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Synthetic Spike-in Standards Improve Run-Specific Systematic Error Analysis for DNA and RNA Sequencing

Figure 3

Comparison of GATK BQSR scores for recalibration based on the genome vs. recalibration based on the spike-in standards.

The differences in quality score recalibration values are calculated for each combination of reported quality score and cycle (a and c) or reported quality score and dinucleotide (b and d) for Illumina (a and b) and SOLiD (c and d). White blocks correspond to very large differences, generally with very few errors. The differences are (genome – spike-in standard), so blue (<0) indicates that genome recalibration would result in recalibrated quality scores that are too low, and yellow/red (>0) results in recalibrated quality scores that are too high. The p values for the differences are shown in Figure S2.

Figure 3

doi: https://doi.org/10.1371/journal.pone.0041356.g003