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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 2011_9K_NB_allplates
Experiment 1Experiment 2matches to markers
between trials
2011_9K_NB_allplates2020_NDSU_Eurofins5
2011_9K_NB_allplates2018_CCRU_50K31
2011_9K_NB_allplates2019_GBS_WBDC0
2011_9K_NB_allplatesUMN_NSGC_GWAS13
2011_9K_NB_allplates2015GBS_MN0
2011_9K_NB_allplates2019N2YUMA3
2011_9K_NB_allplates2015iSelect_MN_plate137
2011_9K_NB_allplates2016GBS_WBDC0
2011_9K_NB_allplates2018_NDSU_Yuma_2R3
2011_9K_NB_allplates2017_NDSU_Yuma_2R4
2011_9K_NB_allplates2016_N2_PYTBC2
2011_9K_NB_allplates2016N2PYTA1
2011_9K_NB_allplates2016_HapMap_WEC0
2011_9K_NB_allplates2015N2PYT2
2011_9K_NB_allplatesWBIP384_HOUH_20131
2011_9K_NB_allplatesWBIP384_ABNAM_20121
2011_9K_NB_allplates2014_NDSU_9K33
2011_9K_NB_allplates2006BOPA1_UT_Plate614
2011_9K_NB_allplatesBOPA1_MN_WB_201114
2011_9K_NB_allplates9K_MN_GEN10_201340
2011_9K_NB_allplates9K_MN_CAP6_201340
2011_9K_NB_allplatesOWB_GBS_20120
2011_9K_NB_allplatesWBIP_9K_Parents36
2011_9K_NB_allplatesVC_MNWC4_2013_3843
2011_9K_NB_allplatesTCFW6_LTT_9K36
2011_9K_NB_allplatesEthiopia_Eritrea_9K37
2011_9K_NB_allplatesVC_MNWC3_2013_3843
2011_9K_NB_allplatesMorexBarke_GBS_20120
2011_9K_NB_allplates2011BOPA1_MN_WC014
2011_9K_NB_allplatesVC_MNWC2_2012_3843
2011_9K_NB_allplatesVC_MNWC1_2011_3843
2011_9K_NB_allplatesVC_MNSC3_2012_3840
2011_9K_NB_allplatesVC_MNSC2_2011_3840
2011_9K_NB_allplates2010BOPA1_MN_GS_PARENTS14
2011_9K_NB_allplates2007BOPA1_MN_PRECAP14
2011_9K_NB_allplatesVC_FHB2010_3840
2011_9K_NB_allplatesCAPV2011_MN_9K34
2011_9K_NB_allplates2011_9K_NB_allplates36
2011_9K_NB_allplates2009BOPA2_AB_Plate55
2011_9K_NB_allplates2009BOPA2_WA_Plate45
2011_9K_NB_allplates2009BOPA2_VT_Plate15
2011_9K_NB_allplates2009BOPA2_UT_Plate65
2011_9K_NB_allplates2009BOPA2_OR_Plate20
2011_9K_NB_allplates2009BOPA2_N6_Plate95
2011_9K_NB_allplates2009BOPA2_N2_Plate85
2011_9K_NB_allplates2009BOPA2_MT_Plate105
2011_9K_NB_allplates2009BOPA2_MN_Plate30
2011_9K_NB_allplates2009BOPA2_BA_Plate75
2011_9K_NB_allplates2009BOPA1_WA_Plate414
2011_9K_NB_allplates2009BOPA1_VT_Plate114
2011_9K_NB_allplates2009BOPA1_UT_Plate614
2011_9K_NB_allplates2009BOPA1_OR_Plate219
2011_9K_NB_allplates2009BOPA1_N6_Plate914
2011_9K_NB_allplates2009BOPA1_N2_Plate814
2011_9K_NB_allplates2009BOPA1_MT_Plate1014
2011_9K_NB_allplates2009BOPA1_MN_Plate319
2011_9K_NB_allplates2009BOPA1_BA_Plate714
2011_9K_NB_allplates2009BOPA1_AB_Plate514
2011_9K_NB_allplates2006BOPA2_UT_Plate65
2011_9K_NB_allplatesPOPA1_Steptoe_Morex_Mapping8
2011_9K_NB_allplatesPOPA1_Oregon_Wolf_Barley_Mapping8
2011_9K_NB_allplatesPOPA1_Morex-Barke_Mapping8
2011_9K_NB_allplatesPOPA1-2_CAPcore8
2011_9K_NB_allplates2008BOPA2_MT_Plate105
