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The definitive result was the mean of the parasite density of the two most concordant reading results.
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These mapped pairs are called concordant reads [ 1].
However, this can introduce additional issues when aligning other concordant reads.
Although only three concordant reads are needed to correct a given error, the optimal result is obtained using 50× of Solexa reads.
In terms of coverage, ~60% of all PA sites in the PolyA_DB have concordant reads observed in our data set.
NextGenMap mapped 9.4% of the pairs discordantly but we don't report this here because we re-align those reads with MaxSSmap.> -wrap-foot> Concoreads reare are pairs that are mapped within 500 base pairs.
Concordant read pairs map in the expected FR orientation, and are thought to correspond to regions that do not differ from the reference genome (in structural terms), whereas pairs with an "everted" RF orientation are indicative of tandem duplications [ 25].
On average, 76.1 % concordant read pairs were uniquely mapped and were kept for further analysis (Table 1).> -wrap-foot> The numbers in Bold is the sums of the three replicates for 2, 5 and 10 dpa fruit, respectively We then used Cufflink program (version 2.2.1) to assemble the aligned reads and to access the transcriptome complexity in early growth fruits.
The number of concordant unique reads in each library was counted with HTseq (http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html).html
To avoid transcription errors, the genotypes were read and entered into our database twice by two independent individuals, and only concordant readings were accepted.
In a concordant study of the custom MPS-SNP panel, only four MPS callings were missing due to coverage reads that were too low (<20), whereas the others were fully concordant with Sanger's sequencing results across the two control samples, that is, 9947A and 9948.
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