Contact Us

• Home
• Select
  • Wizard (Lines, Traits, Trials) Lines by Properties
  • Lines by Phenotype
  • Lines by Haplotype
  • Lines by Genotype Experiment
  • Traits and Trials
  • Markers
  • Subset by Marker Polymorphisms
  • Genetic Map
  • Clear selection
• Analyze
  • Cluster
    • Cluster Lines by Genotype
    • Cluster Lines 3D (pam)
    • Cluster Lines 3D (hclust)
  • Filter outliers
  • Optimize training set
  • Selection Index
  • Traits and Trials statistics
    • Traits and Trials Histogram
    • Traits and Trials Boxplot
    • Traits and Trials Table
  • Canopy Spectral Reflectance
  • Genomic Association and Prediction
  • Compare Trials
  • Track Alleles through Pedigree
  • Parse Purdy Pedigrees
  • Allele Data Conflicts
  • BLAST
  • Haplotype Data
• Download
  • Genotype and Phenotype Data
  • SNP Alleles and Sequences
  • Marker Annotation
  • Bulk Download
  • Android Field Book
  • Genetic Maps
• Search
  • Genes
  • Proteins
  • Pathways
• Reports
  • GWAS Results
  • Variant Effects
  • Marker Alignment to Reference
  • Marker Synonyms by Experiment
  • JBrowse - Genome Browser
    • IBSC v2
• Manage
  • Phenotype Trials
• Resources
  • Overview
  • Tutorials
  • Content Status
  • Data Submission
  • Trait Descriptions
  • Genetic Character Descriptions
  • Contributing Data Programs
  • Data Usage Policy

Quick Links

• Login/Register

• Current selections:
• Lines:
• Markers: All
• Traits: 0
• Genotype Experiments
  
  

