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There are 32.11 Mb common across the three databases, but only about 24 Mb are covered by all four technologies.
In common regions covered by all four technologies, Agilent detects slightly higher number of SNVs, followed by Nextera, TruSeq and Nimblegen.
There are 26.2 Mb of the human genome shared by all four technologies; the majority of which falls in CCDS exonic regions.
A different trend was clear in the 26 Mb region shared by all four technologies, where Agilent detected the highest number of SNVs, followed by Truseq, Nextera, and NimbleGen.
At all the read counts, a disturbing fact was that very few indels were common across the four technologies, especially on CCDS, Ensembl and RefSeq regions.Figure 7B shows a head-to-head comparison of indel detection in the regions covered by all four technologies.
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These 17 pSNMs were validated by all three technologies and considered bona fide pSNMs.
Two regions, 13 bases in katG (codons 312-316) (2175164-2155176) and 17 bases in inhA promoter (-4 to -20), were sequenced by all three technologies.
Transcript and protein ratios across heart and skeletal muscle were shown to be positively correlated for 148 genes detectable by all three technologies.
We therefore focused primarily on the subset of genes detected by all three technologies, through a stringent mapping of MPSS and SAGE tags to known genes, with a further limit to those also present in the oligoarray design.
Spearman correlations and the 95% confidence intervals are presented for all the miRNAs that were present on a platform, or using the 54 sequence-matched miRNAs that were detected by all four microarray technologies.
Concordance correlation coefficients and the 95% confidence intervals are presented for all the miRNAs that were present on a platform, or using the 54 sequence-matched miRNAs that were detected by all four microarray technologies.
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