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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 2011BOPA1_MN_WC0
Experiment 1Experiment 2matches to markers
between trials
2011BOPA1_MN_WC02020_NDSU_Eurofins0
2011BOPA1_MN_WC02018_CCRU_50K1
2011BOPA1_MN_WC02019_GBS_WBDC0
2011BOPA1_MN_WC0UMN_NSGC_GWAS1
2011BOPA1_MN_WC02015GBS_MN0
2011BOPA1_MN_WC02019N2YUMA0
2011BOPA1_MN_WC02015iSelect_MN_plate11
2011BOPA1_MN_WC02016GBS_WBDC0
2011BOPA1_MN_WC02018_NDSU_Yuma_2R0
2011BOPA1_MN_WC02017_NDSU_Yuma_2R0
2011BOPA1_MN_WC02016_N2_PYTBC0
2011BOPA1_MN_WC02016N2PYTA0
2011BOPA1_MN_WC02016_HapMap_WEC0
2011BOPA1_MN_WC02015N2PYT0
2011BOPA1_MN_WC0WBIP384_HOUH_20130
2011BOPA1_MN_WC0WBIP384_ABNAM_20120
2011BOPA1_MN_WC02014_NDSU_9K1
2011BOPA1_MN_WC02006BOPA1_UT_Plate62
2011BOPA1_MN_WC0BOPA1_MN_WB_20112
2011BOPA1_MN_WC09K_MN_GEN10_20132
2011BOPA1_MN_WC09K_MN_CAP6_20132
2011BOPA1_MN_WC0OWB_GBS_20120
2011BOPA1_MN_WC0WBIP_9K_Parents1
2011BOPA1_MN_WC0VC_MNWC4_2013_3840
2011BOPA1_MN_WC0TCFW6_LTT_9K1
2011BOPA1_MN_WC0Ethiopia_Eritrea_9K1
2011BOPA1_MN_WC0VC_MNWC3_2013_3840
2011BOPA1_MN_WC0MorexBarke_GBS_20120
2011BOPA1_MN_WC02011BOPA1_MN_WC02
2011BOPA1_MN_WC0VC_MNWC2_2012_3840
2011BOPA1_MN_WC0VC_MNWC1_2011_3840
2011BOPA1_MN_WC0VC_MNSC3_2012_3840
2011BOPA1_MN_WC0VC_MNSC2_2011_3840
2011BOPA1_MN_WC02010BOPA1_MN_GS_PARENTS2
2011BOPA1_MN_WC02007BOPA1_MN_PRECAP2
2011BOPA1_MN_WC0VC_FHB2010_3840
2011BOPA1_MN_WC0CAPV2011_MN_9K1
2011BOPA1_MN_WC02011_9K_NB_allplates1
2011BOPA1_MN_WC02009BOPA2_AB_Plate50
2011BOPA1_MN_WC02009BOPA2_WA_Plate40
2011BOPA1_MN_WC02009BOPA2_VT_Plate10
2011BOPA1_MN_WC02009BOPA2_UT_Plate60
2011BOPA1_MN_WC02009BOPA2_OR_Plate20
2011BOPA1_MN_WC02009BOPA2_N6_Plate90
2011BOPA1_MN_WC02009BOPA2_N2_Plate80
2011BOPA1_MN_WC02009BOPA2_MT_Plate100
2011BOPA1_MN_WC02009BOPA2_MN_Plate30
2011BOPA1_MN_WC02009BOPA2_BA_Plate70
2011BOPA1_MN_WC02009BOPA1_WA_Plate42
2011BOPA1_MN_WC02009BOPA1_VT_Plate12
2011BOPA1_MN_WC02009BOPA1_UT_Plate62
2011BOPA1_MN_WC02009BOPA1_OR_Plate22
2011BOPA1_MN_WC02009BOPA1_N6_Plate92
2011BOPA1_MN_WC02009BOPA1_N2_Plate82
2011BOPA1_MN_WC02009BOPA1_MT_Plate102
2011BOPA1_MN_WC02009BOPA1_MN_Plate32
2011BOPA1_MN_WC02009BOPA1_BA_Plate72
2011BOPA1_MN_WC02009BOPA1_AB_Plate52
2011BOPA1_MN_WC02006BOPA2_UT_Plate60
2011BOPA1_MN_WC0POPA1_Steptoe_Morex_Mapping1
2011BOPA1_MN_WC0POPA1_Oregon_Wolf_Barley_Mapping1
2011BOPA1_MN_WC0POPA1_Morex-Barke_Mapping1
2011BOPA1_MN_WC0POPA1-2_CAPcore1
2011BOPA1_MN_WC02008BOPA2_MT_Plate100
