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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 OWB_GBS_2012
Experiment 1Experiment 2matches to markers
between trials
OWB_GBS_20122020_NDSU_Eurofins1
OWB_GBS_20122018_CCRU_50K45
OWB_GBS_20122019_GBS_WBDC0
OWB_GBS_2012UMN_NSGC_GWAS25
OWB_GBS_20122015GBS_MN0
OWB_GBS_20122019N2YUMA2
OWB_GBS_20122015iSelect_MN_plate156
OWB_GBS_20122016GBS_WBDC0
OWB_GBS_20122018_NDSU_Yuma_2R2
OWB_GBS_20122017_NDSU_Yuma_2R2
OWB_GBS_20122016_N2_PYTBC2
OWB_GBS_20122016N2PYTA2
OWB_GBS_20122016_HapMap_WEC0
OWB_GBS_20122015N2PYT2
OWB_GBS_2012WBIP384_HOUH_20134
OWB_GBS_2012WBIP384_ABNAM_20124
OWB_GBS_20122014_NDSU_9K50
OWB_GBS_20122006BOPA1_UT_Plate614
OWB_GBS_2012BOPA1_MN_WB_201114
OWB_GBS_20129K_MN_GEN10_201356
OWB_GBS_20129K_MN_CAP6_201356
OWB_GBS_2012OWB_GBS_20121741
OWB_GBS_2012WBIP_9K_Parents54
OWB_GBS_2012VC_MNWC4_2013_3843
OWB_GBS_2012TCFW6_LTT_9K54
OWB_GBS_2012Ethiopia_Eritrea_9K50
OWB_GBS_2012VC_MNWC3_2013_3843
OWB_GBS_2012MorexBarke_GBS_20123595
OWB_GBS_20122011BOPA1_MN_WC014
OWB_GBS_2012VC_MNWC2_2012_3843
OWB_GBS_2012VC_MNWC1_2011_3843
OWB_GBS_2012VC_MNSC3_2012_3843
OWB_GBS_2012VC_MNSC2_2011_3843
OWB_GBS_20122010BOPA1_MN_GS_PARENTS14
OWB_GBS_20122007BOPA1_MN_PRECAP14
OWB_GBS_2012VC_FHB2010_3843
OWB_GBS_2012CAPV2011_MN_9K48
OWB_GBS_20122011_9K_NB_allplates51
OWB_GBS_20122009BOPA2_AB_Plate58
OWB_GBS_20122009BOPA2_WA_Plate48
OWB_GBS_20122009BOPA2_VT_Plate18
OWB_GBS_20122009BOPA2_UT_Plate68
OWB_GBS_20122009BOPA2_OR_Plate20
OWB_GBS_20122009BOPA2_N6_Plate98
OWB_GBS_20122009BOPA2_N2_Plate88
OWB_GBS_20122009BOPA2_MT_Plate108
OWB_GBS_20122009BOPA2_MN_Plate30
OWB_GBS_20122009BOPA2_BA_Plate78
OWB_GBS_20122009BOPA1_WA_Plate414
OWB_GBS_20122009BOPA1_VT_Plate114
OWB_GBS_20122009BOPA1_UT_Plate614
OWB_GBS_20122009BOPA1_OR_Plate222
OWB_GBS_20122009BOPA1_N6_Plate914
OWB_GBS_20122009BOPA1_N2_Plate814
OWB_GBS_20122009BOPA1_MT_Plate1014
OWB_GBS_20122009BOPA1_MN_Plate322
OWB_GBS_20122009BOPA1_BA_Plate714
OWB_GBS_20122009BOPA1_AB_Plate514
OWB_GBS_20122006BOPA2_UT_Plate68
OWB_GBS_2012POPA1_Steptoe_Morex_Mapping14
OWB_GBS_2012POPA1_Oregon_Wolf_Barley_Mapping14
OWB_GBS_2012POPA1_Morex-Barke_Mapping14
OWB_GBS_2012POPA1-2_CAPcore14
OWB_GBS_20122008BOPA2_MT_Plate108
