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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 POPA2_Morex-Barke_Mapping
Experiment 1Experiment 2matches to markers
between trials
POPA2_Morex-Barke_Mapping2020_NDSU_Eurofins0
POPA2_Morex-Barke_Mapping2018_CCRU_50K4
POPA2_Morex-Barke_Mapping2019_GBS_WBDC0
POPA2_Morex-Barke_MappingUMN_NSGC_GWAS3
POPA2_Morex-Barke_Mapping2015GBS_MN0
POPA2_Morex-Barke_Mapping2019N2YUMA0
POPA2_Morex-Barke_Mapping2015iSelect_MN_plate15
POPA2_Morex-Barke_Mapping2016GBS_WBDC0
POPA2_Morex-Barke_Mapping2018_NDSU_Yuma_2R0
POPA2_Morex-Barke_Mapping2017_NDSU_Yuma_2R0
POPA2_Morex-Barke_Mapping2016_N2_PYTBC0
POPA2_Morex-Barke_Mapping2016N2PYTA0
POPA2_Morex-Barke_Mapping2016_HapMap_WEC0
POPA2_Morex-Barke_Mapping2015N2PYT0
POPA2_Morex-Barke_MappingWBIP384_HOUH_20130
POPA2_Morex-Barke_MappingWBIP384_ABNAM_20120
POPA2_Morex-Barke_Mapping2014_NDSU_9K4
POPA2_Morex-Barke_Mapping2006BOPA1_UT_Plate64
POPA2_Morex-Barke_MappingBOPA1_MN_WB_20114
POPA2_Morex-Barke_Mapping9K_MN_GEN10_20135
POPA2_Morex-Barke_Mapping9K_MN_CAP6_20135
POPA2_Morex-Barke_MappingOWB_GBS_20120
POPA2_Morex-Barke_MappingWBIP_9K_Parents5
POPA2_Morex-Barke_MappingVC_MNWC4_2013_3840
POPA2_Morex-Barke_MappingTCFW6_LTT_9K5
POPA2_Morex-Barke_MappingEthiopia_Eritrea_9K5
POPA2_Morex-Barke_MappingVC_MNWC3_2013_3840
POPA2_Morex-Barke_MappingMorexBarke_GBS_20120
POPA2_Morex-Barke_Mapping2011BOPA1_MN_WC04
POPA2_Morex-Barke_MappingVC_MNWC2_2012_3840
POPA2_Morex-Barke_MappingVC_MNWC1_2011_3840
POPA2_Morex-Barke_MappingVC_MNSC3_2012_3840
POPA2_Morex-Barke_MappingVC_MNSC2_2011_3840
POPA2_Morex-Barke_Mapping2010BOPA1_MN_GS_PARENTS4
POPA2_Morex-Barke_Mapping2007BOPA1_MN_PRECAP4
POPA2_Morex-Barke_MappingVC_FHB2010_3840
POPA2_Morex-Barke_MappingCAPV2011_MN_9K5
POPA2_Morex-Barke_Mapping2011_9K_NB_allplates5
POPA2_Morex-Barke_Mapping2009BOPA2_AB_Plate51
POPA2_Morex-Barke_Mapping2009BOPA2_WA_Plate41
POPA2_Morex-Barke_Mapping2009BOPA2_VT_Plate11
POPA2_Morex-Barke_Mapping2009BOPA2_UT_Plate61
POPA2_Morex-Barke_Mapping2009BOPA2_OR_Plate20
POPA2_Morex-Barke_Mapping2009BOPA2_N6_Plate91
POPA2_Morex-Barke_Mapping2009BOPA2_N2_Plate81
POPA2_Morex-Barke_Mapping2009BOPA2_MT_Plate101
POPA2_Morex-Barke_Mapping2009BOPA2_MN_Plate30
POPA2_Morex-Barke_Mapping2009BOPA2_BA_Plate71
POPA2_Morex-Barke_Mapping2009BOPA1_WA_Plate44
POPA2_Morex-Barke_Mapping2009BOPA1_VT_Plate14
POPA2_Morex-Barke_Mapping2009BOPA1_UT_Plate64
POPA2_Morex-Barke_Mapping2009BOPA1_OR_Plate25
POPA2_Morex-Barke_Mapping2009BOPA1_N6_Plate94
POPA2_Morex-Barke_Mapping2009BOPA1_N2_Plate84
POPA2_Morex-Barke_Mapping2009BOPA1_MT_Plate104
POPA2_Morex-Barke_Mapping2009BOPA1_MN_Plate35
POPA2_Morex-Barke_Mapping2009BOPA1_BA_Plate74
POPA2_Morex-Barke_Mapping2009BOPA1_AB_Plate54
POPA2_Morex-Barke_Mapping2006BOPA2_UT_Plate61
POPA2_Morex-Barke_MappingPOPA1_Steptoe_Morex_Mapping4
POPA2_Morex-Barke_MappingPOPA1_Oregon_Wolf_Barley_Mapping4
POPA2_Morex-Barke_MappingPOPA1_Morex-Barke_Mapping4
POPA2_Morex-Barke_MappingPOPA1-2_CAPcore4
POPA2_Morex-Barke_Mapping2008BOPA2_MT_Plate101
