Fig. 3

Results from comparisons made with single base observations from extremely low-coverage sequencing data. Each panel shows the results of 10 comparisons made between four low-coverage subsamples of reads sequenced from two human individuals (NA12891 and NA12892 from the CEU pedigree) using a reference panel of haplotypes from the 1000 Genomes CEU subpopulation. Comparisons made from samples from the same individual are shown in blue, with comparisons made within the sample shown as a dashed line. Comparisons made from samples from different individuals are show in red. At the extremely low coverage of 0.01 % fold, very few usable pairs of SNPs can be found. As coverage increases above 0.1 % fold, the two groups of comparisons are easily separable. Comparisons made within a sample have less extreme LLR values as they were made with less read coverage than across-sample comparisons