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 WBIP_9K_Parents
Experiment 1Experiment 2matches to markers
between trials
WBIP_9K_Parents2020_NDSU_Eurofins5
WBIP_9K_Parents2018_CCRU_50K32
WBIP_9K_Parents2019_GBS_WBDC0
WBIP_9K_ParentsUMN_NSGC_GWAS14
WBIP_9K_Parents2015GBS_MN0
WBIP_9K_Parents2019N2YUMA3
WBIP_9K_Parents2015iSelect_MN_plate138
WBIP_9K_Parents2016GBS_WBDC0
WBIP_9K_Parents2018_NDSU_Yuma_2R3
WBIP_9K_Parents2017_NDSU_Yuma_2R4
WBIP_9K_Parents2016_N2_PYTBC2
WBIP_9K_Parents2016N2PYTA1
WBIP_9K_Parents2016_HapMap_WEC0
WBIP_9K_Parents2015N2PYT2
WBIP_9K_ParentsWBIP384_HOUH_20131
WBIP_9K_ParentsWBIP384_ABNAM_20121
WBIP_9K_Parents2014_NDSU_9K34
WBIP_9K_Parents2006BOPA1_UT_Plate615
WBIP_9K_ParentsBOPA1_MN_WB_201115
WBIP_9K_Parents9K_MN_GEN10_201341
WBIP_9K_Parents9K_MN_CAP6_201341
WBIP_9K_ParentsOWB_GBS_20120
WBIP_9K_ParentsWBIP_9K_Parents37
WBIP_9K_ParentsVC_MNWC4_2013_3843
WBIP_9K_ParentsTCFW6_LTT_9K37
WBIP_9K_ParentsEthiopia_Eritrea_9K38
WBIP_9K_ParentsVC_MNWC3_2013_3843
WBIP_9K_ParentsMorexBarke_GBS_20120
WBIP_9K_Parents2011BOPA1_MN_WC015
WBIP_9K_ParentsVC_MNWC2_2012_3843
WBIP_9K_ParentsVC_MNWC1_2011_3843
WBIP_9K_ParentsVC_MNSC3_2012_3840
WBIP_9K_ParentsVC_MNSC2_2011_3840
WBIP_9K_Parents2010BOPA1_MN_GS_PARENTS15
WBIP_9K_Parents2007BOPA1_MN_PRECAP15
WBIP_9K_ParentsVC_FHB2010_3840
WBIP_9K_ParentsCAPV2011_MN_9K35
WBIP_9K_Parents2011_9K_NB_allplates37
WBIP_9K_Parents2009BOPA2_AB_Plate55
WBIP_9K_Parents2009BOPA2_WA_Plate45
WBIP_9K_Parents2009BOPA2_VT_Plate15
WBIP_9K_Parents2009BOPA2_UT_Plate65
WBIP_9K_Parents2009BOPA2_OR_Plate20
WBIP_9K_Parents2009BOPA2_N6_Plate95
WBIP_9K_Parents2009BOPA2_N2_Plate85
WBIP_9K_Parents2009BOPA2_MT_Plate105
WBIP_9K_Parents2009BOPA2_MN_Plate30
WBIP_9K_Parents2009BOPA2_BA_Plate75
WBIP_9K_Parents2009BOPA1_WA_Plate415
WBIP_9K_Parents2009BOPA1_VT_Plate115
WBIP_9K_Parents2009BOPA1_UT_Plate615
WBIP_9K_Parents2009BOPA1_OR_Plate220
WBIP_9K_Parents2009BOPA1_N6_Plate915
WBIP_9K_Parents2009BOPA1_N2_Plate815
WBIP_9K_Parents2009BOPA1_MT_Plate1015
WBIP_9K_Parents2009BOPA1_MN_Plate320
WBIP_9K_Parents2009BOPA1_BA_Plate715
WBIP_9K_Parents2009BOPA1_AB_Plate515
WBIP_9K_Parents2006BOPA2_UT_Plate65
WBIP_9K_ParentsPOPA1_Steptoe_Morex_Mapping9
WBIP_9K_ParentsPOPA1_Oregon_Wolf_Barley_Mapping9
WBIP_9K_ParentsPOPA1_Morex-Barke_Mapping9
WBIP_9K_ParentsPOPA1-2_CAPcore9
WBIP_9K_Parents2008BOPA2_MT_Plate105
WBIP_9K_Parents2008BOPA1_MT_Plate1015
