Comparative results between cochlea (yellow) and ossicle (green) samples from the same individuals; bold font indicates the samples that were used in Wilcoxon signed-rank test. (A) Endogenous shotgun DNA ratios of the total reads. (B) Complexity as percentage of unique reads expected from 500,000 reads hitting targets. (C) Deamination frequencies on the terminal bases of sequences aligning to the human genome. (D) Contamination estimates calculated by subtracting the rate of mitochondrial matches to the consensus sequence from one (smooth bars) and based on the heterozygosity of the X Chromosome of male individuals (textured bars). Error bars, 95% confidence interval.