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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 2018_CCRU_50K
Experiment 1Experiment 2matches to markers
between trials
2018_CCRU_50K2020_NDSU_Eurofins4
2018_CCRU_50K2018_CCRU_50K26
2018_CCRU_50K2019_GBS_WBDC0
2018_CCRU_50KUMN_NSGC_GWAS9
2018_CCRU_50K2015GBS_MN0
2018_CCRU_50K2019N2YUMA2
2018_CCRU_50K2015iSelect_MN_plate132
2018_CCRU_50K2016GBS_WBDC0
2018_CCRU_50K2018_NDSU_Yuma_2R2
2018_CCRU_50K2017_NDSU_Yuma_2R3
2018_CCRU_50K2016_N2_PYTBC1
2018_CCRU_50K2016N2PYTA0
2018_CCRU_50K2016_HapMap_WEC0
2018_CCRU_50K2015N2PYT1
2018_CCRU_50KWBIP384_HOUH_20131
2018_CCRU_50KWBIP384_ABNAM_20121
2018_CCRU_50K2014_NDSU_9K28
2018_CCRU_50K2006BOPA1_UT_Plate612
2018_CCRU_50KBOPA1_MN_WB_201112
2018_CCRU_50K9K_MN_GEN10_201335
2018_CCRU_50K9K_MN_CAP6_201335
2018_CCRU_50KOWB_GBS_20120
2018_CCRU_50KWBIP_9K_Parents31
2018_CCRU_50KVC_MNWC4_2013_3842
2018_CCRU_50KTCFW6_LTT_9K31
2018_CCRU_50KEthiopia_Eritrea_9K32
2018_CCRU_50KVC_MNWC3_2013_3842
2018_CCRU_50KMorexBarke_GBS_20120
2018_CCRU_50K2011BOPA1_MN_WC012
2018_CCRU_50KVC_MNWC2_2012_3842
2018_CCRU_50KVC_MNWC1_2011_3842
2018_CCRU_50KVC_MNSC3_2012_3840
2018_CCRU_50KVC_MNSC2_2011_3840
2018_CCRU_50K2010BOPA1_MN_GS_PARENTS12
2018_CCRU_50K2007BOPA1_MN_PRECAP12
2018_CCRU_50KVC_FHB2010_3840
2018_CCRU_50KCAPV2011_MN_9K29
2018_CCRU_50K2011_9K_NB_allplates31
2018_CCRU_50K2009BOPA2_AB_Plate55
2018_CCRU_50K2009BOPA2_WA_Plate45
2018_CCRU_50K2009BOPA2_VT_Plate15
2018_CCRU_50K2009BOPA2_UT_Plate65
2018_CCRU_50K2009BOPA2_OR_Plate20
2018_CCRU_50K2009BOPA2_N6_Plate95
2018_CCRU_50K2009BOPA2_N2_Plate85
2018_CCRU_50K2009BOPA2_MT_Plate105
2018_CCRU_50K2009BOPA2_MN_Plate30
2018_CCRU_50K2009BOPA2_BA_Plate75
2018_CCRU_50K2009BOPA1_WA_Plate412
2018_CCRU_50K2009BOPA1_VT_Plate112
2018_CCRU_50K2009BOPA1_UT_Plate612
2018_CCRU_50K2009BOPA1_OR_Plate217
2018_CCRU_50K2009BOPA1_N6_Plate912
2018_CCRU_50K2009BOPA1_N2_Plate812
2018_CCRU_50K2009BOPA1_MT_Plate1012
2018_CCRU_50K2009BOPA1_MN_Plate317
2018_CCRU_50K2009BOPA1_BA_Plate712
2018_CCRU_50K2009BOPA1_AB_Plate512
2018_CCRU_50K2006BOPA2_UT_Plate65
2018_CCRU_50KPOPA1_Steptoe_Morex_Mapping8
2018_CCRU_50KPOPA1_Oregon_Wolf_Barley_Mapping8
2018_CCRU_50KPOPA1_Morex-Barke_Mapping8
2018_CCRU_50KPOPA1-2_CAPcore8
2018_CCRU_50K2008BOPA2_MT_Plate105
2018_CCRU_50K2008BOPA1_MT_Plate1012
