The binning of the sequenced reads (demultiplexing) allowed a maximum of one mismatch in each index. The demultiplexed libraries were processed and mapped using the EAGER (v 1.92.54) pipeline (33). The adapter sequences were clipped, and reads were filtered for the ones longer than 30 base pairs using AdapterRemoval (v2.2.0) (34). Adapter-clipped reads were aligned to the UCSC genome browser human genome reference hg19 using BWA aln/samse alignment software (v0.7.12) (35) with a lenient stringency parameter (“-n 0.01”) and by retaining only reads with Phred-scaled mapping quality scores ≥ 30. Duplicate reads were removed with DeDup v0.12.2 (33). To eliminate genotyping bases with retained damage, the two terminal positions in each read were clipped, and subsequently, a pseudo-diploid genotype was reconstructed for each individual using pileupCaller by performing a random choice between high-quality bases (Phred-scaled base quality score ≥ 30) aligning to each targeted SNP position (https://github.com/stschiff/sequenceTools).

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