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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 UMN_NSGC_GWAS
Experiment 1Experiment 2matches to markers
between trials
UMN_NSGC_GWAS2020_NDSU_Eurofins3
UMN_NSGC_GWAS2018_CCRU_50K10
UMN_NSGC_GWAS2019_GBS_WBDC0
UMN_NSGC_GWASUMN_NSGC_GWAS2
UMN_NSGC_GWAS2015GBS_MN0
UMN_NSGC_GWAS2019N2YUMA2
UMN_NSGC_GWAS2015iSelect_MN_plate113
UMN_NSGC_GWAS2016GBS_WBDC0
UMN_NSGC_GWAS2018_NDSU_Yuma_2R2
UMN_NSGC_GWAS2017_NDSU_Yuma_2R2
UMN_NSGC_GWAS2016_N2_PYTBC1
UMN_NSGC_GWAS2016N2PYTA0
UMN_NSGC_GWAS2016_HapMap_WEC0
UMN_NSGC_GWAS2015N2PYT1
UMN_NSGC_GWASWBIP384_HOUH_20130
UMN_NSGC_GWASWBIP384_ABNAM_20120
UMN_NSGC_GWAS2014_NDSU_9K12
UMN_NSGC_GWAS2006BOPA1_UT_Plate68
UMN_NSGC_GWASBOPA1_MN_WB_20118
UMN_NSGC_GWAS9K_MN_GEN10_201315
UMN_NSGC_GWAS9K_MN_CAP6_201315
UMN_NSGC_GWASOWB_GBS_20120
UMN_NSGC_GWASWBIP_9K_Parents13
UMN_NSGC_GWASVC_MNWC4_2013_3840
UMN_NSGC_GWASTCFW6_LTT_9K13
UMN_NSGC_GWASEthiopia_Eritrea_9K14
UMN_NSGC_GWASVC_MNWC3_2013_3840
UMN_NSGC_GWASMorexBarke_GBS_20120
UMN_NSGC_GWAS2011BOPA1_MN_WC08
UMN_NSGC_GWASVC_MNWC2_2012_3840
UMN_NSGC_GWASVC_MNWC1_2011_3840
UMN_NSGC_GWASVC_MNSC3_2012_3840
UMN_NSGC_GWASVC_MNSC2_2011_3840
UMN_NSGC_GWAS2010BOPA1_MN_GS_PARENTS8
UMN_NSGC_GWAS2007BOPA1_MN_PRECAP8
UMN_NSGC_GWASVC_FHB2010_3840
UMN_NSGC_GWASCAPV2011_MN_9K13
UMN_NSGC_GWAS2011_9K_NB_allplates13
UMN_NSGC_GWAS2009BOPA2_AB_Plate53
UMN_NSGC_GWAS2009BOPA2_WA_Plate43
UMN_NSGC_GWAS2009BOPA2_VT_Plate13
UMN_NSGC_GWAS2009BOPA2_UT_Plate63
UMN_NSGC_GWAS2009BOPA2_OR_Plate20
UMN_NSGC_GWAS2009BOPA2_N6_Plate93
UMN_NSGC_GWAS2009BOPA2_N2_Plate83
UMN_NSGC_GWAS2009BOPA2_MT_Plate103
UMN_NSGC_GWAS2009BOPA2_MN_Plate30
UMN_NSGC_GWAS2009BOPA2_BA_Plate73
UMN_NSGC_GWAS2009BOPA1_WA_Plate48
UMN_NSGC_GWAS2009BOPA1_VT_Plate18
UMN_NSGC_GWAS2009BOPA1_UT_Plate68
UMN_NSGC_GWAS2009BOPA1_OR_Plate211
UMN_NSGC_GWAS2009BOPA1_N6_Plate98
UMN_NSGC_GWAS2009BOPA1_N2_Plate88
UMN_NSGC_GWAS2009BOPA1_MT_Plate108
UMN_NSGC_GWAS2009BOPA1_MN_Plate311
UMN_NSGC_GWAS2009BOPA1_BA_Plate78
UMN_NSGC_GWAS2009BOPA1_AB_Plate58
UMN_NSGC_GWAS2006BOPA2_UT_Plate63
UMN_NSGC_GWASPOPA1_Steptoe_Morex_Mapping6
UMN_NSGC_GWASPOPA1_Oregon_Wolf_Barley_Mapping6
UMN_NSGC_GWASPOPA1_Morex-Barke_Mapping6
UMN_NSGC_GWASPOPA1-2_CAPcore6
UMN_NSGC_GWAS2008BOPA2_MT_Plate103
