Here, we show that the short-term consumption of diets composed entirely of animal or plant products alters microbial community structure and overwhelms inter-individual differences in microbial gene expression. Long-term diet influences the structure and activity of the trillions of microorganisms residing in the human gut1–5, but it remains unclear how rapidly and reproducibly the human gut microbiome responds to short-term macronutrient change. We estimated that the error rate of raw genotype calls is as high as 1 in 10–15kb, but the error rate of post-filtered calls is reduced to 1 in 100–200kb without significant compromise on the sensitivity. By investigating false heterozygous calls in the haploid genome, we identified the erroneous realignment in low-complexity regions and the incomplete reference genome with respect to the sample as the two major sources of errors, which press for continued improvements in these two areas. Results: We made ten SNP and INDEL call sets with two read mappers and five variant callers, both on a haploid human genome and a diploid genome at a similar coverage. However, in the lack of an unbiased whole-genome truth set, the global error rate of variant calls and the leading causal artifacts still remain unclear even given the great efforts in the evaluation of variant calling methods. Motivation: Whole-genome high-coverage sequencing has been widely used for personal and cancer genomics as well as in various research areas.
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