From: Lacey S. <la...@ma...> - 2009-10-30 19:59:25
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I am seeing a discrepancy between the source listed in the details page and the correct one. If I hide all tracks containing Redberry sourced SNPs and then choose one (ex: L01827A) The details page still shows the source as Redberry. Notice that in the example shown below there isn't even a Redberry SNP at that position!!! I haven't done any configuration to the details page for the SNP feature and the track link = AUTO. I'm using Gbrowse 1.66 You can look at the gbrowse installation here: http://128.233.29.40/cgi-bin/gbrowse/Medicago_test/ Thanks for any help! I'm completely stumped! Lacey Details page for the same SNP (Names are unique to each SNP): Name: Lc_TOG895724_1_003_00001_Nov08_883 Type: SNP Source: Redberry Position: chr07:24031174..24031174 Length: 1 Score: 50 Note: "Source:UC Davis Cos Genotype:C Comment:RBvs827/P17" load_id: Redberry_TOG895724_chr07_24031174 >Lc_TOG895724_1_003_00001_Nov08_883 class=Sequence position=chr07:24031174..24031174 A Note: This page uses cookies to save and restore preference information. No information is shared. Generic genome browser version 1.66 The offending lines in the GFF: chr07 L01827A SNP 24031174 24031174 50 . . ID = L01827A_TOG895724_chr07_24031174 ;Name=Lc_TOG895724_1_003_00001_Nov08_883;Note="Source:UC Davis Cos,Genotype:A,Comment:RBvs827/P17" chr07 P172815 SNP 24031174 24031174 50 . . ID = P172815_TOG895724_chr07_24031174 ;Name=Lc_TOG895724_1_003_00001_Nov08_883;Note="Source:UC Davis Cos,Genotype:A,Comment:RBvs827/P17" Track Stanzas: [SNP_Eston_lensCOS] feature = SNP:Eston glyph = diamond category = Lentil:Polymorphisms description = 0 height = 10 fgcolor = white bgcolor = sub { my $feature = shift; my @note = $feature->notes; if ($note[1] =~ /.*Genotype:T.*/) { return "crimson"; } elsif ($note[1] =~ /.*Genotype:A.*/) { return "lawngreen"; } elsif ($note[1] =~ /.*Genotype:C.*/) { return "blue"; } elsif ($note[1] =~ /.*Genotype:G.*/) { return "black"; } else { return "yellow"; }} label = 0 link = AUTO key = Eston SNPs citation = SNPs generated from the UC Davis COS TOGs for the Eston line. The background colours indicate the base at that location: T- red, A-green, C-blue, G-black. [SNP_Redberry:lensCOS] feature = SNP:Redberry glyph = diamond category = Lentil:Polymorphisms description = 0 height = 10 fgcolor = white bgcolor = sub { my $feature = shift; my @note = $feature->notes; if ($note[1] =~ /.*Genotype:T.*/) { return "crimson"; } elsif ($note[1] =~ /.*Genotype:A.*/) { return "lawngreen"; } elsif ($note[1] =~ /.*Genotype:C.*/) { return "blue"; } elsif ($note[1] =~ /.*Genotype:G.*/) { return "black"; } else { return "yellow"; }} label = 0 link = AUTO key = Redberry SNPs citation = SNPs generated from the UC Davis COS TOGs for the Redberry line. The background colours indicate the base at that location: T- red, A-green, C-blue, G-black. [SNP_L01827A_lensCOS] feature = SNP:L01827A glyph = diamond category = Lentil:Polymorphisms description = 0 height = 10 fgcolor = white bgcolor = sub { my $feature = shift; my @note = $feature->notes; if ($note[1] =~ /.*Genotype:T.*/) { return "crimson"; } elsif ($note[1] =~ /.*Genotype:A.*/) { return "lawngreen"; } elsif ($note[1] =~ /.*Genotype:C.*/) { return "blue"; } elsif ($note[1] =~ /.*Genotype:G.*/) { return "black"; } else { return "yellow"; }} label = 0 link = AUTO key = L01827A SNPs citation = SNPs generated from the UC Davis COS TOGs for the L01-827A line. The background colours indicate the base at that location: T- red, A-green, C-blue, G-black. [SNP_P172815_lensCOS] feature = SNP:P172815 glyph = diamond category = Lentil:Polymorphisms description = 0 height = 10 fgcolor = white bgcolor = sub { my $feature = shift; my @note = $feature->notes; if ($note[1] =~ /.*Genotype:T.*/) { return "crimson"; } elsif ($note[1] =~ /.*Genotype:A.*/) { return "lawngreen"; } elsif ($note[1] =~ /.*Genotype:C.*/) { return "blue"; } elsif ($note[1] =~ /.*Genotype:G.*/) { return "black"; } else { return "yellow"; }} label = 0 link = AUTO key = P172815 SNPs citation = SNPs generated from the UC Davis COS TOGs for the P172815 line. The background colours indicate the base at that location: T- red, A-green, C-blue, G-black. |