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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 POPA1_Oregon_Wolf_Barley_Mapping
Experiment 1Experiment 2matches to markers
between trials
POPA1_Oregon_Wolf_Barley_Mapping2020_NDSU_Eurofins1
POPA1_Oregon_Wolf_Barley_Mapping2018_CCRU_50K5
POPA1_Oregon_Wolf_Barley_Mapping2019_GBS_WBDC0
POPA1_Oregon_Wolf_Barley_MappingUMN_NSGC_GWAS4
POPA1_Oregon_Wolf_Barley_Mapping2015GBS_MN0
POPA1_Oregon_Wolf_Barley_Mapping2019N2YUMA1
POPA1_Oregon_Wolf_Barley_Mapping2015iSelect_MN_plate15
POPA1_Oregon_Wolf_Barley_Mapping2016GBS_WBDC0
POPA1_Oregon_Wolf_Barley_Mapping2018_NDSU_Yuma_2R1
POPA1_Oregon_Wolf_Barley_Mapping2017_NDSU_Yuma_2R1
POPA1_Oregon_Wolf_Barley_Mapping2016_N2_PYTBC1
POPA1_Oregon_Wolf_Barley_Mapping2016N2PYTA1
POPA1_Oregon_Wolf_Barley_Mapping2016_HapMap_WEC0
POPA1_Oregon_Wolf_Barley_Mapping2015N2PYT1
POPA1_Oregon_Wolf_Barley_MappingWBIP384_HOUH_20131
POPA1_Oregon_Wolf_Barley_MappingWBIP384_ABNAM_20121
POPA1_Oregon_Wolf_Barley_Mapping2014_NDSU_9K5
POPA1_Oregon_Wolf_Barley_Mapping2006BOPA1_UT_Plate64
POPA1_Oregon_Wolf_Barley_MappingBOPA1_MN_WB_20114
POPA1_Oregon_Wolf_Barley_Mapping9K_MN_GEN10_20138
POPA1_Oregon_Wolf_Barley_Mapping9K_MN_CAP6_20138
POPA1_Oregon_Wolf_Barley_MappingOWB_GBS_20120
POPA1_Oregon_Wolf_Barley_MappingWBIP_9K_Parents5
POPA1_Oregon_Wolf_Barley_MappingVC_MNWC4_2013_3841
POPA1_Oregon_Wolf_Barley_MappingTCFW6_LTT_9K5
POPA1_Oregon_Wolf_Barley_MappingEthiopia_Eritrea_9K7
POPA1_Oregon_Wolf_Barley_MappingVC_MNWC3_2013_3841
POPA1_Oregon_Wolf_Barley_MappingMorexBarke_GBS_20120
POPA1_Oregon_Wolf_Barley_Mapping2011BOPA1_MN_WC04
POPA1_Oregon_Wolf_Barley_MappingVC_MNWC2_2012_3841
POPA1_Oregon_Wolf_Barley_MappingVC_MNWC1_2011_3841
POPA1_Oregon_Wolf_Barley_MappingVC_MNSC3_2012_3840
POPA1_Oregon_Wolf_Barley_MappingVC_MNSC2_2011_3840
POPA1_Oregon_Wolf_Barley_Mapping2010BOPA1_MN_GS_PARENTS4
POPA1_Oregon_Wolf_Barley_Mapping2007BOPA1_MN_PRECAP4
POPA1_Oregon_Wolf_Barley_MappingVC_FHB2010_3840
POPA1_Oregon_Wolf_Barley_MappingCAPV2011_MN_9K5
POPA1_Oregon_Wolf_Barley_Mapping2011_9K_NB_allplates5
POPA1_Oregon_Wolf_Barley_Mapping2009BOPA2_AB_Plate54
POPA1_Oregon_Wolf_Barley_Mapping2009BOPA2_WA_Plate44
POPA1_Oregon_Wolf_Barley_Mapping2009BOPA2_VT_Plate14
POPA1_Oregon_Wolf_Barley_Mapping2009BOPA2_UT_Plate64
POPA1_Oregon_Wolf_Barley_Mapping2009BOPA2_OR_Plate20
