Contact Us

  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 2014_NDSU_9K
Experiment 1Experiment 2matches to markers
between trials
2014_NDSU_9K2020_NDSU_Eurofins5
2014_NDSU_9K2018_CCRU_50K28
2014_NDSU_9K2019_GBS_WBDC0
2014_NDSU_9KUMN_NSGC_GWAS12
2014_NDSU_9K2015GBS_MN0
2014_NDSU_9K2019N2YUMA3
2014_NDSU_9K2015iSelect_MN_plate134
2014_NDSU_9K2016GBS_WBDC0
2014_NDSU_9K2018_NDSU_Yuma_2R3
2014_NDSU_9K2017_NDSU_Yuma_2R4
2014_NDSU_9K2016_N2_PYTBC2
2014_NDSU_9K2016N2PYTA1
2014_NDSU_9K2016_HapMap_WEC0
2014_NDSU_9K2015N2PYT2
2014_NDSU_9KWBIP384_HOUH_20131
2014_NDSU_9KWBIP384_ABNAM_20121
2014_NDSU_9K2014_NDSU_9K33
2014_NDSU_9K2006BOPA1_UT_Plate614
2014_NDSU_9KBOPA1_MN_WB_201114
2014_NDSU_9K9K_MN_GEN10_201337
2014_NDSU_9K9K_MN_CAP6_201337
2014_NDSU_9KOWB_GBS_20120
2014_NDSU_9KWBIP_9K_Parents33
2014_NDSU_9KVC_MNWC4_2013_3843
2014_NDSU_9KTCFW6_LTT_9K33
2014_NDSU_9KEthiopia_Eritrea_9K35
2014_NDSU_9KVC_MNWC3_2013_3843
2014_NDSU_9KMorexBarke_GBS_20120
2014_NDSU_9K2011BOPA1_MN_WC014
2014_NDSU_9KVC_MNWC2_2012_3843
2014_NDSU_9KVC_MNWC1_2011_3843
2014_NDSU_9KVC_MNSC3_2012_3840
2014_NDSU_9KVC_MNSC2_2011_3840
2014_NDSU_9K2010BOPA1_MN_GS_PARENTS14
2014_NDSU_9K2007BOPA1_MN_PRECAP14
2014_NDSU_9KVC_FHB2010_3840
2014_NDSU_9KCAPV2011_MN_9K32
2014_NDSU_9K2011_9K_NB_allplates33
2014_NDSU_9K2009BOPA2_AB_Plate53
2014_NDSU_9K2009BOPA2_WA_Plate43
2014_NDSU_9K2009BOPA2_VT_Plate13
2014_NDSU_9K2009BOPA2_UT_Plate63
2014_NDSU_9K2009BOPA2_OR_Plate20
2014_NDSU_9K2009BOPA2_N6_Plate93
2014_NDSU_9K2009BOPA2_N2_Plate83
2014_NDSU_9K2009BOPA2_MT_Plate103
2014_NDSU_9K2009BOPA2_MN_Plate30
2014_NDSU_9K2009BOPA2_BA_Plate73
2014_NDSU_9K2009BOPA1_WA_Plate414
2014_NDSU_9K2009BOPA1_VT_Plate114
2014_NDSU_9K2009BOPA1_UT_Plate614
2014_NDSU_9K2009BOPA1_OR_Plate217
2014_NDSU_9K2009BOPA1_N6_Plate914
2014_NDSU_9K2009BOPA1_N2_Plate814
2014_NDSU_9K2009BOPA1_MT_Plate1014
2014_NDSU_9K2009BOPA1_MN_Plate317
2014_NDSU_9K2009BOPA1_BA_Plate714
2014_NDSU_9K2009BOPA1_AB_Plate514
2014_NDSU_9K2006BOPA2_UT_Plate63
2014_NDSU_9KPOPA1_Steptoe_Morex_Mapping8
2014_NDSU_9KPOPA1_Oregon_Wolf_Barley_Mapping8
2014_NDSU_9KPOPA1_Morex-Barke_Mapping8
2014_NDSU_9KPOPA1-2_CAPcore8
2014_NDSU_9K2008BOPA2_MT_Plate103
2014_NDSU_9K2008BOPA1_MT_Plate1014
