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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 MorexBarke_GBS_2012
Experiment 1Experiment 2matches to markers
between trials
MorexBarke_GBS_20122020_NDSU_Eurofins3
MorexBarke_GBS_20122018_CCRU_50K72
MorexBarke_GBS_20122019_GBS_WBDC0
MorexBarke_GBS_2012UMN_NSGC_GWAS44
MorexBarke_GBS_20122015GBS_MN0
MorexBarke_GBS_20122019N2YUMA5
MorexBarke_GBS_20122015iSelect_MN_plate182
MorexBarke_GBS_20122016GBS_WBDC0
MorexBarke_GBS_20122018_NDSU_Yuma_2R5
MorexBarke_GBS_20122017_NDSU_Yuma_2R5
MorexBarke_GBS_20122016_N2_PYTBC5
MorexBarke_GBS_20122016N2PYTA5
MorexBarke_GBS_20122016_HapMap_WEC0
MorexBarke_GBS_20122015N2PYT5
MorexBarke_GBS_2012WBIP384_HOUH_20134
MorexBarke_GBS_2012WBIP384_ABNAM_20124
MorexBarke_GBS_20122014_NDSU_9K78
MorexBarke_GBS_20122006BOPA1_UT_Plate616
MorexBarke_GBS_2012BOPA1_MN_WB_201116
MorexBarke_GBS_20129K_MN_GEN10_201382
MorexBarke_GBS_20129K_MN_CAP6_201382
MorexBarke_GBS_2012OWB_GBS_20123841
MorexBarke_GBS_2012WBIP_9K_Parents82
MorexBarke_GBS_2012VC_MNWC4_2013_3845
MorexBarke_GBS_2012TCFW6_LTT_9K80
MorexBarke_GBS_2012Ethiopia_Eritrea_9K78
MorexBarke_GBS_2012VC_MNWC3_2013_3845
MorexBarke_GBS_2012MorexBarke_GBS_20121176
MorexBarke_GBS_20122011BOPA1_MN_WC016
MorexBarke_GBS_2012VC_MNWC2_2012_3845
MorexBarke_GBS_2012VC_MNWC1_2011_3845
MorexBarke_GBS_2012VC_MNSC3_2012_3843
MorexBarke_GBS_2012VC_MNSC2_2011_3843
MorexBarke_GBS_20122010BOPA1_MN_GS_PARENTS16
MorexBarke_GBS_20122007BOPA1_MN_PRECAP16
MorexBarke_GBS_2012VC_FHB2010_3843
MorexBarke_GBS_2012CAPV2011_MN_9K79
MorexBarke_GBS_20122011_9K_NB_allplates79
MorexBarke_GBS_20122009BOPA2_AB_Plate511
MorexBarke_GBS_20122009BOPA2_WA_Plate411
MorexBarke_GBS_20122009BOPA2_VT_Plate111
MorexBarke_GBS_20122009BOPA2_UT_Plate611
MorexBarke_GBS_20122009BOPA2_OR_Plate20
MorexBarke_GBS_20122009BOPA2_N6_Plate911
MorexBarke_GBS_20122009BOPA2_N2_Plate811
MorexBarke_GBS_20122009BOPA2_MT_Plate1011
MorexBarke_GBS_20122009BOPA2_MN_Plate30
MorexBarke_GBS_20122009BOPA2_BA_Plate711
MorexBarke_GBS_20122009BOPA1_WA_Plate416
MorexBarke_GBS_20122009BOPA1_VT_Plate116
MorexBarke_GBS_20122009BOPA1_UT_Plate616
MorexBarke_GBS_20122009BOPA1_OR_Plate227
MorexBarke_GBS_20122009BOPA1_N6_Plate916
MorexBarke_GBS_20122009BOPA1_N2_Plate816
MorexBarke_GBS_20122009BOPA1_MT_Plate1016
MorexBarke_GBS_20122009BOPA1_MN_Plate327
MorexBarke_GBS_20122009BOPA1_BA_Plate716
MorexBarke_GBS_20122009BOPA1_AB_Plate516
MorexBarke_GBS_20122006BOPA2_UT_Plate611
MorexBarke_GBS_2012POPA1_Steptoe_Morex_Mapping10
MorexBarke_GBS_2012POPA1_Oregon_Wolf_Barley_Mapping10
MorexBarke_GBS_2012POPA1_Morex-Barke_Mapping10
MorexBarke_GBS_2012POPA1-2_CAPcore10
MorexBarke_GBS_20122008BOPA2_MT_Plate1011
MorexBarke_GBS_20122008BOPA1_MT_Plate1016
