NDSU_Eurofins0
2015N2PYT2018_CCRU_50K1
2015N2PYT2019_GBS_WBDC0
2015N2PYTUMN_NSGC_GWAS0
2015N2PYT2015GBS_MN0
2015N2PYT2019N2YUMA0
2015N2PYT2015iSelect_MN_plate11
2015N2PYT2016GBS_WBDC0
2015N2PYT2018_NDSU_Yuma_2R0
2015N2PYT2017_NDSU_Yuma_2R0
2015N2PYT2016_N2_PYTBC0
2015N2PYT2016N2PYTA0
2015N2PYT2016_HapMap_WEC0
2015N2PYT2015N2PYT0
2015N2PYTWBIP384_HOUH_20130
2015N2PYTWBIP384_ABNAM_20120
2015N2PYT2014_NDSU_9K1
2015N2PYT2006BOPA1_UT_Plate61
2015N2PYTBOPA1_MN_WB_20111
2015N2PYT9K_MN_GEN10_20131
2015N2PYT9K_MN_CAP6_20131
2015N2PYTOWB_GBS_20120
2015N2PYTWBIP_9K_Parents1
2015N2PYTVC_MNWC4_2013_3840
2015N2PYTTCFW6_LTT_9K1
2015N2PYTEthiopia_Eritrea_9K1
2015N2PYTVC_MNWC3_2013_3840
2015N2PYTMorexBarke_GBS_20120
2015N2PYT2011BOPA1_MN_WC01
2015N2PYTVC_MNWC2_2012_3840
2015N2PYTVC_MNWC1_2011_3840
2015N2PYTVC_MNSC3_2012_3840
2015N2PYTVC_MNSC2_2011_3840
2015N2PYT2010BOPA1_MN_GS_PARENTS1
2015N2PYT2007BOPA1_MN_PRECAP1
2015N2PYTVC_FHB2010_3840
2015N2PYTCAPV2011_MN_9K1
2015N2PYT2011_9K_NB_allplates1
2015N2PYT2009BOPA2_AB_Plate50
2015N2PYT2009BOPA2_WA_Plate40
2015N2PYT2009BOPA2_VT_Plate10
2015N2PYT2009BOPA2_UT_Plate60
2015N2PYT2009BOPA2_OR_Plate20
2015N2PYT2009BOPA2_N6_Plate90
2015N2PYT2009BOPA2_N2_Plate80
2015N2PYT2009BOPA2_MT_Plate100
2015N2PYT2009BOPA2_MN_Plate30
2015N2PYT2009BOPA2_BA_Plate70
2015N2PYT2009BOPA1_WA_Plate41
2015N2PYT2009BOPA1_VT_Plate11
2015N2PYT2009BOPA1_UT_Plate61
2015N2PYT2009BOPA1_OR_Plate21
2015N2PYT2009BOPA1_N6_Plate91
2015N2PYT2009BOPA1_N2_Plate81
2015N2PYT2009BOPA1_MT_Plate101
2015N2PYT2009BOPA1_MN_Plate31
2015N2PYT2009BOPA1_BA_Plate71
2015N2PYT2009BOPA1_AB_Plate51
2015N2PYT2006BOPA2_UT_Plate60
2015N2PYTPOPA1_Steptoe_Morex_Mapping1
2015N2PYTPOPA1_Oregon_Wolf_Barley_Mapping1
2015N2PYTPOPA1_Morex-Barke_Mapping1
2015N2PYTPOPA1-2_CAPcore1
2015N2PYT2008BOPA2_MT_Plate100
2015N2PYT2008BOPA1_MT_Plate101
2015N2PYT2008BOPA2_WA_Plate40
2015N2PYT2008BOPA1_WA_Plate41
2015N2PYT2008BOPA2_VT_Plate10
2015N2PYT2008BOPA1_VT_Plate11
2015N2PYT2008BOPA2_UT_Plate60
2015N2PYT2008BOPA1_UT_Plate61
2015N2PYT2008BOPA2_OR_Plate20
2015N2PYT2008BOPA1_OR_Plate21
2015N2PYT2008BOPA2_N6_Plate90
2015N2PYT2008BOPA1_N6_Plate91
2015N2PYT2008BOPA2_N2_Plate80
2015N2PYT2008BOPA1_N2_Plate81
2015N2PYT2008BOPA2_MN_Plate30
2015N2PYT2008BOPA1_MN_Plate31
2015N2PYT2008BOPA2_BA_Plate70
2015N2PYT2008BOPA1_BA_Plate71
2015N2PYT2008BOPA2_AB_Plate50
2015N2PYT2008BOPA1_AB_Plate51
2015N2PYTPOPA2_Steptoe-Morex_Mapping0
2015N2PYTPOPA2_OWB_Mapping0
2015N2PYTPOPA2_CAPcore0
2015N2PYTPOPA2_Morex-Barke_Mapping0
2015N2PYTPOPA3_Morex-Barke_Mapping0
2015N2PYTPOPA3_Steptoe-Morex_Mapping0
2015N2PYTPOPA3_OWB_Mapping0
2015N2PYTPOPA3_CAPcore0
2015N2PYT2006BOPA2_OR_Plate20
2015N2PYT2007BOPA2_WA_Plate40
2015N2PYT2007BOPA2_VT_Plate10
2015N2PYT2007BOPA2_OR_Plate20
2015N2PYT2007BOPA2_N6_Plate90
2015N2PYT2007BOPA2_N2_Plate80
2015N2PYT2007BOPA2_MT_Plate100
2015N2PYT2007BOPA2_MN_Plate30
2015N2PYT2007BOPA2_BA_Plate70
2015N2PYT2007BOPA2_UT_Plate60
2015N2PYT2007BOPA2_AB_Plate50
2015N2PYT2007BOPA1_WA_Plate41
2015N2PYT2007BOPA1_VT_Plate11
2015N2PYT2007BOPA1_OR_Plate21
2015N2PYT2007BOPA1_N6_Plate91
2015N2PYT2007BOPA1_N2_Plate81
2015N2PYT2007BOPA1_MT_Plate101
2015N2PYT2007BOPA1_MN_Plate31
2015N2PYT2007BOPA1_BA_Plate71
2015N2PYT2007BOPA1_UT_Plate61
2015N2PYT2007BOPA1_AB_Plate51
2015N2PYT2006BOPA2_WA_Plate40
2015N2PYT2006BOPA2_VT_Plate10
2015N2PYT2006BOPA2_N6_Plate90
2015N2PYT2006BOPA2_N2_Plate80
2015N2PYT2006BOPA2_MT_Plate100
2015N2PYT2006BOPA2_MN_Plate30
2015N2PYT2006BOPA2_BA_Plate70
2015N2PYT2006BOPA2_AB_Plate50
2015N2PYT2006BOPA1_WA_Plate41
2015N2PYT2006BOPA1_VT_Plate11
2015N2PYT2006BOPA1_OR_Plate21
2015N2PYT2006BOPA1_N6_Plate91
2015N2PYT2006BOPA1_N2_Plate81
2015N2PYT2006BOPA1_MT_Plate101
2015N2PYT2006BOPA1_MN_Plate31
2015N2PYT2006BOPA1_BA_Plate71
2015N2PYT2006BOPA1_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.