Table S2. SNPs identified on chromosome 3
PCR amplicon namea / Predicted cytologyb / Genomic positionb / Context [+]c / Base present in:d / Assay
P[w+]-P[w+] /

y w-iso

/ mutant
3L:8.9a / 66E / 3L:8,891,419-8,891,617 / - / - / - / - / SSCP
3L:8.9b / 66E / 3L:8,900,023 / CATTTTAGTTCTAATTATATG / C / C / A / SEQ
3L:8.9c / 66E / 3L:8,906,203 / CACAGAACAAAGATTTTTGCG / A / A / T / SEQ
3L:8.9d / 66E / 3L:8,916,597 / AGCAAATTACGTGCAACTTCT / G / G / T / SEQ
3L:8.9e / 66E / 3L:8,924,387 / GATGACCTTCATATCAAGTTG / A / A / T / SEQ
3L:8.9f / 66E / 3l:8,929,952-8,930,229 / - / - / - / - / SSCP
3L:8.9g / 66E / 3L:8,934,422 / ATGTTTATTGAGCTTCATTTA / A / A / T / SEQ
3L:8.9h / 66E / 3L:8,937,619-8,938,001 / - / - / - / - / SSCP
3L:9.0a / 66F / 3L:8,962,678-8,962,849 / - / - / - / - / SSCP
3L:9.0b / 66F / 3L:8,967,141-8,967,364 / - / - / - / - / SSCP
3L:9.0c / 66F / 3L:8,980,756-8,980,935 / - / - / - / - / SSCP
3L:9.0d / 66F / 3L:9,059,586-9,059,759 / - / - / - / - / SSCP

a PCR amplicons of ~ 1 kb in length were sequenced for initial identification of SNPs.

b Based on the D. melanogaster Genome Release 3.2.

c The SNP is indicated with a black highlight in the context of 20 bp of flanking genomic sequence.

d ‘P[w+]-P[w+]’refers to theisogenizedl(3)s2383s2383-l(3)j2B9j2B9recombinant mapping chromosome; ‘mutant’ refers to the isogenized pix3c3 mutant chromosome; both the mapping and mutant chromosomes were put in trans with an isogenized third chromosome derived from a y w strain (‘y w-iso’) in order to unambiguously identify dimorphic SNPs.