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It therefore follows that in order to develop a model based on geographical features one would either need to identify a key feature that can be mapped on multiple geographical scales, or a combination of geographical features that can exist across multiple scales.
Even after this restrictive procedure, single RNA sequences can be mapped on multiple locations due to the genomic repeats contained in the genome such as transposable elements and tRNA.
DROMPA can accept multiple mapped reads (reads mapped on multiple loci of the reference genome), whereas most available peak-calling programs can only accept uniquely mapped reads (reads mapped onto the reference genome only once).
Therefore, if this estimation can be generalized, the AHGS and AhTE markers mapped on multiple maps can be considered as potential sources for obtaining polymorphic markers in other mapping populations.
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In this mapping analysis, when a read could be mapped to multiple positions on the reference sequence, the one where the number of mismatches was the smallest was chosen; if there were multiple candidates for the least mismatch, the read was mapped to every position as if it was multiplied.
A total of 14 QTLs were mapped on chromosome 6 alone; multiple major genes for good traits have been pyramided in R1128, including Sd1 for plant height, Hd1 and Ehd1 for heading date, Gn1a for grain number and IPA1 for ideal plant shape.
We did gene enrichment analyses of the significant QTL mapped on Chr 9 with multiple parameters that included linkage, gene ontology, variation in gene expression, polymorphism, co-citation networks, and biological relevance.
In this analysis, the reads that were mapped to multiple positions on the genome were excluded.
Reads that mapped onto multiple locations on the genome were removed with Filter SAM (version 1.0.0).
How do they deal with the reads that can be mapped to multiple locations on a reference genome?
The work reported in this manuscript effectively generates 20-base pair tags and the % of tags mapped to multiple locations on genome would be slightly higher.
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