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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
Experiment 1Experiment 2matches to markers
between trials
2020_NDSU_Eurofins0
2018_CCRU_50K1
2019_GBS_WBDC0
UMN_NSGC_GWAS0
2015GBS_MN0
2019N2YUMA0
2015iSelect_MN_plate11
2016GBS_WBDC0
2018_NDSU_Yuma_2R0
2017_NDSU_Yuma_2R0
2016_N2_PYTBC0
2016N2PYTA0
2016_HapMap_WEC0
2015N2PYT0
WBIP384_HOUH_20130
WBIP384_ABNAM_20120
2014_NDSU_9K1
2006BOPA1_UT_Plate61
BOPA1_MN_WB_20111
9K_MN_GEN10_20131
9K_MN_CAP6_20131
OWB_GBS_20120
WBIP_9K_Parents1
VC_MNWC4_2013_3840
TCFW6_LTT_9K1
Ethiopia_Eritrea_9K1
VC_MNWC3_2013_3840
MorexBarke_GBS_20120
2011BOPA1_MN_WC01
VC_MNWC2_2012_3840
VC_MNWC1_2011_3840
VC_MNSC3_2012_3840
VC_MNSC2_2011_3840
2010BOPA1_MN_GS_PARENTS1
2007BOPA1_MN_PRECAP1
VC_FHB2010_3840
CAPV2011_MN_9K1
2011_9K_NB_allplates1
2009BOPA2_AB_Plate50
2009BOPA2_WA_Plate40
2009BOPA2_VT_Plate10
2009BOPA2_UT_Plate60
2009BOPA2_OR_Plate20
2009BOPA2_N6_Plate90
2009BOPA2_N2_Plate80
2009BOPA2_MT_Plate100
2009BOPA2_MN_Plate30
2009BOPA2_BA_Plate70
2009BOPA1_WA_Plate41
2009BOPA1_VT_Plate11
2009BOPA1_UT_Plate61
2009BOPA1_OR_Plate21
2009BOPA1_N6_Plate91
2009BOPA1_N2_Plate81
2009BOPA1_MT_Plate101
2009BOPA1_MN_Plate31
2009BOPA1_BA_Plate71
2009BOPA1_AB_Plate51
2006BOPA2_UT_Plate60
POPA1_Steptoe_Morex_Mapping1
POPA1_Oregon_Wolf_Barley_Mapping1
POPA1_Morex-Barke_Mapping1
POPA1-2_CAPcore1
2008BOPA2_MT_Plate100
2008BOPA1_MT_Plate101
2008BOPA2_WA_Plate40
2008BOPA1_WA_Plate41
2008BOPA2_VT_Plate10
2008BOPA1_VT_Plate11
2008BOPA2_UT_Plate60
2008BOPA1_UT_Plate61
2008BOPA2_OR_Plate20
2008BOPA1_OR_Plate21
2008BOPA2_N6_Plate90
2008BOPA1_N6_Plate91
2008BOPA2_N2_Plate80
2008BOPA1_N2_Plate81
2008BOPA2_MN_Plate30
2008BOPA1_MN_Plate31
2008BOPA2_BA_Plate70
2008BOPA1_BA_Plate71
2008BOPA2_AB_Plate50
2008BOPA1_AB_Plate51
POPA2_Steptoe-Morex_Mapping0
POPA2_OWB_Mapping0
POPA2_CAPcore0
POPA2_Morex-Barke_Mapping0
POPA3_Morex-Barke_Mapping0
POPA3_Steptoe-Morex_Mapping0
POPA3_OWB_Mapping0
POPA3_CAPcore0
2006BOPA2_OR_Plate20
2007BOPA2_WA_Plate40
2007BOPA2_VT_Plate10
2007BOPA2_OR_Plate20
2007BOPA2_N6_Plate90
2007BOPA2_N2_Plate80
2007BOPA2_MT_Plate100
2007BOPA2_MN_Plate30
2007BOPA2_BA_Plate70
2007BOPA2_UT_Plate60
2007BOPA2_AB_Plate50
2007BOPA1_WA_Plate41
2007BOPA1_VT_Plate11
2007BOPA1_OR_Plate21
2007BOPA1_N6_Plate91
2007BOPA1_N2_Plate81
2007BOPA1_MT_Plate101
2007BOPA1_MN_Plate31
2007BOPA1_BA_Plate71
2007BOPA1_UT_Plate61
2007BOPA1_AB_Plate51
2006BOPA2_WA_Plate40
2006BOPA2_VT_Plate10
2006BOPA2_N6_Plate90
2006BOPA2_N2_Plate80
2006BOPA2_MT_Plate100
2006BOPA2_MN_Plate30
2006BOPA2_BA_Plate70
2006BOPA2_AB_Plate50
2006BOPA1_WA_Plate41
2006BOPA1_VT_Plate11
2006BOPA1_OR_Plate21
2006BOPA1_N6_Plate91
2006BOPA1_N2_Plate81
2006BOPA1_MT_Plate101
2006BOPA1_MN_Plate31
2006BOPA1_BA_Plate71
2006BOPA1_AB_Plate51

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.