Appendix SmartPhase

where n is the number of reads overlapping two variant positions, ntrans is the number of reads supporting a trans configuration while giving equal evidence to both variants, ncis is the number of reads containing both variants, qk is the Phred quality score of a read at a particular position k, and l represents the length of the variant allele being examined in this read (either v1 or v2). The Phred quality score assesses the quality of base determination during sequencing and is logarithmically related to the base-calling error probability. A Phred quality score of 10 corresponds to a base call accuracy of 90% while a Phred quality score of 60 represents a base call