IHS/BFS/2/1

This page describes a signal of selection found in the Burkina Faso An. gambiae populationusing the IHS (Cite et al. 20XX) statistic.The focus of this signal is on chromosome arm 2R between positions 28,260,000 and 28,540,000. The evidence supporting this signal is strong (\Delta_{i} >= 100 on both flanks).

This signal overlaps the Cyp6p locus, a genome region with prior evidence of an association with insecticide resistance and/or recent positive selection in Anopheles mosquitoes.

Signal location. Blue markers show the values of the selection statistic. The dashed black line shows the fitted peak model. The shaded red area shows the focus of the selection signal. The shaded blue area shows the genomic region in linkage with the selection event. Use the mouse wheel or the controls at the top right of the plot to zoom in, and hover over genes to see gene names and descriptions.

Genes

The following 32 genes overlap the focal region: AGAP002845, AGAP002846 (Trunk), AGAP013388 (Niemann-Pick Type C-2), AGAP002847 (Niemann-Pick Type C-2), AGAP002848 (Niemann-Pick Type C-2), AGAP002849 (Niemann-Pick Type C-2), AGAP002850 (Niemann-Pick Type C-2), AGAP002851 (Niemann-Pick C2 protein), AGAP002852, AGAP002853, AGAP002854, AGAP002855, AGAP002856, AGAP013529, AGAP013314, AGAP002857, AGAP002858 (Sodium/potassium-transporting ATPase subunit alpha), AGAP002859 (solute carrier family 8 (sodium/calcium exchanger)), AGAP0028621 (CYP6AA1 - cytochrome P450), AGAP0131281 (CYP6AA2 - cytochrome P450), AGAP0028631 (COEAE6O - carboxylesterase alpha esterase), AGAP0028641 (CYP6P15P - cytochrome P450), AGAP0028651 (CYP6P3 - cytochrome P450), AGAP0028661 (CYP6P5 - cytochrome P450), AGAP0028671 (CYP6P4 - cytochrome P450), AGAP0028681 (CYP6P1 - cytochrome P450), AGAP0028691 (CYP6P2 - cytochrome P450), AGAP0028701 (CYP6AD1 - cytochrome P450), AGAP013202, AGAP000586, AGAP002872 (lipase), AGAP002873.

The following 15 genes are within 50 kbp of the focal region: AGAP013404, AGAP002839 (WD repeat-containing protein 85), AGAP002840, AGAP013351, AGAP002841 (pyridoxal phosphate phosphatase PHOSPHO2), AGAP002842 (CLIPD1 protein), AGAP013069, AGAP002874, AGAP002875 (protein HEXIM1/2), AGAP013244 (adenosine deaminase, tRNA-specific 2, TAD2 homolog), AGAP002876 (single-strand selective monofunctional uracil DNA glycosylase), AGAP002877 (Tetratricopeptide repeat protein 30 homolog), AGAP002878 (Cystatin-like protein), AGAP002879 (cathepsin F), AGAP002880 (COP9 signalosome complex subunit 5).

Key to insecticide resistance candidate gene types: 1 metabolic; 2 target-site; 3 behavioural; 4 cuticular.

Overlapping selection signals

The following selection signals have a focus which overlaps with the focus of this signal.

Signal Statistic Population Focus Peak model \Delta_{i} Max. percentile Known locus
IHS/UGS/2/1 IHS Uganda An. gambiae 2R:28,280,000-28,700,000 1,661 100.0% Cyp6p
H12/UGS/2/1 H12 Uganda An. gambiae 2R:28,460,000-28,500,000 1,567 99.2% Cyp6p
IHS/CMS/2/1 IHS Cameroon An. gambiae 2R:28,240,000-28,560,000 1,249 100.0% Cyp6p
IHS/GNS/2/1 IHS Guinea An. gambiae 2R:28,440,000-28,700,000 1,134 99.8% Cyp6p
H12/CMS/2/1 H12 Cameroon An. gambiae 2R:28,460,000-28,560,000 1,124 100.0% Cyp6p
H12/GNS/2/2 H12 Guinea An. gambiae 2R:28,420,000-28,460,000 1,073 98.5% Cyp6p
H12/BFS/2/2 H12 Burkina Faso An. gambiae 2R:28,440,000-28,480,000 976 98.4% Cyp6p
XPEHH/UGS.GWA/2/1 XPEHH Uganda An. gambiae 2R:28,460,000-28,600,000 758 99.7% Cyp6p
XPEHH/UGS.BFS/2/1 XPEHH Uganda An. gambiae 2R:27,980,000-28,280,000 753 99.9% nan
XPEHH/BFS.GWA/2/3 XPEHH Burkina Faso An. gambiae 2R:28,420,000-28,500,000 697 99.1% Cyp6p
XPEHH/CMS.GWA/2/2 XPEHH Cameroon An. gambiae 2R:28,420,000-28,620,000 578 98.7% Cyp6p
XPEHH/BFM.GWA/2/3 XPEHH Burkina Faso An. coluzzii 2R:28,380,000-28,520,000 495 99.2% Cyp6p
H12/BFM/2/4 H12 Burkina Faso An. coluzzii 2R:28,420,000-28,520,000 366 98.5% Cyp6p
H12/AOM/2/6 H12 Angola An. coluzzii 2R:28,440,000-28,480,000 235 97.8% Cyp6p
XPEHH/AOM.GWA/2/7 XPEHH Angola An. coluzzii 2R:28,480,000-28,520,000 92 84.1% Cyp6p

Diagnostics

The information below provides some diagnostics from the Peak modelling algorithm.

Selection signal in context. @@TODO

Peak targetting. @@TODO

Peak fitting diagnostics. @@TODO

Model fit reports

Peak model:

[[Model]]
    Model(skewed_exponential_peak)
[[Fit Statistics]]
    # function evals   = 33
    # data points      = 693
    # variables        = 4
    chi-square         = 151.489
    reduced chi-square = 0.220
    Akaike info crit   = -1045.719
    Bayesian info crit = -1027.555
[[Variables]]
    center:      0 (fixed)
    amplitude:   3.64297423 +/- 0.066902 (1.84%) (init= 3)
    decay:       2.31050173 +/- 0.111168 (4.81%) (init= 0.5)
    skew:       -0.48408098 +/- 0.028458 (5.88%) (init= 0)
    baseline:    1.54373488 +/- 0.048031 (3.11%) (init= 1)
    ceiling:     100 (fixed)
    floor:       0 (fixed)
[[Correlations]] (unreported correlations are <  0.100)
    C(decay, baseline)           = -0.827
    C(amplitude, baseline)       = -0.335
    C(decay, skew)               =  0.268
    C(skew, baseline)            = -0.219
    C(amplitude, skew)           =  0.133

Null model:

[[Model]]
    Model(constant)
[[Fit Statistics]]
    # function evals   = 11
    # data points      = 692
    # variables        = 1
    chi-square         = 818.972
    reduced chi-square = 1.185
    Akaike info crit   = 118.577
    Bayesian info crit = 123.116
[[Variables]]
    c:   2.66758545 +/- 0.041384 (1.55%) (init= 1)

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