POPA1_Oregon_Wolf_Barley_Mapping2009BOPA2_N6_Plate94
POPA1_Oregon_Wolf_Barley_Mapping2009BOPA2_N2_Plate84
POPA1_Oregon_Wolf_Barley_Mapping2009BOPA2_MT_Plate104
POPA1_Oregon_Wolf_Barley_Mapping2009BOPA2_MN_Plate30
POPA1_Oregon_Wolf_Barley_Mapping2009BOPA2_BA_Plate74
POPA1_Oregon_Wolf_Barley_Mapping2009BOPA1_WA_Plate44
POPA1_Oregon_Wolf_Barley_Mapping2009BOPA1_VT_Plate14
POPA1_Oregon_Wolf_Barley_Mapping2009BOPA1_UT_Plate64
POPA1_Oregon_Wolf_Barley_Mapping2009BOPA1_OR_Plate28
POPA1_Oregon_Wolf_Barley_Mapping2009BOPA1_N6_Plate94
POPA1_Oregon_Wolf_Barley_Mapping2009BOPA1_N2_Plate84
POPA1_Oregon_Wolf_Barley_Mapping2009BOPA1_MT_Plate104
POPA1_Oregon_Wolf_Barley_Mapping2009BOPA1_MN_Plate38
POPA1_Oregon_Wolf_Barley_Mapping2009BOPA1_BA_Plate74
POPA1_Oregon_Wolf_Barley_Mapping2009BOPA1_AB_Plate54
POPA1_Oregon_Wolf_Barley_Mapping2006BOPA2_UT_Plate64
POPA1_Oregon_Wolf_Barley_MappingPOPA1_Steptoe_Morex_Mapping4
POPA1_Oregon_Wolf_Barley_MappingPOPA1_Oregon_Wolf_Barley_Mapping4
POPA1_Oregon_Wolf_Barley_MappingPOPA1_Morex-Barke_Mapping4
POPA1_Oregon_Wolf_Barley_MappingPOPA1-2_CAPcore4
POPA1_Oregon_Wolf_Barley_Mapping2008BOPA2_MT_Plate104
POPA1_Oregon_Wolf_Barley_Mapping2008BOPA1_MT_Plate104
POPA1_Oregon_Wolf_Barley_Mapping2008BOPA2_WA_Plate44
POPA1_Oregon_Wolf_Barley_Mapping2008BOPA1_WA_Plate44
POPA1_Oregon_Wolf_Barley_Mapping2008BOPA2_VT_Plate14
POPA1_Oregon_Wolf_Barley_Mapping2008BOPA1_VT_Plate14
POPA1_Oregon_Wolf_Barley_Mapping2008BOPA2_UT_Plate64
POPA1_Oregon_Wolf_Barley_Mapping2008BOPA1_UT_Plate64
POPA1_Oregon_Wolf_Barley_Mapping2008BOPA2_OR_Plate24
POPA1_Oregon_Wolf_Barley_Mapping2008BOPA1_OR_Plate24
POPA1_Oregon_Wolf_Barley_Mapping2008BOPA2_N6_Plate94
POPA1_Oregon_Wolf_Barley_Mapping2008BOPA1_N6_Plate94
POPA1_Oregon_Wolf_Barley_Mapping2008BOPA2_N2_Plate84
POPA1_Oregon_Wolf_Barley_Mapping2008BOPA1_N2_Plate84
POPA1_Oregon_Wolf_Barley_Mapping2008BOPA2_MN_Plate34
POPA1_Oregon_Wolf_Barley_Mapping2008BOPA1_MN_Plate34
POPA1_Oregon_Wolf_Barley_Mapping2008BOPA2_BA_Plate74
POPA1_Oregon_Wolf_Barley_Mapping2008BOPA1_BA_Plate74
POPA1_Oregon_Wolf_Barley_Mapping2008BOPA2_AB_Plate54
POPA1_Oregon_Wolf_Barley_Mapping2008BOPA1_AB_Plate54
POPA1_Oregon_Wolf_Barley_MappingPOPA2_Steptoe-Morex_Mapping4
POPA1_Oregon_Wolf_Barley_MappingPOPA2_OWB_Mapping4
POPA1_Oregon_Wolf_Barley_MappingPOPA2_CAPcore4
