Contact Us

  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 POPA1-2_CAPcore
Experiment 1Experiment 2matches to markers
between trials
POPA1-2_CAPcore2020_NDSU_Eurofins1
POPA1-2_CAPcore2018_CCRU_50K5
POPA1-2_CAPcore2019_GBS_WBDC0
POPA1-2_CAPcoreUMN_NSGC_GWAS4
POPA1-2_CAPcore2015GBS_MN0
POPA1-2_CAPcore2019N2YUMA1
POPA1-2_CAPcore2015iSelect_MN_plate15
POPA1-2_CAPcore2016GBS_WBDC0
POPA1-2_CAPcore2018_NDSU_Yuma_2R1
POPA1-2_CAPcore2017_NDSU_Yuma_2R1
POPA1-2_CAPcore2016_N2_PYTBC1
POPA1-2_CAPcore2016N2PYTA1
POPA1-2_CAPcore2016_HapMap_WEC0
POPA1-2_CAPcore2015N2PYT1
POPA1-2_CAPcoreWBIP384_HOUH_20131
POPA1-2_CAPcoreWBIP384_ABNAM_20121
POPA1-2_CAPcore2014_NDSU_9K5
POPA1-2_CAPcore2006BOPA1_UT_Plate64
POPA1-2_CAPcoreBOPA1_MN_WB_20114
POPA1-2_CAPcore9K_MN_GEN10_20138
POPA1-2_CAPcore9K_MN_CAP6_20138
POPA1-2_CAPcoreOWB_GBS_20120
POPA1-2_CAPcoreWBIP_9K_Parents5
POPA1-2_CAPcoreVC_MNWC4_2013_3841
POPA1-2_CAPcoreTCFW6_LTT_9K5
POPA1-2_CAPcoreEthiopia_Eritrea_9K7
POPA1-2_CAPcoreVC_MNWC3_2013_3841
POPA1-2_CAPcoreMorexBarke_GBS_20120
POPA1-2_CAPcore2011BOPA1_MN_WC04
POPA1-2_CAPcoreVC_MNWC2_2012_3841
POPA1-2_CAPcoreVC_MNWC1_2011_3841
POPA1-2_CAPcoreVC_MNSC3_2012_3840
POPA1-2_CAPcoreVC_MNSC2_2011_3840
POPA1-2_CAPcore2010BOPA1_MN_GS_PARENTS4
POPA1-2_CAPcore2007BOPA1_MN_PRECAP4
POPA1-2_CAPcoreVC_FHB2010_3840
POPA1-2_CAPcoreCAPV2011_MN_9K5
POPA1-2_CAPcore2011_9K_NB_allplates5
POPA1-2_CAPcore2009BOPA2_AB_Plate54
POPA1-2_CAPcore2009BOPA2_WA_Plate44
POPA1-2_CAPcore2009BOPA2_VT_Plate14
POPA1-2_CAPcore2009BOPA2_UT_Plate64
POPA1-2_CAPcore2009BOPA2_OR_Plate20
POPA1-2_CAPcore2009BOPA2_N6_Plate94
POPA1-2_CAPcore2009BOPA2_N2_Plate84
POPA1-2_CAPcore2009BOPA2_MT_Plate104
POPA1-2_CAPcore2009BOPA2_MN_Plate30
POPA1-2_CAPcore2009BOPA2_BA_Plate74
POPA1-2_CAPcore2009BOPA1_WA_Plate44
POPA1-2_CAPcore2009BOPA1_VT_Plate14
POPA1-2_CAPcore2009BOPA1_UT_Plate64
POPA1-2_CAPcore2009BOPA1_OR_Plate28
POPA1-2_CAPcore2009BOPA1_N6_Plate94
POPA1-2_CAPcore2009BOPA1_N2_Plate84
POPA1-2_CAPcore2009BOPA1_MT_Plate104
POPA1-2_CAPcore2009BOPA1_MN_Plate38
POPA1-2_CAPcore2009BOPA1_BA_Plate74
POPA1-2_CAPcore2009BOPA1_AB_Plate54
POPA1-2_CAPcore2006BOPA2_UT_Plate64
POPA1-2_CAPcorePOPA1_Steptoe_Morex_Mapping4
POPA1-2_CAPcorePOPA1_Oregon_Wolf_Barley_Mapping4
POPA1-2_CAPcorePOPA1_Morex-Barke_Mapping4
POPA1-2_CAPcorePOPA1-2_CAPcore4
POPA1-2_CAPcore2008BOPA2_MT_Plate104
POPA1-2_CAPcore2008BOPA1_MT_Plate104
