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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 9K_MN_CAP6_2013
Experiment 1Experiment 2matches to markers
between trials
9K_MN_CAP6_20132020_NDSU_Eurofins5
9K_MN_CAP6_20132018_CCRU_50K36
9K_MN_CAP6_20132019_GBS_WBDC0
9K_MN_CAP6_2013UMN_NSGC_GWAS16
9K_MN_CAP6_20132015GBS_MN0
9K_MN_CAP6_20132019N2YUMA3
9K_MN_CAP6_20132015iSelect_MN_plate143
9K_MN_CAP6_20132016GBS_WBDC0
9K_MN_CAP6_20132018_NDSU_Yuma_2R3
9K_MN_CAP6_20132017_NDSU_Yuma_2R4
9K_MN_CAP6_20132016_N2_PYTBC2
9K_MN_CAP6_20132016N2PYTA1
9K_MN_CAP6_20132016_HapMap_WEC0
9K_MN_CAP6_20132015N2PYT2
9K_MN_CAP6_2013WBIP384_HOUH_20131
9K_MN_CAP6_2013WBIP384_ABNAM_20121
9K_MN_CAP6_20132014_NDSU_9K38
9K_MN_CAP6_20132006BOPA1_UT_Plate617
9K_MN_CAP6_2013BOPA1_MN_WB_201117
9K_MN_CAP6_20139K_MN_GEN10_201346
9K_MN_CAP6_20139K_MN_CAP6_201346
9K_MN_CAP6_2013OWB_GBS_20120
9K_MN_CAP6_2013WBIP_9K_Parents41
9K_MN_CAP6_2013VC_MNWC4_2013_3843
9K_MN_CAP6_2013TCFW6_LTT_9K41
9K_MN_CAP6_2013Ethiopia_Eritrea_9K42
9K_MN_CAP6_2013VC_MNWC3_2013_3843
9K_MN_CAP6_2013MorexBarke_GBS_20120
9K_MN_CAP6_20132011BOPA1_MN_WC017
9K_MN_CAP6_2013VC_MNWC2_2012_3843
9K_MN_CAP6_2013VC_MNWC1_2011_3843
9K_MN_CAP6_2013VC_MNSC3_2012_3840
9K_MN_CAP6_2013VC_MNSC2_2011_3840
9K_MN_CAP6_20132010BOPA1_MN_GS_PARENTS17
9K_MN_CAP6_20132007BOPA1_MN_PRECAP17
9K_MN_CAP6_2013VC_FHB2010_3840
9K_MN_CAP6_2013CAPV2011_MN_9K39
9K_MN_CAP6_20132011_9K_NB_allplates41
9K_MN_CAP6_20132009BOPA2_AB_Plate57
9K_MN_CAP6_20132009BOPA2_WA_Plate47
9K_MN_CAP6_20132009BOPA2_VT_Plate17
9K_MN_CAP6_20132009BOPA2_UT_Plate67
9K_MN_CAP6_20132009BOPA2_OR_Plate20
9K_MN_CAP6_20132009BOPA2_N6_Plate97
9K_MN_CAP6_20132009BOPA2_N2_Plate87
9K_MN_CAP6_20132009BOPA2_MT_Plate107
9K_MN_CAP6_20132009BOPA2_MN_Plate30
9K_MN_CAP6_20132009BOPA2_BA_Plate77
9K_MN_CAP6_20132009BOPA1_WA_Plate417
9K_MN_CAP6_20132009BOPA1_VT_Plate117
9K_MN_CAP6_20132009BOPA1_UT_Plate617
9K_MN_CAP6_20132009BOPA1_OR_Plate224
9K_MN_CAP6_20132009BOPA1_N6_Plate917
9K_MN_CAP6_20132009BOPA1_N2_Plate817
9K_MN_CAP6_20132009BOPA1_MT_Plate1017
9K_MN_CAP6_20132009BOPA1_MN_Plate324
9K_MN_CAP6_20132009BOPA1_BA_Plate717
9K_MN_CAP6_20132009BOPA1_AB_Plate517
9K_MN_CAP6_20132006BOPA2_UT_Plate67
9K_MN_CAP6_2013POPA1_Steptoe_Morex_Mapping12
9K_MN_CAP6_2013POPA1_Oregon_Wolf_Barley_Mapping12
9K_MN_CAP6_2013POPA1_Morex-Barke_Mapping12
9K_MN_CAP6_2013POPA1-2_CAPcore12
9K_MN_CAP6_20132008BOPA2_MT_Plate107