POPA2_Morex-Barke_Mapping2008BOPA1_MT_Plate104
POPA2_Morex-Barke_Mapping2008BOPA2_WA_Plate41
POPA2_Morex-Barke_Mapping2008BOPA1_WA_Plate44
POPA2_Morex-Barke_Mapping2008BOPA2_VT_Plate11
POPA2_Morex-Barke_Mapping2008BOPA1_VT_Plate14
POPA2_Morex-Barke_Mapping2008BOPA2_UT_Plate61
POPA2_Morex-Barke_Mapping2008BOPA1_UT_Plate64
POPA2_Morex-Barke_Mapping2008BOPA2_OR_Plate21
POPA2_Morex-Barke_Mapping2008BOPA1_OR_Plate24
POPA2_Morex-Barke_Mapping2008BOPA2_N6_Plate91
POPA2_Morex-Barke_Mapping2008BOPA1_N6_Plate94
POPA2_Morex-Barke_Mapping2008BOPA2_N2_Plate81
POPA2_Morex-Barke_Mapping2008BOPA1_N2_Plate84
POPA2_Morex-Barke_Mapping2008BOPA2_MN_Plate31
POPA2_Morex-Barke_Mapping2008BOPA1_MN_Plate34
POPA2_Morex-Barke_Mapping2008BOPA2_BA_Plate71
POPA2_Morex-Barke_Mapping2008BOPA1_BA_Plate74
POPA2_Morex-Barke_Mapping2008BOPA2_AB_Plate51
POPA2_Morex-Barke_Mapping2008BOPA1_AB_Plate54
POPA2_Morex-Barke_MappingPOPA2_Steptoe-Morex_Mapping0
POPA2_Morex-Barke_MappingPOPA2_OWB_Mapping0
POPA2_Morex-Barke_MappingPOPA2_CAPcore0
POPA2_Morex-Barke_MappingPOPA2_Morex-Barke_Mapping0
POPA2_Morex-Barke_MappingPOPA3_Morex-Barke_Mapping1
POPA2_Morex-Barke_MappingPOPA3_Steptoe-Morex_Mapping1
POPA2_Morex-Barke_MappingPOPA3_OWB_Mapping1
POPA2_Morex-Barke_MappingPOPA3_CAPcore1
POPA2_Morex-Barke_Mapping2006BOPA2_OR_Plate21
POPA2_Morex-Barke_Mapping2007BOPA2_WA_Plate41
POPA2_Morex-Barke_Mapping2007BOPA2_VT_Plate11
POPA2_Morex-Barke_Mapping2007BOPA2_OR_Plate21
POPA2_Morex-Barke_Mapping2007BOPA2_N6_Plate91
POPA2_Morex-Barke_Mapping2007BOPA2_N2_Plate81
POPA2_Morex-Barke_Mapping2007BOPA2_MT_Plate101
POPA2_Morex-Barke_Mapping2007BOPA2_MN_Plate31
POPA2_Morex-Barke_Mapping2007BOPA2_BA_Plate71
POPA2_Morex-Barke_Mapping2007BOPA2_UT_Plate61
POPA2_Morex-Barke_Mapping2007BOPA2_AB_Plate51
POPA2_Morex-Barke_Mapping2007BOPA1_WA_Plate44
POPA2_Morex-Barke_Mapping2007BOPA1_VT_Plate14
POPA2_Morex-Barke_Mapping2007BOPA1_OR_Plate24
POPA2_Morex-Barke_Mapping2007BOPA1_N6_Plate94
POPA2_Morex-Barke_Mapping2007BOPA1_N2_Plate84
POPA2_Morex-Barke_Mapping2007BOPA1_MT_Plate104
POPA2_Morex-Barke_Mapping2007BOPA1_MN_Plate34
POPA2_Morex-Barke_Mapping2007BOPA1_BA_Plate74
POPA2_Morex-Barke_Mapping2007BOPA1_UT_Plate64
POPA2_Morex-Barke_Mapping2007BOPA1_AB_Plate54
POPA2_Morex-Barke_Mapping2006BOPA2_WA_Plate41
POPA2_Morex-Barke_Mapping2006BOPA2_VT_Plate11
POPA2_Morex-Barke_Mapping2006BOPA2_N6_Plate91
POPA2_Morex-Barke_Mapping2006BOPA2_N2_Plate81
POPA2_Morex-Barke_Mapping2006BOPA2_MT_Plate101
POPA2_Morex-Barke_Mapping2006BOPA2_MN_Plate31
POPA2_Morex-Barke_Mapping2006BOPA2_BA_Plate71
POPA2_Morex-Barke_Mapping2006BOPA2_AB_Plate51
POPA2_Morex-Barke_Mapping2006BOPA1_WA_Plate44
POPA2_Morex-Barke_Mapping2006BOPA1_VT_Plate14
POPA2_Morex-Barke_Mapping2006BOPA1_OR_Plate24
POPA2_Morex-Barke_Mapping2006BOPA1_N6_Plate94
POPA2_Morex-Barke_Mapping2006BOPA1_N2_Plate84
POPA2_Morex-Barke_Mapping2006BOPA1_MT_Plate104
POPA2_Morex-Barke_Mapping2006BOPA1_MN_Plate34
POPA2_Morex-Barke_Mapping2006BOPA1_BA_Plate74
POPA2_Morex-Barke_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.