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. 2013 May;23(5):843–854. doi: 10.1101/gr.147686.112

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© 2013, Published by Cold Spring Harbor Laboratory Press

This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see http://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 3.0 Unported License), as described at http://creativecommons.org/licenses/by-nc/3.0/.

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Figure 3. — Substitution error rates as a function of expected and observed nucleotide during gap-fill. (A) Schematic illustrating mononucleotide and dinucleotide substitution dependencies being considered. All rates are shown for a given expected gap-fill mono- or dinucleotide, which is the complementary nucleotide(s) to the nucleotide(s) present in the target genomic DNA, considering only ≥Q41 fr-read base-calls and Q60 smc-read base-calls at putative homozygous positions based on GATK calls. (B) Distributions of substitution error rates for eight HapMap cell line and 45 clinical cancer samples, comparing fr-reads and smc-reads, and all substitutions other than C>A or G>A (W>N + N>B, left) to only C>A (middle), or G>A (right). (C) Distributions of substitution error rates comparing fr-reads and smc-reads, and all G>A substitutions occurring in the non-CG dinucleotide context (DG>DA + GN>AN, left) to G>A substitutions occurring only in the CG dinucleotide context (CG>CA, right).