MorexBarke_GBS_20122008BOPA2_WA_Plate411
MorexBarke_GBS_20122008BOPA1_WA_Plate416
MorexBarke_GBS_20122008BOPA2_VT_Plate111
MorexBarke_GBS_20122008BOPA1_VT_Plate116
MorexBarke_GBS_20122008BOPA2_UT_Plate611
MorexBarke_GBS_20122008BOPA1_UT_Plate616
MorexBarke_GBS_20122008BOPA2_OR_Plate211
MorexBarke_GBS_20122008BOPA1_OR_Plate216
MorexBarke_GBS_20122008BOPA2_N6_Plate911
MorexBarke_GBS_20122008BOPA1_N6_Plate916
MorexBarke_GBS_20122008BOPA2_N2_Plate811
MorexBarke_GBS_20122008BOPA1_N2_Plate816
MorexBarke_GBS_20122008BOPA2_MN_Plate311
MorexBarke_GBS_20122008BOPA1_MN_Plate316
MorexBarke_GBS_20122008BOPA2_BA_Plate711
MorexBarke_GBS_20122008BOPA1_BA_Plate716
MorexBarke_GBS_20122008BOPA2_AB_Plate511
MorexBarke_GBS_20122008BOPA1_AB_Plate516
MorexBarke_GBS_2012POPA2_Steptoe-Morex_Mapping8
MorexBarke_GBS_2012POPA2_OWB_Mapping8
MorexBarke_GBS_2012POPA2_CAPcore8
MorexBarke_GBS_2012POPA2_Morex-Barke_Mapping8
MorexBarke_GBS_2012POPA3_Morex-Barke_Mapping9
MorexBarke_GBS_2012POPA3_Steptoe-Morex_Mapping9
MorexBarke_GBS_2012POPA3_OWB_Mapping9
MorexBarke_GBS_2012POPA3_CAPcore9
MorexBarke_GBS_20122006BOPA2_OR_Plate211
MorexBarke_GBS_20122007BOPA2_WA_Plate411
MorexBarke_GBS_20122007BOPA2_VT_Plate111
MorexBarke_GBS_20122007BOPA2_OR_Plate211
MorexBarke_GBS_20122007BOPA2_N6_Plate911
MorexBarke_GBS_20122007BOPA2_N2_Plate811
MorexBarke_GBS_20122007BOPA2_MT_Plate1011
MorexBarke_GBS_20122007BOPA2_MN_Plate311
MorexBarke_GBS_20122007BOPA2_BA_Plate711
MorexBarke_GBS_20122007BOPA2_UT_Plate611
MorexBarke_GBS_20122007BOPA2_AB_Plate511
MorexBarke_GBS_20122007BOPA1_WA_Plate416
MorexBarke_GBS_20122007BOPA1_VT_Plate116
MorexBarke_GBS_20122007BOPA1_OR_Plate216
MorexBarke_GBS_20122007BOPA1_N6_Plate916
MorexBarke_GBS_20122007BOPA1_N2_Plate816
MorexBarke_GBS_20122007BOPA1_MT_Plate1016
MorexBarke_GBS_20122007BOPA1_MN_Plate316
MorexBarke_GBS_20122007BOPA1_BA_Plate716
MorexBarke_GBS_20122007BOPA1_UT_Plate616
MorexBarke_GBS_20122007BOPA1_AB_Plate516
MorexBarke_GBS_20122006BOPA2_WA_Plate411
MorexBarke_GBS_20122006BOPA2_VT_Plate111
MorexBarke_GBS_20122006BOPA2_N6_Plate911
MorexBarke_GBS_20122006BOPA2_N2_Plate811
MorexBarke_GBS_20122006BOPA2_MT_Plate1011
MorexBarke_GBS_20122006BOPA2_MN_Plate311
MorexBarke_GBS_20122006BOPA2_BA_Plate711
MorexBarke_GBS_20122006BOPA2_AB_Plate511
MorexBarke_GBS_20122006BOPA1_WA_Plate416
MorexBarke_GBS_20122006BOPA1_VT_Plate116
MorexBarke_GBS_20122006BOPA1_OR_Plate216
MorexBarke_GBS_20122006BOPA1_N6_Plate916
MorexBarke_GBS_20122006BOPA1_N2_Plate816
MorexBarke_GBS_20122006BOPA1_MT_Plate1016
MorexBarke_GBS_20122006BOPA1_MN_Plate316
MorexBarke_GBS_20122006BOPA1_BA_Plate716
MorexBarke_GBS_20122006BOPA1_AB_Plate516

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.