OWB_GBS_20122008BOPA1_MT_Plate1014
OWB_GBS_20122008BOPA2_WA_Plate48
OWB_GBS_20122008BOPA1_WA_Plate414
OWB_GBS_20122008BOPA2_VT_Plate18
OWB_GBS_20122008BOPA1_VT_Plate114
OWB_GBS_20122008BOPA2_UT_Plate68
OWB_GBS_20122008BOPA1_UT_Plate614
OWB_GBS_20122008BOPA2_OR_Plate28
OWB_GBS_20122008BOPA1_OR_Plate214
OWB_GBS_20122008BOPA2_N6_Plate98
OWB_GBS_20122008BOPA1_N6_Plate914
OWB_GBS_20122008BOPA2_N2_Plate88
OWB_GBS_20122008BOPA1_N2_Plate814
OWB_GBS_20122008BOPA2_MN_Plate38
OWB_GBS_20122008BOPA1_MN_Plate314
OWB_GBS_20122008BOPA2_BA_Plate78
OWB_GBS_20122008BOPA1_BA_Plate714
OWB_GBS_20122008BOPA2_AB_Plate58
OWB_GBS_20122008BOPA1_AB_Plate514
OWB_GBS_2012POPA2_Steptoe-Morex_Mapping5
OWB_GBS_2012POPA2_OWB_Mapping5
OWB_GBS_2012POPA2_CAPcore5
OWB_GBS_2012POPA2_Morex-Barke_Mapping5
OWB_GBS_2012POPA3_Morex-Barke_Mapping3
OWB_GBS_2012POPA3_Steptoe-Morex_Mapping3
OWB_GBS_2012POPA3_OWB_Mapping3
OWB_GBS_2012POPA3_CAPcore3
OWB_GBS_20122006BOPA2_OR_Plate28
OWB_GBS_20122007BOPA2_WA_Plate48
OWB_GBS_20122007BOPA2_VT_Plate18
OWB_GBS_20122007BOPA2_OR_Plate28
OWB_GBS_20122007BOPA2_N6_Plate98
OWB_GBS_20122007BOPA2_N2_Plate88
OWB_GBS_20122007BOPA2_MT_Plate108
OWB_GBS_20122007BOPA2_MN_Plate38
OWB_GBS_20122007BOPA2_BA_Plate78
OWB_GBS_20122007BOPA2_UT_Plate68
OWB_GBS_20122007BOPA2_AB_Plate58
OWB_GBS_20122007BOPA1_WA_Plate414
OWB_GBS_20122007BOPA1_VT_Plate114
OWB_GBS_20122007BOPA1_OR_Plate214
OWB_GBS_20122007BOPA1_N6_Plate914
OWB_GBS_20122007BOPA1_N2_Plate814
OWB_GBS_20122007BOPA1_MT_Plate1014
OWB_GBS_20122007BOPA1_MN_Plate314
OWB_GBS_20122007BOPA1_BA_Plate714
OWB_GBS_20122007BOPA1_UT_Plate614
OWB_GBS_20122007BOPA1_AB_Plate514
OWB_GBS_20122006BOPA2_WA_Plate48
OWB_GBS_20122006BOPA2_VT_Plate18
OWB_GBS_20122006BOPA2_N6_Plate98
OWB_GBS_20122006BOPA2_N2_Plate88
OWB_GBS_20122006BOPA2_MT_Plate108
OWB_GBS_20122006BOPA2_MN_Plate38
OWB_GBS_20122006BOPA2_BA_Plate78
OWB_GBS_20122006BOPA2_AB_Plate58
OWB_GBS_20122006BOPA1_WA_Plate414
OWB_GBS_20122006BOPA1_VT_Plate114
OWB_GBS_20122006BOPA1_OR_Plate214
OWB_GBS_20122006BOPA1_N6_Plate914
OWB_GBS_20122006BOPA1_N2_Plate814
OWB_GBS_20122006BOPA1_MT_Plate1014
OWB_GBS_20122006BOPA1_MN_Plate314
OWB_GBS_20122006BOPA1_BA_Plate714
OWB_GBS_20122006BOPA1_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.