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Does anyone know the details about which line they are using to sequence as the Drosophila melanogaster reference genome?

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That was surprisingly buried.

I found this in a paper describing genome build 3 - See "Materials and Methods". I imagine that this is consistent through to the current build. In any case it should get you started.

"Sequencing templates were made from P1, BAC and WGS DNA libraries using the D. melanogaster strain yellow (y1); cinnabar (cn1) brown (bw1) speck (sp1)."

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