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The median sequence count was 2 (range: 2-29) patientient.
A total of 3,722,656 sequences passed all quality control filters, with a median sequence count of 41970 per sample.
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Another interesting point is that performance of MetaPSICOV with 200 effective sequences is roughly the same as the best individual covariation-based method with a median effective sequence count of 621 (the median for the original PSICOV test set).
The total consensus sequence count was 25965.
The range of reads mapped to a gene was comparable across runs, with the 9 lanes of increased sequence counts displaying a slight increase in median read number per gene.
Sequencing Count Matrices Document S2.
The 167 genes found to be significant by 454 cDNA sequencing, but not by microarray analysis, were mostly characterized by low fold changes from baseline (median fold change as estimated from 454 cDNA sequencing counts = 1.75); or conversely, registered low hybridization intensities in the microarray analysis (median rank among 4844 probe sets = 343).
The 1 716 022 loci and their flanking sequences harboured a median count of 1.47 SNP per 100 bp (SNP/hbp), and 1.35 SNP/hbp for the 6 bp of the seed sites that match nucleotides 2 7 of the miRNA seed motifs (Table 1).
The differential cell counts showed a median (range) lymphocyte count of 21% (0 75%) and neutrophil count of 79% (10 95%).
The median CD4 count is 331 mm3, and the median viral load was 714 copies/ml.
Median mitotic count was 2/50 high-power fields, with the highest count being 13/50 high-power fields.
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