2011BOPA1_MN_WC02008BOPA1_MT_Plate102
2011BOPA1_MN_WC02008BOPA2_WA_Plate40
2011BOPA1_MN_WC02008BOPA1_WA_Plate42
2011BOPA1_MN_WC02008BOPA2_VT_Plate10
2011BOPA1_MN_WC02008BOPA1_VT_Plate12
2011BOPA1_MN_WC02008BOPA2_UT_Plate60
2011BOPA1_MN_WC02008BOPA1_UT_Plate62
2011BOPA1_MN_WC02008BOPA2_OR_Plate20
2011BOPA1_MN_WC02008BOPA1_OR_Plate22
2011BOPA1_MN_WC02008BOPA2_N6_Plate90
2011BOPA1_MN_WC02008BOPA1_N6_Plate92
2011BOPA1_MN_WC02008BOPA2_N2_Plate80
2011BOPA1_MN_WC02008BOPA1_N2_Plate82
2011BOPA1_MN_WC02008BOPA2_MN_Plate30
2011BOPA1_MN_WC02008BOPA1_MN_Plate32
2011BOPA1_MN_WC02008BOPA2_BA_Plate70
2011BOPA1_MN_WC02008BOPA1_BA_Plate72
2011BOPA1_MN_WC02008BOPA2_AB_Plate50
2011BOPA1_MN_WC02008BOPA1_AB_Plate52
2011BOPA1_MN_WC0POPA2_Steptoe-Morex_Mapping1
2011BOPA1_MN_WC0POPA2_OWB_Mapping1
2011BOPA1_MN_WC0POPA2_CAPcore1
2011BOPA1_MN_WC0POPA2_Morex-Barke_Mapping1
2011BOPA1_MN_WC0POPA3_Morex-Barke_Mapping0
2011BOPA1_MN_WC0POPA3_Steptoe-Morex_Mapping0
2011BOPA1_MN_WC0POPA3_OWB_Mapping0
2011BOPA1_MN_WC0POPA3_CAPcore0
2011BOPA1_MN_WC02006BOPA2_OR_Plate20
2011BOPA1_MN_WC02007BOPA2_WA_Plate40
2011BOPA1_MN_WC02007BOPA2_VT_Plate10
2011BOPA1_MN_WC02007BOPA2_OR_Plate20
2011BOPA1_MN_WC02007BOPA2_N6_Plate90
2011BOPA1_MN_WC02007BOPA2_N2_Plate80
2011BOPA1_MN_WC02007BOPA2_MT_Plate100
2011BOPA1_MN_WC02007BOPA2_MN_Plate30
2011BOPA1_MN_WC02007BOPA2_BA_Plate70
2011BOPA1_MN_WC02007BOPA2_UT_Plate60
2011BOPA1_MN_WC02007BOPA2_AB_Plate50
2011BOPA1_MN_WC02007BOPA1_WA_Plate42
2011BOPA1_MN_WC02007BOPA1_VT_Plate12
2011BOPA1_MN_WC02007BOPA1_OR_Plate22
2011BOPA1_MN_WC02007BOPA1_N6_Plate92
2011BOPA1_MN_WC02007BOPA1_N2_Plate82
2011BOPA1_MN_WC02007BOPA1_MT_Plate102
2011BOPA1_MN_WC02007BOPA1_MN_Plate32
2011BOPA1_MN_WC02007BOPA1_BA_Plate72
2011BOPA1_MN_WC02007BOPA1_UT_Plate62
2011BOPA1_MN_WC02007BOPA1_AB_Plate52
2011BOPA1_MN_WC02006BOPA2_WA_Plate40
2011BOPA1_MN_WC02006BOPA2_VT_Plate10
2011BOPA1_MN_WC02006BOPA2_N6_Plate90
2011BOPA1_MN_WC02006BOPA2_N2_Plate80
2011BOPA1_MN_WC02006BOPA2_MT_Plate100
2011BOPA1_MN_WC02006BOPA2_MN_Plate30
2011BOPA1_MN_WC02006BOPA2_BA_Plate70
2011BOPA1_MN_WC02006BOPA2_AB_Plate50
2011BOPA1_MN_WC02006BOPA1_WA_Plate42
2011BOPA1_MN_WC02006BOPA1_VT_Plate12
2011BOPA1_MN_WC02006BOPA1_OR_Plate22
2011BOPA1_MN_WC02006BOPA1_N6_Plate92
2011BOPA1_MN_WC02006BOPA1_N2_Plate82
2011BOPA1_MN_WC02006BOPA1_MT_Plate102
2011BOPA1_MN_WC02006BOPA1_MN_Plate32
2011BOPA1_MN_WC02006BOPA1_BA_Plate72
2011BOPA1_MN_WC02006BOPA1_AB_Plate52

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.