2018_CCRU_50K2008BOPA2_WA_Plate45
2018_CCRU_50K2008BOPA1_WA_Plate412
2018_CCRU_50K2008BOPA2_VT_Plate15
2018_CCRU_50K2008BOPA1_VT_Plate112
2018_CCRU_50K2008BOPA2_UT_Plate65
2018_CCRU_50K2008BOPA1_UT_Plate612
2018_CCRU_50K2008BOPA2_OR_Plate25
2018_CCRU_50K2008BOPA1_OR_Plate212
2018_CCRU_50K2008BOPA2_N6_Plate95
2018_CCRU_50K2008BOPA1_N6_Plate912
2018_CCRU_50K2008BOPA2_N2_Plate85
2018_CCRU_50K2008BOPA1_N2_Plate812
2018_CCRU_50K2008BOPA2_MN_Plate35
2018_CCRU_50K2008BOPA1_MN_Plate312
2018_CCRU_50K2008BOPA2_BA_Plate75
2018_CCRU_50K2008BOPA1_BA_Plate712
2018_CCRU_50K2008BOPA2_AB_Plate55
2018_CCRU_50K2008BOPA1_AB_Plate512
2018_CCRU_50KPOPA2_Steptoe-Morex_Mapping7
2018_CCRU_50KPOPA2_OWB_Mapping7
2018_CCRU_50KPOPA2_CAPcore7
2018_CCRU_50KPOPA2_Morex-Barke_Mapping7
2018_CCRU_50KPOPA3_Morex-Barke_Mapping2
2018_CCRU_50KPOPA3_Steptoe-Morex_Mapping2
2018_CCRU_50KPOPA3_OWB_Mapping2
2018_CCRU_50KPOPA3_CAPcore2
2018_CCRU_50K2006BOPA2_OR_Plate25
2018_CCRU_50K2007BOPA2_WA_Plate45
2018_CCRU_50K2007BOPA2_VT_Plate15
2018_CCRU_50K2007BOPA2_OR_Plate25
2018_CCRU_50K2007BOPA2_N6_Plate95
2018_CCRU_50K2007BOPA2_N2_Plate85
2018_CCRU_50K2007BOPA2_MT_Plate105
2018_CCRU_50K2007BOPA2_MN_Plate35
2018_CCRU_50K2007BOPA2_BA_Plate75
2018_CCRU_50K2007BOPA2_UT_Plate65
2018_CCRU_50K2007BOPA2_AB_Plate55
2018_CCRU_50K2007BOPA1_WA_Plate412
2018_CCRU_50K2007BOPA1_VT_Plate112
2018_CCRU_50K2007BOPA1_OR_Plate212
2018_CCRU_50K2007BOPA1_N6_Plate912
2018_CCRU_50K2007BOPA1_N2_Plate812
2018_CCRU_50K2007BOPA1_MT_Plate1012
2018_CCRU_50K2007BOPA1_MN_Plate312
2018_CCRU_50K2007BOPA1_BA_Plate712
2018_CCRU_50K2007BOPA1_UT_Plate612
2018_CCRU_50K2007BOPA1_AB_Plate512
2018_CCRU_50K2006BOPA2_WA_Plate45
2018_CCRU_50K2006BOPA2_VT_Plate15
2018_CCRU_50K2006BOPA2_N6_Plate95
2018_CCRU_50K2006BOPA2_N2_Plate85
2018_CCRU_50K2006BOPA2_MT_Plate105
2018_CCRU_50K2006BOPA2_MN_Plate35
2018_CCRU_50K2006BOPA2_BA_Plate75
2018_CCRU_50K2006BOPA2_AB_Plate55
2018_CCRU_50K2006BOPA1_WA_Plate412
2018_CCRU_50K2006BOPA1_VT_Plate112
2018_CCRU_50K2006BOPA1_OR_Plate212
2018_CCRU_50K2006BOPA1_N6_Plate912
2018_CCRU_50K2006BOPA1_N2_Plate812
2018_CCRU_50K2006BOPA1_MT_Plate1012
2018_CCRU_50K2006BOPA1_MN_Plate312
2018_CCRU_50K2006BOPA1_BA_Plate712
2018_CCRU_50K2006BOPA1_AB_Plate512

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.