SNP Calling Consed can detect SNPs (including indels) and calculate the SNP quality (the probability that there is actually no SNP but all of the non-reference bases are base-calling errors) using the method of Li as implemented by MAQ (Li, H., J. Ruan, and R. Durbin, Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res, 2008. 18(11): p. 1851-8). The list of SNPs can be displayed in consed. The user can click on a SNP to view the reads and bases at that location, or can repeatedly click "next" to sequentially view locations of each SNP in the list. Consed can also generate in batch a VCF format report of SNPs. Our implementation differs from that in MAQ in that we always consider the reference base to be one of the 2 possible alleles, regardless of its observed frequency in the reads. We assign prior probabilities of 1-R, 2R/3, and R/3 to homozygous reference, heterozygous, and homozygous alternate respectively, where R=.001. Our filters are slightly different: No position is considered unless it has a non-reference base (or indel) of quality 20. We ignore any bases with quality < 10, we ignore any reads with mapping quality < 10, and we require at least 3 reads that pass these filters. We require at least one read to have a mapping quality 20. We do not discard snps flanking a potential indel nor do we discard clusters of potential SNPs in a 10-base window since these filters were designed to handle problems from an ungapped alignment which are not problems with gapped aligners such as our phaster (P. Green unpublished). MAQ's methods include a factor of 0.85**k where k is the number of discrepant reads, but we do not allow this factor to get smaller than 0.85**20 regardless of the number of reads.