Can ZOOM utilize the quality score of reads to enhance mapping results?
Answer. Yes. For Illumina/Solexa data, ZOOM adopts two ways to utilize quality score to enhance mapping results. The first way is to only count mismatches occurring on high quality positions. The second one is to utilize quality score of each base of read to compute the mapping probability of possible alignments for each read and choose best or top N mapping results according to the mapping probability. For ABI SOLiD data, because ZOOM can differentiate possible genomic differences from sequencing errors on color space, ZOOM computes the mapping probability of alignments for each read utilizing both quality scores and the probability of a SNP occurring in the organism you sequenced. Then it uses the mapping probability to assess and choose best or top N mapping results for each read.