2011_9K_NB_allplates2008BOPA1_MT_Plate1014
2011_9K_NB_allplates2008BOPA2_WA_Plate45
2011_9K_NB_allplates2008BOPA1_WA_Plate414
2011_9K_NB_allplates2008BOPA2_VT_Plate15
2011_9K_NB_allplates2008BOPA1_VT_Plate114
2011_9K_NB_allplates2008BOPA2_UT_Plate65
2011_9K_NB_allplates2008BOPA1_UT_Plate614
2011_9K_NB_allplates2008BOPA2_OR_Plate25
2011_9K_NB_allplates2008BOPA1_OR_Plate214
2011_9K_NB_allplates2008BOPA2_N6_Plate95
2011_9K_NB_allplates2008BOPA1_N6_Plate914
2011_9K_NB_allplates2008BOPA2_N2_Plate85
2011_9K_NB_allplates2008BOPA1_N2_Plate814
2011_9K_NB_allplates2008BOPA2_MN_Plate35
2011_9K_NB_allplates2008BOPA1_MN_Plate314
2011_9K_NB_allplates2008BOPA2_BA_Plate75
2011_9K_NB_allplates2008BOPA1_BA_Plate714
2011_9K_NB_allplates2008BOPA2_AB_Plate55
2011_9K_NB_allplates2008BOPA1_AB_Plate514
2011_9K_NB_allplatesPOPA2_Steptoe-Morex_Mapping9
2011_9K_NB_allplatesPOPA2_OWB_Mapping9
2011_9K_NB_allplatesPOPA2_CAPcore9
2011_9K_NB_allplatesPOPA2_Morex-Barke_Mapping9
2011_9K_NB_allplatesPOPA3_Morex-Barke_Mapping2
2011_9K_NB_allplatesPOPA3_Steptoe-Morex_Mapping2
2011_9K_NB_allplatesPOPA3_OWB_Mapping2
2011_9K_NB_allplatesPOPA3_CAPcore2
2011_9K_NB_allplates2006BOPA2_OR_Plate25
2011_9K_NB_allplates2007BOPA2_WA_Plate45
2011_9K_NB_allplates2007BOPA2_VT_Plate15
2011_9K_NB_allplates2007BOPA2_OR_Plate25
2011_9K_NB_allplates2007BOPA2_N6_Plate95
2011_9K_NB_allplates2007BOPA2_N2_Plate85
2011_9K_NB_allplates2007BOPA2_MT_Plate105
2011_9K_NB_allplates2007BOPA2_MN_Plate35
2011_9K_NB_allplates2007BOPA2_BA_Plate75
2011_9K_NB_allplates2007BOPA2_UT_Plate65
2011_9K_NB_allplates2007BOPA2_AB_Plate55
2011_9K_NB_allplates2007BOPA1_WA_Plate414
2011_9K_NB_allplates2007BOPA1_VT_Plate114
2011_9K_NB_allplates2007BOPA1_OR_Plate214
2011_9K_NB_allplates2007BOPA1_N6_Plate914
2011_9K_NB_allplates2007BOPA1_N2_Plate814
2011_9K_NB_allplates2007BOPA1_MT_Plate1014
2011_9K_NB_allplates2007BOPA1_MN_Plate314
2011_9K_NB_allplates2007BOPA1_BA_Plate714
2011_9K_NB_allplates2007BOPA1_UT_Plate614
2011_9K_NB_allplates2007BOPA1_AB_Plate514
2011_9K_NB_allplates2006BOPA2_WA_Plate45
2011_9K_NB_allplates2006BOPA2_VT_Plate15
2011_9K_NB_allplates2006BOPA2_N6_Plate95
2011_9K_NB_allplates2006BOPA2_N2_Plate85
2011_9K_NB_allplates2006BOPA2_MT_Plate105
2011_9K_NB_allplates2006BOPA2_MN_Plate35
2011_9K_NB_allplates2006BOPA2_BA_Plate75
2011_9K_NB_allplates2006BOPA2_AB_Plate55
2011_9K_NB_allplates2006BOPA1_WA_Plate414
2011_9K_NB_allplates2006BOPA1_VT_Plate114
2011_9K_NB_allplates2006BOPA1_OR_Plate214
2011_9K_NB_allplates2006BOPA1_N6_Plate914
2011_9K_NB_allplates2006BOPA1_N2_Plate814
2011_9K_NB_allplates2006BOPA1_MT_Plate1014
2011_9K_NB_allplates2006BOPA1_MN_Plate314
2011_9K_NB_allplates2006BOPA1_BA_Plate714
2011_9K_NB_allplates2006BOPA1_AB_Plate514

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.