2014_NDSU_9K2008BOPA2_WA_Plate43
2014_NDSU_9K2008BOPA1_WA_Plate414
2014_NDSU_9K2008BOPA2_VT_Plate13
2014_NDSU_9K2008BOPA1_VT_Plate114
2014_NDSU_9K2008BOPA2_UT_Plate63
2014_NDSU_9K2008BOPA1_UT_Plate614
2014_NDSU_9K2008BOPA2_OR_Plate23
2014_NDSU_9K2008BOPA1_OR_Plate214
2014_NDSU_9K2008BOPA2_N6_Plate93
2014_NDSU_9K2008BOPA1_N6_Plate914
2014_NDSU_9K2008BOPA2_N2_Plate83
2014_NDSU_9K2008BOPA1_N2_Plate814
2014_NDSU_9K2008BOPA2_MN_Plate33
2014_NDSU_9K2008BOPA1_MN_Plate314
2014_NDSU_9K2008BOPA2_BA_Plate73
2014_NDSU_9K2008BOPA1_BA_Plate714
2014_NDSU_9K2008BOPA2_AB_Plate53
2014_NDSU_9K2008BOPA1_AB_Plate514
2014_NDSU_9KPOPA2_Steptoe-Morex_Mapping8
2014_NDSU_9KPOPA2_OWB_Mapping8
2014_NDSU_9KPOPA2_CAPcore8
2014_NDSU_9KPOPA2_Morex-Barke_Mapping8
2014_NDSU_9KPOPA3_Morex-Barke_Mapping1
2014_NDSU_9KPOPA3_Steptoe-Morex_Mapping1
2014_NDSU_9KPOPA3_OWB_Mapping1
2014_NDSU_9KPOPA3_CAPcore1
2014_NDSU_9K2006BOPA2_OR_Plate23
2014_NDSU_9K2007BOPA2_WA_Plate43
2014_NDSU_9K2007BOPA2_VT_Plate13
2014_NDSU_9K2007BOPA2_OR_Plate23
2014_NDSU_9K2007BOPA2_N6_Plate93
2014_NDSU_9K2007BOPA2_N2_Plate83
2014_NDSU_9K2007BOPA2_MT_Plate103
2014_NDSU_9K2007BOPA2_MN_Plate33
2014_NDSU_9K2007BOPA2_BA_Plate73
2014_NDSU_9K2007BOPA2_UT_Plate63
2014_NDSU_9K2007BOPA2_AB_Plate53
2014_NDSU_9K2007BOPA1_WA_Plate414
2014_NDSU_9K2007BOPA1_VT_Plate114
2014_NDSU_9K2007BOPA1_OR_Plate214
2014_NDSU_9K2007BOPA1_N6_Plate914
2014_NDSU_9K2007BOPA1_N2_Plate814
2014_NDSU_9K2007BOPA1_MT_Plate1014
2014_NDSU_9K2007BOPA1_MN_Plate314
2014_NDSU_9K2007BOPA1_BA_Plate714
2014_NDSU_9K2007BOPA1_UT_Plate614
2014_NDSU_9K2007BOPA1_AB_Plate514
2014_NDSU_9K2006BOPA2_WA_Plate43
2014_NDSU_9K2006BOPA2_VT_Plate13
2014_NDSU_9K2006BOPA2_N6_Plate93
2014_NDSU_9K2006BOPA2_N2_Plate83
2014_NDSU_9K2006BOPA2_MT_Plate103
2014_NDSU_9K2006BOPA2_MN_Plate33
2014_NDSU_9K2006BOPA2_BA_Plate73
2014_NDSU_9K2006BOPA2_AB_Plate53
2014_NDSU_9K2006BOPA1_WA_Plate414
2014_NDSU_9K2006BOPA1_VT_Plate114
2014_NDSU_9K2006BOPA1_OR_Plate214
2014_NDSU_9K2006BOPA1_N6_Plate914
2014_NDSU_9K2006BOPA1_N2_Plate814
2014_NDSU_9K2006BOPA1_MT_Plate1014
2014_NDSU_9K2006BOPA1_MN_Plate314
2014_NDSU_9K2006BOPA1_BA_Plate714
2014_NDSU_9K2006BOPA1_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.