SNP sequences identified among Canton S, Oregon R, w;iso2;iso3, y;cnbwsp, and pairwise combinations of 17 P element strains. Identified SNPs are listed according to the STS from which they were derived. For each SNP entry, the approximate cytological location and ~10 bp of sequence flanking the polymorphic site are indicated. Cytological locations are derived from the P1-based genome physical map (Kimmerly et al. 1996), and confirmed by comparison of the STS sequence to a database of Release 1 genome sequences with associated cytological locations (Adams et al. 2000). "Nucleotide Position" refers to nucleotide positions within sequence assemblies and is included to provide relative, rather than absolute positions for each polymorphism. The identity of the dimorphic base for each SNP is listed for each strain, and the corresponding Phred quality score of that base in the sequence trace is listed parenthetically. Sequences from the y;cn bw sp strain were derived from the Release 1 sequence where available. Restriction endonucl eases listed under "RFLP?" are those for which the recognition site is present in one allele and absent in the other. The location of P element insertions (designated as Q1040, etc.) is indicated, and SNP sequences are listed between each pairwise set of P element strains that can be used for eye color-based selection of recombinants in that interval. All polymorphisms between the w;iso2;iso3 and P element strains were initially detected by Denaturing HPLC.