UMN_NSGC_GWAS2008BOPA1_MT_Plate108
UMN_NSGC_GWAS2008BOPA2_WA_Plate43
UMN_NSGC_GWAS2008BOPA1_WA_Plate48
UMN_NSGC_GWAS2008BOPA2_VT_Plate13
UMN_NSGC_GWAS2008BOPA1_VT_Plate18
UMN_NSGC_GWAS2008BOPA2_UT_Plate63
UMN_NSGC_GWAS2008BOPA1_UT_Plate68
UMN_NSGC_GWAS2008BOPA2_OR_Plate23
UMN_NSGC_GWAS2008BOPA1_OR_Plate28
UMN_NSGC_GWAS2008BOPA2_N6_Plate93
UMN_NSGC_GWAS2008BOPA1_N6_Plate98
UMN_NSGC_GWAS2008BOPA2_N2_Plate83
UMN_NSGC_GWAS2008BOPA1_N2_Plate88
UMN_NSGC_GWAS2008BOPA2_MN_Plate33
UMN_NSGC_GWAS2008BOPA1_MN_Plate38
UMN_NSGC_GWAS2008BOPA2_BA_Plate73
UMN_NSGC_GWAS2008BOPA1_BA_Plate78
UMN_NSGC_GWAS2008BOPA2_AB_Plate53
UMN_NSGC_GWAS2008BOPA1_AB_Plate58
UMN_NSGC_GWASPOPA2_Steptoe-Morex_Mapping4
UMN_NSGC_GWASPOPA2_OWB_Mapping4
UMN_NSGC_GWASPOPA2_CAPcore4
UMN_NSGC_GWASPOPA2_Morex-Barke_Mapping4
UMN_NSGC_GWASPOPA3_Morex-Barke_Mapping1
UMN_NSGC_GWASPOPA3_Steptoe-Morex_Mapping1
UMN_NSGC_GWASPOPA3_OWB_Mapping1
UMN_NSGC_GWASPOPA3_CAPcore1
UMN_NSGC_GWAS2006BOPA2_OR_Plate23
UMN_NSGC_GWAS2007BOPA2_WA_Plate43
UMN_NSGC_GWAS2007BOPA2_VT_Plate13
UMN_NSGC_GWAS2007BOPA2_OR_Plate23
UMN_NSGC_GWAS2007BOPA2_N6_Plate93
UMN_NSGC_GWAS2007BOPA2_N2_Plate83
UMN_NSGC_GWAS2007BOPA2_MT_Plate103
UMN_NSGC_GWAS2007BOPA2_MN_Plate33
UMN_NSGC_GWAS2007BOPA2_BA_Plate73
UMN_NSGC_GWAS2007BOPA2_UT_Plate63
UMN_NSGC_GWAS2007BOPA2_AB_Plate53
UMN_NSGC_GWAS2007BOPA1_WA_Plate48
UMN_NSGC_GWAS2007BOPA1_VT_Plate18
UMN_NSGC_GWAS2007BOPA1_OR_Plate28
UMN_NSGC_GWAS2007BOPA1_N6_Plate98
UMN_NSGC_GWAS2007BOPA1_N2_Plate88
UMN_NSGC_GWAS2007BOPA1_MT_Plate108
UMN_NSGC_GWAS2007BOPA1_MN_Plate38
UMN_NSGC_GWAS2007BOPA1_BA_Plate78
UMN_NSGC_GWAS2007BOPA1_UT_Plate68
UMN_NSGC_GWAS2007BOPA1_AB_Plate58
UMN_NSGC_GWAS2006BOPA2_WA_Plate43
UMN_NSGC_GWAS2006BOPA2_VT_Plate13
UMN_NSGC_GWAS2006BOPA2_N6_Plate93
UMN_NSGC_GWAS2006BOPA2_N2_Plate83
UMN_NSGC_GWAS2006BOPA2_MT_Plate103
UMN_NSGC_GWAS2006BOPA2_MN_Plate33
UMN_NSGC_GWAS2006BOPA2_BA_Plate73
UMN_NSGC_GWAS2006BOPA2_AB_Plate53
UMN_NSGC_GWAS2006BOPA1_WA_Plate48
UMN_NSGC_GWAS2006BOPA1_VT_Plate18
UMN_NSGC_GWAS2006BOPA1_OR_Plate28
UMN_NSGC_GWAS2006BOPA1_N6_Plate98
UMN_NSGC_GWAS2006BOPA1_N2_Plate88
UMN_NSGC_GWAS2006BOPA1_MT_Plate108
UMN_NSGC_GWAS2006BOPA1_MN_Plate38
UMN_NSGC_GWAS2006BOPA1_BA_Plate78
UMN_NSGC_GWAS2006BOPA1_AB_Plate58

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.