Fig. 3

Read counts, automatic genotype calls and validation results for the 60-loci libraries. a: Specific read counts for E reactions for 12 samples at each of 60 L1 loci. Blue and black circles represent, respectively, the present and absent calls made based on the clustering of read counts. Crosses indicate genotypes with a quality score less than 7. Triangles (locus 28) indicate genotypes that would be called “present” (blue) because of high read count but that were called “absent” because the L1 sequence was detected in the reads (in the case of very short L1 insertions). b: Specific read counts obtained for E reactions for loci that passed quality control. Green and red circles indicate, respectively, concordant and discordant calls for 25 loci that were validated individually using single-locus PCR reactions and gel electrophoresis. All calls were concordant. Locus 41 was excluded from the analysis because the primers did not work. c: Same as a but for the G libraries. d: Same as b for 23 loci that passed quality control and that were individually validated. All calls were concordant