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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.

marker 1marker 2% homologylength
12_2148211_11153100121
12_2147111_11090100121
12_2095412_31167100121
12_1026411_20332100121
12_2023711_10150100121
12_1011411_20193100121
12_3153611_10627100121
12_3139811_11435100121
12_3116712_20954100121
12_3110011_21406100121
12_31064BK_11100121
12_31050BK_04100121
12_30871BK_1499.16119
12_3040411_20260100121
BK_1711_20188100202
SCRI_RS_115208SCRI_RS_188905100121
SCRI_RS_121003SCRI_RS_187354100121
SCRI_RS_13017712_3096010073
SCRI_RS_131218SCRI_RS_188893100121
SCRI_RS_172357SCRI_RS_17944799.14116
SCRI_RS_174946SCRI_RS_144101100121
SCRI_RS_179447SCRI_RS_17235799.14116
SCRI_RS_181112SCRI_RS_18262799.17121
SCRI_RS_182627SCRI_RS_18111299.17121
SCRI_RS_187354SCRI_RS_121003100121
SCRI_RS_188893SCRI_RS_131218100121
SCRI_RS_188905SCRI_RS_115208100121
SCRI_RS_188912SCRI_RS_8447099.17121
SCRI_RS_222748SCRI_RS_198854100121
SCRI_RS_32890SCRI_RS_185058100121
SCRI_RS_84470SCRI_RS_18891299.17121

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.