What's New

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 CAPV2011_MN_9K

Experiment 1	Experiment 2	matches to markers between trials
CAPV2011_MN_9K	2020_NDSU_Eurofins	5
CAPV2011_MN_9K	2018_CCRU_50K	30
CAPV2011_MN_9K	2019_GBS_WBDC	0
CAPV2011_MN_9K	UMN_NSGC_GWAS	13
CAPV2011_MN_9K	2015GBS_MN	0
CAPV2011_MN_9K	2019N2YUMA	3
CAPV2011_MN_9K	2015iSelect_MN_plate1	36
CAPV2011_MN_9K	2016GBS_WBDC	0
CAPV2011_MN_9K	2018_NDSU_Yuma_2R	3
CAPV2011_MN_9K	2017_NDSU_Yuma_2R	4
CAPV2011_MN_9K	2016_N2_PYTBC	2
CAPV2011_MN_9K	2016N2PYTA	1
CAPV2011_MN_9K	2016_HapMap_WEC	0
CAPV2011_MN_9K	2015N2PYT	2
CAPV2011_MN_9K	WBIP384_HOUH_2013	1
CAPV2011_MN_9K	WBIP384_ABNAM_2012	1
CAPV2011_MN_9K	2014_NDSU_9K	33
CAPV2011_MN_9K	2006BOPA1_UT_Plate6	14
CAPV2011_MN_9K	BOPA1_MN_WB_2011	14
CAPV2011_MN_9K	9K_MN_GEN10_2013	39
CAPV2011_MN_9K	9K_MN_CAP6_2013	39
CAPV2011_MN_9K	OWB_GBS_2012	0
CAPV2011_MN_9K	WBIP_9K_Parents	35
CAPV2011_MN_9K	VC_MNWC4_2013_384	2
CAPV2011_MN_9K	TCFW6_LTT_9K	35
CAPV2011_MN_9K	Ethiopia_Eritrea_9K	37
CAPV2011_MN_9K	VC_MNWC3_2013_384	2
CAPV2011_MN_9K	MorexBarke_GBS_2012	0
CAPV2011_MN_9K	2011BOPA1_MN_WC0	14
CAPV2011_MN_9K	VC_MNWC2_2012_384	2
CAPV2011_MN_9K	VC_MNWC1_2011_384	2
CAPV2011_MN_9K	VC_MNSC3_2012_384	0
CAPV2011_MN_9K	VC_MNSC2_2011_384	0
CAPV2011_MN_9K	2010BOPA1_MN_GS_PARENTS	14
CAPV2011_MN_9K	2007BOPA1_MN_PRECAP	14
CAPV2011_MN_9K	VC_FHB2010_384	0
CAPV2011_MN_9K	CAPV2011_MN_9K	34
CAPV2011_MN_9K	2011_9K_NB_allplates	35
CAPV2011_MN_9K	2009BOPA2_AB_Plate5	5
CAPV2011_MN_9K	2009BOPA2_WA_Plate4	5
CAPV2011_MN_9K	2009BOPA2_VT_Plate1	5
CAPV2011_MN_9K	2009BOPA2_UT_Plate6	5
CAPV2011_MN_9K	2009BOPA2_OR_Plate2	0
CAPV2011_MN_9K	2009BOPA2_N6_Plate9	5
CAPV2011_MN_9K	2009BOPA2_N2_Plate8	5
CAPV2011_MN_9K	2009BOPA2_MT_Plate10	5
CAPV2011_MN_9K	2009BOPA2_MN_Plate3	0
CAPV2011_MN_9K	2009BOPA2_BA_Plate7	5
CAPV2011_MN_9K	2009BOPA1_WA_Plate4	14
CAPV2011_MN_9K	2009BOPA1_VT_Plate1	14
CAPV2011_MN_9K	2009BOPA1_UT_Plate6	14
CAPV2011_MN_9K	2009BOPA1_OR_Plate2	19
CAPV2011_MN_9K	2009BOPA1_N6_Plate9	14
CAPV2011_MN_9K	2009BOPA1_N2_Plate8	14
CAPV2011_MN_9K	2009BOPA1_MT_Plate10	14
CAPV2011_MN_9K	2009BOPA1_MN_Plate3	19
CAPV2011_MN_9K	2009BOPA1_BA_Plate7	14
CAPV2011_MN_9K	2009BOPA1_AB_Plate5	14
CAPV2011_MN_9K	2006BOPA2_UT_Plate6	5
CAPV2011_MN_9K	POPA1_Steptoe_Morex_Mapping	9
CAPV2011_MN_9K	POPA1_Oregon_Wolf_Barley_Mapping	9
CAPV2011_MN_9K	POPA1_Morex-Barke_Mapping	9
CAPV2011_MN_9K	POPA1-2_CAPcore	9
CAPV2011_MN_9K	2008BOPA2_MT_Plate10	5
CAPV2011_MN_9K	2008BOPA1_MT_Plate10	14
