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Question: Interpretation of Tassel MLM output
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I've performermed GWAS by MLM in Tassel and got a tables with results. What is the meaning and biological interpretation of Effect and MarkerR2 columns of tables below (short example): Table1

Trait   Marker  Locus   Site    Allele  Effect  Obs
H   S01_13979   1   13979   C   -2,34E+01 57
H   S01_13979   1   13979   G   -2,98E+01   19
H   S01_13979   1   13979   S   0   1
H   S01_15671   1   15671   A   12,17981    63
H   S01_15671   1   15671   T   0   10
H   S01_60519   1   60519   A   4,98562 59
H   S01_60519   1   60519   G   0   12

Table2:

Trait   Marker  Chr Pos df  F   p   add_effect  add_F   add_p   dom_effect  dom_F   dom_p   errordf MarkerR2    Genetic Var Residual Var    -2LnLikelihood
H   None            0   NaN NaN NaN NaN NaN NaN NaN NaN 118 NaN 98,50852    174,05853   981,70492
H   S01_13979   1   13979   2   1,94541 0,15047 3,23034 1,3632  0,24689 26,59698    2,85018 0,09575 77  0,04521 98,50852    174,05853   981,70492   
H   S01_15671   1   15671   1   3,39907 0,06959 NaN NaN NaN NaN NaN NaN 73  0,04054 98,50852    174,05853   981,70492
H   S01_60519   1   60519   1   0,52195 0,47256 NaN NaN NaN NaN NaN NaN 71  0,00616 98,50852    174,05853   981,70492

Thanks, Denis

ADD COMMENTlink 15 months ago Denis • 70
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1

Regarding the Effect: it is the effect that your allele has on the phenotype (usually one allele arbitrarily receives an effect of 0). You might find this link useful.

Regarding the MarkerR2, here it is briefly explained (not sure how much this can help!)

ADD REPLYlink 15 months ago
Fabio Marroni
♦ 2.2k

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