Fig. 1

Exemplary output file from real patient data generated by Illumina NextSeq. Relative number of reads at seven positions analyzed in case of sample “Example_Illumina”. Reference bases are plotted at the negative y axis, detected bases in the mapped reads are plotted at the positive y axis (marked 5% threshold). Likely SNV at chr1:115,258,747 (reference C, ∼70% of the reads with high-quality C and ∼30% of the reads with high-quality T). No variant at chr2:25,467,204 (reference G, ∼100% of the reads with high-quality G). Unlikely SNV at chr2:198,267,280 (reference C, ∼95% of the reads with low-quality C, ∼5% of the reads with low-quality A). Likely deletion at chr4:106,157,106 (reference A, ∼75% of the reads with high quality A, ∼25% of the reads with deleted A). Known homozygous SNP at chr17:7,579,472 (reference G, polymorphism C displayed as additional reference base, ∼100% of the reads with high-quality C). Possible insertion of a “G”, but unlikely deletion at chr20:31,022,442 (reference G, ∼97% of the reads with high-quality G, ∼3% of the reads with deleted G, ∼30% of the reads with inserted high-quality G). Likely SNV at chr21:44,514,777 (reference T, ∼65% of the reads with high-quality T, ∼35% of the reads with high-quality G)