9K_MN_CAP6_20132008BOPA1_MT_Plate1017
9K_MN_CAP6_20132008BOPA2_WA_Plate47
9K_MN_CAP6_20132008BOPA1_WA_Plate417
9K_MN_CAP6_20132008BOPA2_VT_Plate17
9K_MN_CAP6_20132008BOPA1_VT_Plate117
9K_MN_CAP6_20132008BOPA2_UT_Plate67
9K_MN_CAP6_20132008BOPA1_UT_Plate617
9K_MN_CAP6_20132008BOPA2_OR_Plate27
9K_MN_CAP6_20132008BOPA1_OR_Plate217
9K_MN_CAP6_20132008BOPA2_N6_Plate97
9K_MN_CAP6_20132008BOPA1_N6_Plate917
9K_MN_CAP6_20132008BOPA2_N2_Plate87
9K_MN_CAP6_20132008BOPA1_N2_Plate817
9K_MN_CAP6_20132008BOPA2_MN_Plate37
9K_MN_CAP6_20132008BOPA1_MN_Plate317
9K_MN_CAP6_20132008BOPA2_BA_Plate77
9K_MN_CAP6_20132008BOPA1_BA_Plate717
9K_MN_CAP6_20132008BOPA2_AB_Plate57
9K_MN_CAP6_20132008BOPA1_AB_Plate517
9K_MN_CAP6_2013POPA2_Steptoe-Morex_Mapping10
9K_MN_CAP6_2013POPA2_OWB_Mapping10
9K_MN_CAP6_2013POPA2_CAPcore10
9K_MN_CAP6_2013POPA2_Morex-Barke_Mapping10
9K_MN_CAP6_2013POPA3_Morex-Barke_Mapping2
9K_MN_CAP6_2013POPA3_Steptoe-Morex_Mapping2
9K_MN_CAP6_2013POPA3_OWB_Mapping2
9K_MN_CAP6_2013POPA3_CAPcore2
9K_MN_CAP6_20132006BOPA2_OR_Plate27
9K_MN_CAP6_20132007BOPA2_WA_Plate47
9K_MN_CAP6_20132007BOPA2_VT_Plate17
9K_MN_CAP6_20132007BOPA2_OR_Plate27
9K_MN_CAP6_20132007BOPA2_N6_Plate97
9K_MN_CAP6_20132007BOPA2_N2_Plate87
9K_MN_CAP6_20132007BOPA2_MT_Plate107
9K_MN_CAP6_20132007BOPA2_MN_Plate37
9K_MN_CAP6_20132007BOPA2_BA_Plate77
9K_MN_CAP6_20132007BOPA2_UT_Plate67
9K_MN_CAP6_20132007BOPA2_AB_Plate57
9K_MN_CAP6_20132007BOPA1_WA_Plate417
9K_MN_CAP6_20132007BOPA1_VT_Plate117
9K_MN_CAP6_20132007BOPA1_OR_Plate217
9K_MN_CAP6_20132007BOPA1_N6_Plate917
9K_MN_CAP6_20132007BOPA1_N2_Plate817
9K_MN_CAP6_20132007BOPA1_MT_Plate1017
9K_MN_CAP6_20132007BOPA1_MN_Plate317
9K_MN_CAP6_20132007BOPA1_BA_Plate717
9K_MN_CAP6_20132007BOPA1_UT_Plate617
9K_MN_CAP6_20132007BOPA1_AB_Plate517
9K_MN_CAP6_20132006BOPA2_WA_Plate47
9K_MN_CAP6_20132006BOPA2_VT_Plate17
9K_MN_CAP6_20132006BOPA2_N6_Plate97
9K_MN_CAP6_20132006BOPA2_N2_Plate87
9K_MN_CAP6_20132006BOPA2_MT_Plate107
9K_MN_CAP6_20132006BOPA2_MN_Plate37
9K_MN_CAP6_20132006BOPA2_BA_Plate77
9K_MN_CAP6_20132006BOPA2_AB_Plate57
9K_MN_CAP6_20132006BOPA1_WA_Plate417
9K_MN_CAP6_20132006BOPA1_VT_Plate117
9K_MN_CAP6_20132006BOPA1_OR_Plate217
9K_MN_CAP6_20132006BOPA1_N6_Plate917
9K_MN_CAP6_20132006BOPA1_N2_Plate817
9K_MN_CAP6_20132006BOPA1_MT_Plate1017
9K_MN_CAP6_20132006BOPA1_MN_Plate317
9K_MN_CAP6_20132006BOPA1_BA_Plate717
9K_MN_CAP6_20132006BOPA1_AB_Plate517

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.