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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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Did you check the genome publication –  GWW Jul 26 '12 at 20:15
    
I just quickly went through it, but did not find any clue. –  Pengyao Jul 26 '12 at 20:46
    
As far as I know they just used a generic D. melanogaster lab strain. –  GWW Jul 26 '12 at 21:10
    
Do you know which lab strain? Oregan R? –  Pengyao Jul 27 '12 at 1:43
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does this help? fruitfly.org/annot/release3.html#strain –  Michael Kuhn Jul 27 '12 at 8:38
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up vote 5 down vote accepted

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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