CAPV2011_MN_9K	2008BOPA2_WA_Plate4	5
CAPV2011_MN_9K	2008BOPA1_WA_Plate4	14
CAPV2011_MN_9K	2008BOPA2_VT_Plate1	5
CAPV2011_MN_9K	2008BOPA1_VT_Plate1	14
CAPV2011_MN_9K	2008BOPA2_UT_Plate6	5
CAPV2011_MN_9K	2008BOPA1_UT_Plate6	14
CAPV2011_MN_9K	2008BOPA2_OR_Plate2	5
CAPV2011_MN_9K	2008BOPA1_OR_Plate2	14
CAPV2011_MN_9K	2008BOPA2_N6_Plate9	5
CAPV2011_MN_9K	2008BOPA1_N6_Plate9	14
CAPV2011_MN_9K	2008BOPA2_N2_Plate8	5
CAPV2011_MN_9K	2008BOPA1_N2_Plate8	14
CAPV2011_MN_9K	2008BOPA2_MN_Plate3	5
CAPV2011_MN_9K	2008BOPA1_MN_Plate3	14
CAPV2011_MN_9K	2008BOPA2_BA_Plate7	5
CAPV2011_MN_9K	2008BOPA1_BA_Plate7	14
CAPV2011_MN_9K	2008BOPA2_AB_Plate5	5
CAPV2011_MN_9K	2008BOPA1_AB_Plate5	14
CAPV2011_MN_9K	POPA2_Steptoe-Morex_Mapping	8
CAPV2011_MN_9K	POPA2_OWB_Mapping	8
CAPV2011_MN_9K	POPA2_CAPcore	8
CAPV2011_MN_9K	POPA2_Morex-Barke_Mapping	8
CAPV2011_MN_9K	POPA3_Morex-Barke_Mapping	2
CAPV2011_MN_9K	POPA3_Steptoe-Morex_Mapping	2
CAPV2011_MN_9K	POPA3_OWB_Mapping	2
CAPV2011_MN_9K	POPA3_CAPcore	2
CAPV2011_MN_9K	2006BOPA2_OR_Plate2	5
CAPV2011_MN_9K	2007BOPA2_WA_Plate4	5
CAPV2011_MN_9K	2007BOPA2_VT_Plate1	5
CAPV2011_MN_9K	2007BOPA2_OR_Plate2	5
CAPV2011_MN_9K	2007BOPA2_N6_Plate9	5
CAPV2011_MN_9K	2007BOPA2_N2_Plate8	5
CAPV2011_MN_9K	2007BOPA2_MT_Plate10	5
CAPV2011_MN_9K	2007BOPA2_MN_Plate3	5
CAPV2011_MN_9K	2007BOPA2_BA_Plate7	5
CAPV2011_MN_9K	2007BOPA2_UT_Plate6	5
CAPV2011_MN_9K	2007BOPA2_AB_Plate5	5
CAPV2011_MN_9K	2007BOPA1_WA_Plate4	14
CAPV2011_MN_9K	2007BOPA1_VT_Plate1	14
CAPV2011_MN_9K	2007BOPA1_OR_Plate2	14
CAPV2011_MN_9K	2007BOPA1_N6_Plate9	14
CAPV2011_MN_9K	2007BOPA1_N2_Plate8	14
CAPV2011_MN_9K	2007BOPA1_MT_Plate10	14
CAPV2011_MN_9K	2007BOPA1_MN_Plate3	14
CAPV2011_MN_9K	2007BOPA1_BA_Plate7	14
CAPV2011_MN_9K	2007BOPA1_UT_Plate6	14
CAPV2011_MN_9K	2007BOPA1_AB_Plate5	14
CAPV2011_MN_9K	2006BOPA2_WA_Plate4	5
CAPV2011_MN_9K	2006BOPA2_VT_Plate1	5
CAPV2011_MN_9K	2006BOPA2_N6_Plate9	5
CAPV2011_MN_9K	2006BOPA2_N2_Plate8	5
CAPV2011_MN_9K	2006BOPA2_MT_Plate10	5
CAPV2011_MN_9K	2006BOPA2_MN_Plate3	5
CAPV2011_MN_9K	2006BOPA2_BA_Plate7	5
CAPV2011_MN_9K	2006BOPA2_AB_Plate5	5
CAPV2011_MN_9K	2006BOPA1_WA_Plate4	14
CAPV2011_MN_9K	2006BOPA1_VT_Plate1	14
CAPV2011_MN_9K	2006BOPA1_OR_Plate2	14
CAPV2011_MN_9K	2006BOPA1_N6_Plate9	14
CAPV2011_MN_9K	2006BOPA1_N2_Plate8	14
CAPV2011_MN_9K	2006BOPA1_MT_Plate10	14
CAPV2011_MN_9K	2006BOPA1_MN_Plate3	14
CAPV2011_MN_9K	2006BOPA1_BA_Plate7	14
CAPV2011_MN_9K	2006BOPA1_AB_Plate5	14

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.