POPA1_Oregon_Wolf_Barley_MappingPOPA2_Morex-Barke_Mapping4
POPA1_Oregon_Wolf_Barley_MappingPOPA3_Morex-Barke_Mapping0
POPA1_Oregon_Wolf_Barley_MappingPOPA3_Steptoe-Morex_Mapping0
POPA1_Oregon_Wolf_Barley_MappingPOPA3_OWB_Mapping0
POPA1_Oregon_Wolf_Barley_MappingPOPA3_CAPcore0
POPA1_Oregon_Wolf_Barley_Mapping2006BOPA2_OR_Plate24
POPA1_Oregon_Wolf_Barley_Mapping2007BOPA2_WA_Plate44
POPA1_Oregon_Wolf_Barley_Mapping2007BOPA2_VT_Plate14
POPA1_Oregon_Wolf_Barley_Mapping2007BOPA2_OR_Plate24
POPA1_Oregon_Wolf_Barley_Mapping2007BOPA2_N6_Plate94
POPA1_Oregon_Wolf_Barley_Mapping2007BOPA2_N2_Plate84
POPA1_Oregon_Wolf_Barley_Mapping2007BOPA2_MT_Plate104
POPA1_Oregon_Wolf_Barley_Mapping2007BOPA2_MN_Plate34
POPA1_Oregon_Wolf_Barley_Mapping2007BOPA2_BA_Plate74
POPA1_Oregon_Wolf_Barley_Mapping2007BOPA2_UT_Plate64
POPA1_Oregon_Wolf_Barley_Mapping2007BOPA2_AB_Plate54
POPA1_Oregon_Wolf_Barley_Mapping2007BOPA1_WA_Plate44
POPA1_Oregon_Wolf_Barley_Mapping2007BOPA1_VT_Plate14
POPA1_Oregon_Wolf_Barley_Mapping2007BOPA1_OR_Plate24
POPA1_Oregon_Wolf_Barley_Mapping2007BOPA1_N6_Plate94
POPA1_Oregon_Wolf_Barley_Mapping2007BOPA1_N2_Plate84
POPA1_Oregon_Wolf_Barley_Mapping2007BOPA1_MT_Plate104
POPA1_Oregon_Wolf_Barley_Mapping2007BOPA1_MN_Plate34
POPA1_Oregon_Wolf_Barley_Mapping2007BOPA1_BA_Plate74
POPA1_Oregon_Wolf_Barley_Mapping2007BOPA1_UT_Plate64
POPA1_Oregon_Wolf_Barley_Mapping2007BOPA1_AB_Plate54
POPA1_Oregon_Wolf_Barley_Mapping2006BOPA2_WA_Plate44
POPA1_Oregon_Wolf_Barley_Mapping2006BOPA2_VT_Plate14
POPA1_Oregon_Wolf_Barley_Mapping2006BOPA2_N6_Plate94
POPA1_Oregon_Wolf_Barley_Mapping2006BOPA2_N2_Plate84
POPA1_Oregon_Wolf_Barley_Mapping2006BOPA2_MT_Plate104
POPA1_Oregon_Wolf_Barley_Mapping2006BOPA2_MN_Plate34
POPA1_Oregon_Wolf_Barley_Mapping2006BOPA2_BA_Plate74
POPA1_Oregon_Wolf_Barley_Mapping2006BOPA2_AB_Plate54
POPA1_Oregon_Wolf_Barley_Mapping2006BOPA1_WA_Plate44
POPA1_Oregon_Wolf_Barley_Mapping2006BOPA1_VT_Plate14
POPA1_Oregon_Wolf_Barley_Mapping2006BOPA1_OR_Plate24
POPA1_Oregon_Wolf_Barley_Mapping2006BOPA1_N6_Plate94
POPA1_Oregon_Wolf_Barley_Mapping2006BOPA1_N2_Plate84
POPA1_Oregon_Wolf_Barley_Mapping2006BOPA1_MT_Plate104
POPA1_Oregon_Wolf_Barley_Mapping2006BOPA1_MN_Plate34
POPA1_Oregon_Wolf_Barley_Mapping2006BOPA1_BA_Plate74
POPA1_Oregon_Wolf_Barley_Mapping2006BOPA1_AB_Plate54

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.