Sequencing templates were made from P1, BAC and WGS DNA libraries using the D. melanogaster strain yellow (y1); cinnabar (cn1) brown (bw1) speck (sp1). This isogenic strain was constructed in the early 1990s [26 (link)]; the P1 [27 (link)], BAC [11 (link)] and WGS DNA libraries [1 (link)] were made in 1990, 1998 and 1999, respectively. Although we have not determined the single-nucleotide polymorphism rate between the libraries, we observed four cases of insertional polymorphisms in which BACs contain transposable elements that are absent from the Release 2 WGS assembly; two on the X, a gtwin element in BACR33A08 and a 412 element in BACR29P19; one on chromosome 2, a roo in BACR01K07 and one on chromosome 3, a roo in BACR02C22. We have confirmed the molecular mutation of the y1 allele as an A to C transversion in the ATG translation initiation codon as first determined by Geyer et al. [28 (link)]. We determined the molecular lesion of the cn1 allele to be a 1,832 bp deletion relative to wild type. The mutation in bw1 was known to be associated with an uncharacterized insertion [29 (link)]. We have identified the insertion to be a 412 transposable element mapping to the third exon. The wild-type sp gene, located genetically and cytologically to 60 C, has not yet been molecularly characterized. However, sp1 is known to be suppressible by suppressor of sable [30 (link)], a known suppressor of 412 elements. Two 412 elements map to 60 C, one in Dat and another near Nop60B.