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After read mapping, we discarded the reads mapped to multiple chromosomal positions and unmapped reads.
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In our experiments, to avoid mapping errors, we discarded all hits with an identity score lower than 95% as well as those with a starting alignment position beyond the third base.
If a single locus aligned to multiple map loci, we discarded all alignments for that locus.
Hence, the average number of sequences mapped by chance to the genome in 5 or fewer sites (since we discarded reads mapping to >5 positions in our analysis), M, is given by: (2) where N is the number of sequences to be mapped in each step.
We discarded reads mapped to multiple genomic positions.
SNPs with skewed segregations (P < 0.05) were used for mapping and discarded only if unlinked.
If a mapping presented the same percentage of identity and coverage to more than one gene, the mapping was discarded.
We modified our insertion site analysis pipeline such that any experimental sequence read not meeting the minimum required length for accurate and unique mapping was discarded.
Then we obtained all the 3' most tags in the transcriptome, checked if they were unique in the transcriptome mapping, and discarded those genes with non-unique 3' most tags.
Reads that either mapped to multiple locations or did not map were discarded.
Variations with an occurrence below 99%% in the mapping step were discarded from the study.
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