POPA1-2_CAPcore2008BOPA2_WA_Plate44
POPA1-2_CAPcore2008BOPA1_WA_Plate44
POPA1-2_CAPcore2008BOPA2_VT_Plate14
POPA1-2_CAPcore2008BOPA1_VT_Plate14
POPA1-2_CAPcore2008BOPA2_UT_Plate64
POPA1-2_CAPcore2008BOPA1_UT_Plate64
POPA1-2_CAPcore2008BOPA2_OR_Plate24
POPA1-2_CAPcore2008BOPA1_OR_Plate24
POPA1-2_CAPcore2008BOPA2_N6_Plate94
POPA1-2_CAPcore2008BOPA1_N6_Plate94
POPA1-2_CAPcore2008BOPA2_N2_Plate84
POPA1-2_CAPcore2008BOPA1_N2_Plate84
POPA1-2_CAPcore2008BOPA2_MN_Plate34
POPA1-2_CAPcore2008BOPA1_MN_Plate34
POPA1-2_CAPcore2008BOPA2_BA_Plate74
POPA1-2_CAPcore2008BOPA1_BA_Plate74
POPA1-2_CAPcore2008BOPA2_AB_Plate54
POPA1-2_CAPcore2008BOPA1_AB_Plate54
POPA1-2_CAPcorePOPA2_Steptoe-Morex_Mapping4
POPA1-2_CAPcorePOPA2_OWB_Mapping4
POPA1-2_CAPcorePOPA2_CAPcore4
POPA1-2_CAPcorePOPA2_Morex-Barke_Mapping4
POPA1-2_CAPcorePOPA3_Morex-Barke_Mapping0
POPA1-2_CAPcorePOPA3_Steptoe-Morex_Mapping0
POPA1-2_CAPcorePOPA3_OWB_Mapping0
POPA1-2_CAPcorePOPA3_CAPcore0
POPA1-2_CAPcore2006BOPA2_OR_Plate24
POPA1-2_CAPcore2007BOPA2_WA_Plate44
POPA1-2_CAPcore2007BOPA2_VT_Plate14
POPA1-2_CAPcore2007BOPA2_OR_Plate24
POPA1-2_CAPcore2007BOPA2_N6_Plate94
POPA1-2_CAPcore2007BOPA2_N2_Plate84
POPA1-2_CAPcore2007BOPA2_MT_Plate104
POPA1-2_CAPcore2007BOPA2_MN_Plate34
POPA1-2_CAPcore2007BOPA2_BA_Plate74
POPA1-2_CAPcore2007BOPA2_UT_Plate64
POPA1-2_CAPcore2007BOPA2_AB_Plate54
POPA1-2_CAPcore2007BOPA1_WA_Plate44
POPA1-2_CAPcore2007BOPA1_VT_Plate14
POPA1-2_CAPcore2007BOPA1_OR_Plate24
POPA1-2_CAPcore2007BOPA1_N6_Plate94
POPA1-2_CAPcore2007BOPA1_N2_Plate84
POPA1-2_CAPcore2007BOPA1_MT_Plate104
POPA1-2_CAPcore2007BOPA1_MN_Plate34
POPA1-2_CAPcore2007BOPA1_BA_Plate74
POPA1-2_CAPcore2007BOPA1_UT_Plate64
POPA1-2_CAPcore2007BOPA1_AB_Plate54
POPA1-2_CAPcore2006BOPA2_WA_Plate44
POPA1-2_CAPcore2006BOPA2_VT_Plate14
POPA1-2_CAPcore2006BOPA2_N6_Plate94
POPA1-2_CAPcore2006BOPA2_N2_Plate84
POPA1-2_CAPcore2006BOPA2_MT_Plate104
POPA1-2_CAPcore2006BOPA2_MN_Plate34
POPA1-2_CAPcore2006BOPA2_BA_Plate74
POPA1-2_CAPcore2006BOPA2_AB_Plate54
POPA1-2_CAPcore2006BOPA1_WA_Plate44
POPA1-2_CAPcore2006BOPA1_VT_Plate14
POPA1-2_CAPcore2006BOPA1_OR_Plate24
POPA1-2_CAPcore2006BOPA1_N6_Plate94
POPA1-2_CAPcore2006BOPA1_N2_Plate84
POPA1-2_CAPcore2006BOPA1_MT_Plate104
POPA1-2_CAPcore2006BOPA1_MN_Plate34
POPA1-2_CAPcore2006BOPA1_BA_Plate74
POPA1-2_CAPcore2006BOPA1_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.