WBIP_9K_Parents2008BOPA2_WA_Plate45
WBIP_9K_Parents2008BOPA1_WA_Plate415
WBIP_9K_Parents2008BOPA2_VT_Plate15
WBIP_9K_Parents2008BOPA1_VT_Plate115
WBIP_9K_Parents2008BOPA2_UT_Plate65
WBIP_9K_Parents2008BOPA1_UT_Plate615
WBIP_9K_Parents2008BOPA2_OR_Plate25
WBIP_9K_Parents2008BOPA1_OR_Plate215
WBIP_9K_Parents2008BOPA2_N6_Plate95
WBIP_9K_Parents2008BOPA1_N6_Plate915
WBIP_9K_Parents2008BOPA2_N2_Plate85
WBIP_9K_Parents2008BOPA1_N2_Plate815
WBIP_9K_Parents2008BOPA2_MN_Plate35
WBIP_9K_Parents2008BOPA1_MN_Plate315
WBIP_9K_Parents2008BOPA2_BA_Plate75
WBIP_9K_Parents2008BOPA1_BA_Plate715
WBIP_9K_Parents2008BOPA2_AB_Plate55
WBIP_9K_Parents2008BOPA1_AB_Plate515
WBIP_9K_ParentsPOPA2_Steptoe-Morex_Mapping9
WBIP_9K_ParentsPOPA2_OWB_Mapping9
WBIP_9K_ParentsPOPA2_CAPcore9
WBIP_9K_ParentsPOPA2_Morex-Barke_Mapping9
WBIP_9K_ParentsPOPA3_Morex-Barke_Mapping2
WBIP_9K_ParentsPOPA3_Steptoe-Morex_Mapping2
WBIP_9K_ParentsPOPA3_OWB_Mapping2
WBIP_9K_ParentsPOPA3_CAPcore2
WBIP_9K_Parents2006BOPA2_OR_Plate25
WBIP_9K_Parents2007BOPA2_WA_Plate45
WBIP_9K_Parents2007BOPA2_VT_Plate15
WBIP_9K_Parents2007BOPA2_OR_Plate25
WBIP_9K_Parents2007BOPA2_N6_Plate95
WBIP_9K_Parents2007BOPA2_N2_Plate85
WBIP_9K_Parents2007BOPA2_MT_Plate105
WBIP_9K_Parents2007BOPA2_MN_Plate35
WBIP_9K_Parents2007BOPA2_BA_Plate75
WBIP_9K_Parents2007BOPA2_UT_Plate65
WBIP_9K_Parents2007BOPA2_AB_Plate55
WBIP_9K_Parents2007BOPA1_WA_Plate415
WBIP_9K_Parents2007BOPA1_VT_Plate115
WBIP_9K_Parents2007BOPA1_OR_Plate215
WBIP_9K_Parents2007BOPA1_N6_Plate915
WBIP_9K_Parents2007BOPA1_N2_Plate815
WBIP_9K_Parents2007BOPA1_MT_Plate1015
WBIP_9K_Parents2007BOPA1_MN_Plate315
WBIP_9K_Parents2007BOPA1_BA_Plate715
WBIP_9K_Parents2007BOPA1_UT_Plate615
WBIP_9K_Parents2007BOPA1_AB_Plate515
WBIP_9K_Parents2006BOPA2_WA_Plate45
WBIP_9K_Parents2006BOPA2_VT_Plate15
WBIP_9K_Parents2006BOPA2_N6_Plate95
WBIP_9K_Parents2006BOPA2_N2_Plate85
WBIP_9K_Parents2006BOPA2_MT_Plate105
WBIP_9K_Parents2006BOPA2_MN_Plate35
WBIP_9K_Parents2006BOPA2_BA_Plate75
WBIP_9K_Parents2006BOPA2_AB_Plate55
WBIP_9K_Parents2006BOPA1_WA_Plate415
WBIP_9K_Parents2006BOPA1_VT_Plate115
WBIP_9K_Parents2006BOPA1_OR_Plate215
WBIP_9K_Parents2006BOPA1_N6_Plate915
WBIP_9K_Parents2006BOPA1_N2_Plate815
WBIP_9K_Parents2006BOPA1_MT_Plate1015
WBIP_9K_Parents2006BOPA1_MN_Plate315
WBIP_9K_Parents2006BOPA1_BA_Plate715
WBIP_9K_Parents2006BOPA1_AB_Plate515

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.