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Redundant reads were subtracted before variant callings.
Redundant reads were discarded within each replicate.
Redundant reads sharing 100% identity were removed using CD-HIT-454 [ 41].
Redundant reads were removed using the duplicate removal plugin in CLC.
Redundant reads were removed, and those from the two biological replicates were merged into a single data set.
Redundant reads were reduced to 46,646 contigs with the average contig length of 297 bases covering 13.85 Mb.
Redundant reads resulting in duplicate base calls were filtered at a threshold of a Euclid distance ≤ 3 and a mismatch rate of ≤ 0.1.
The impact of redundant reads would most likely have influenced allelic balance and genotype calling results.
In seedling, greater than 30% of the ∼21-nt ∼21-ntant redundantched to known mireads
Consistent with previous reports, the 21-nt small RNAs comprised many redundant reads, whereas the 24-nt class comprised primarily unique or low abundance reads.
Non-perfectly redundant reads weredundantapped onto the human genome, readsring the alignment to start werein thanfirst three nucleotides and to possess a mappedm onto0% identhey.
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