Analysis_Plots_afterSync_2018.md

Ancestral Pi for Novoalign

Fst Plots:

Generation 38:

Generation 77:

Generation 115:

Fst Comparisons:

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meanFst: Selection vs. Conrtrol: Generation 38

meanFst: Control vs. Control: Generation38

meanFst: Selection vs. Selection: Generation38

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meanFst: Selection vs. Conrtrol: Generation 77

meanFst: Control vs. Control: Generation77

meanFst: Selection vs. Selection: Generation77

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meanFst: Selection vs. Control: Generation115

meanFst: Control vs. Control: Generation115

meanFst: Selection vs. Selection: Generation115

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Model Outputs:

Treatment x Generation -log10(meanP-value) for model output:

Treatment x Generation: -log10(meanP) with Bonferroni Correction for multiple comparisons:

Treatment x Generation -log10(meanP-value) for model output: colours dictate the qunatiles (the top 1% in dark grey, green being the top 0.01% of positions)

Just the top 1% of positions (~ 32000 positions)

Comparison Of Model and Fst

Full Chromosome:

-- Numbers/ peaks do not line up perfectly (product of how they are plotted/ measured (windows vs. positions)

Individual chromosome plots:

-- line up per position, but the fst have 1/500th (ish) data points (windows of 500 used)

X Chromosome

2L Chromosome

2R Chromosome

3L Chromosome

3R Chromosome

4 Chromosome

The 2L peak seems consistant and present in both Fst and Model output:

2L:4991444..5304468 in flybase.org