Relationship between number of sequence reads, missing data, sequencing depth and the number of SNP calls.

(a) The average percentage of missing data per SNP in each sequenced sample is plotted as function of the number of sequence reads in that sample. (b) Histogram of missing data per SNP. (c) The number of SNP calls plotted against the minimum depth at a variant position in a given sample to make a successful genotype call. All SNP calls were made with the SAMtools pipeline. The minor allele frequency was set to 30% and the maximum rate of missing data was set to 50%. The sequencing platforms used for this study include Illumina HiSeq2000 (black), Ion Torrent PGM (green) and Ion Torrent Proton (red). The color code for all panels is given in the legend to (a).