Amplification bias and uniformity.

<p>(A) Local mapping density from properly mapped reads (at fixed 5x sampling depth), normalized to average 1, as a function of position along the reference sequence, for single-cell MDA (microfluidic in red, microfluidic+tube in orange). (B) Same as panel A, but for single-cell MALBAC and bulk NEB-WGA. (C) Fractional genome coverage from properly mapped read pairs, plotted as a function of gain. Here, each set of properly mapped read pairs was randomly down-sampled to 5x depth. Experiments that did not generate this many properly mapped reads were not included in the figure. (D) Fraction of the genome covered by mapped read pairs when the set of <i>raw</i> read pairs was down-sampled to a fixed depth of 20x, plotted as a function of gain. Filled symbols signify bulk experiments, open symbols single-cell experiments.