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Bioinformatically predicted mapping positions were validated using oat × maize chromosome addition and radiation hybrid lines [ 18, 21].
Estimated PCR duplicates (pairs of reads defining fragments with identical start and stop mapping positions) were also filtered out.
When multiple mapping positions were obtained for the same read, a single hit was considered (the most significant one).
The advantage of this genetic map for QTL analysis was that mapping positions were represented by nonconflicting and nonoverlapping markers such that a genome scan procedure was appropriate for all traits.
For cis-NATs mapping, all clean reads from the 8 libraries from both leaf and root were mapped to Arabidopsis cis-NATs pairs regions with no mismatch allowed and all mapping positions were kept for each read.
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Based on SAM files all samples were anonymized before downstream analysis so only information about reads mapping positions was used.
For convenient visualization, the genomic mapping positions are combined with expression profiles in.igv files (http://www.broadinstitute.org/igv/).org/igv/
Such an integrative approach is advantageous over simply using the rank of feature positions, since mapping positions are not always uniformly distributed and the spatial patterns may be of interest in experiments like DMR detection.
Using NCBI Build 35, 16,097 unique map positions were defined with a median interval between mapped elements of 54.8 Kb.
Genetic analysis showed that all the markers segregated in the expected 1 1 ratio and map positions were determined for all 23 loci.
Precise gene orders were often left unresolved because map positions were typically determined by comparing two-point recombination frequencies rather than by analyzing definitive three-point backcrosses.
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