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Chunk #2 — Results — Sequencing statistics

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A comparison of BeadChip and WGS genotyping outputs using partial validation by sanger sequencing.
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Table 1 lists the sequencing statistics for the three sequenced samples. FastQC reports are available as Additional files 1, 2, 3, 4, 5 and 6 for sample_001, sample_002, sample_003, respectively. Percentage of reads falling into a category with averaged Phred scaled sequencing quality above 30 is shown by %Q. The absence of unpaired reads, repeatability in terms of GC content and more than 90% of bases exceeding sequencing quality of 30 was used as a mark of confidence in data quality. Table 1Raw sequencing data statistics summarySampleRead orientationMean read quality (Phred score)Number of reads% GC% Q > 30Number of bases (1e6)Mean read length (bp)001R139.3139903635841.0795.5659855.45150.0R236.7639903635841.2186.1759855.45150.1002R139.2837590016841.0695.4756385.03150.2R236.837590016841.2286.3256385.03150.3003R139.3238582601240.9595.5957873.9150.4R236.4938582601241.0885.1557873.9150.5The table describes the raw sequencing data quality metrics for all sequenced samples; GC Guanine-cytosine sequence content