IHS/GNS/X/1

This page describes a signal of selection found in the Guinea An. gambiae populationusing the IHS (Cite et al. 20XX) statistic.The focus of this signal is on chromosome arm X between positions 15,240,000 and 15,780,000. The evidence supporting this signal is strong (\Delta_{i} >= 100 on both flanks).

This signal overlaps the Cyp9k1 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: AGAP0008181 (CYP9K1 - cytochrome P450), AGAP000819 (nuclear receptor subfamily 2 group E member (Tailless)), AGAP0008204 (CPR125 - cuticular protein RR-2 family 125), AGAP000821, AGAP000822, AGAP000823 (CD81 antigen), AGAP000824 (bone morphogenetic protein 5), AGAP000825, AGAP000826 (cap-specific mRNA (nucleoside-2’-O-)-methyltransferase 1), AGAP000829 (calpain-15), AGAP000830 (CASPS7 - short caspase 7), AGAP000831 (DnaJ homolog subfamily C member 25), AGAP000832 (Derlin-2/3), AGAP000833 (MIP - myoinhibitory-like peptide), AGAP000834, AGAP000835, AGAP028655, AGAP013506, AGAP000840 (amiloride-sensitive sodium channel, other), AGAP000841 (Ras-related protein Rab-40), AGAP013101, AGAP000842 (NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, assembly factor 1), AGAP000843 (cardiolipin synthase), AGAP000844 (Progestin and adipoQ receptor family member 4), AGAP000847 (CDC-like kinase), AGAP000848, AGAP000849 (NADH dehydrogenase (ubiquinone) 1 beta subcomplex 1), AGAP000850, AGAP0008511 (cytochrome c oxidase subunit 6a, mitochrondrial), AGAP000852 (Small ubiquitin-related modifier), AGAP000853 (gamma-glutamyltranspeptidase), AGAP000854.

The following 5 genes are within 50 kbp of the focal region: AGAP000855, AGAP0008561 (tRNA-dihydrouridine synthase 2), AGAP000857 (mRpL3 - 39S ribosomal protein L3, mitochondrial), AGAP013097, AGAP012991 (Fascin).

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
H12/BFM/X/1 H12 Burkina Faso An. coluzzii X:15,100,000-15,300,000 1,267 100.0% Cyp9k1
XPEHH/BFM.GWA/X/1 XPEHH Burkina Faso An. coluzzii X:15,060,000-15,260,000 852 99.4% Cyp9k1
H12/BFS/X/1 H12 Burkina Faso An. gambiae X:15,100,000-15,240,000 815 98.5% Cyp9k1
XPEHH/BFM.BFS/X/1 XPEHH Burkina Faso An. coluzzii X:15,580,000-15,800,000 718 99.9% nan
IHS/UGS/X/1 IHS Uganda An. gambiae X:14,640,000-15,360,000 517 96.7% Cyp9k1
IHS/BFM/X/1 IHS Burkina Faso An. coluzzii X:14,760,000-15,620,000 501 100.0% Cyp9k1
H12/UGS/X/1 H12 Uganda An. gambiae X:15,160,000-15,480,000 348 94.9% Cyp9k1
XPEHH/UGS.CMS/X/1 XPEHH Uganda An. gambiae X:15,240,000-15,460,000 284 99.9% Cyp9k1
XPEHH/UGS.BFS/X/1 XPEHH Uganda An. gambiae X:14,960,000-15,320,000 204 89.8% Cyp9k1
IHS/CMS/X/1 IHS Cameroon An. gambiae X:15,520,000-15,560,000 162 96.6% nan

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_gaussian)
[[Fit Statistics]]
    # function evals   = 43
    # data points      = 311
    # variables        = 4
    chi-square         = 52.624
    reduced chi-square = 0.171
    Akaike info crit   = -544.527
    Bayesian info crit = -529.568
[[Variables]]
    center:      0 (fixed)
    amplitude:   3.13251252 +/- 0.085309 (2.72%) (init= 3)
    sigma:       1.15142874 +/- 0.035262 (3.06%) (init= 0.5)
    skew:        0.46466950 +/- 0.031142 (6.70%) (init= 0)
    baseline:    1.84106998 +/- 0.032327 (1.76%) (init= 1)
    ceiling:     100 (fixed)
    floor:       0 (fixed)
[[Correlations]] (unreported correlations are <  0.100)
    C(sigma, baseline)           = -0.474
    C(amplitude, sigma)          = -0.394
    C(sigma, skew)               = -0.264
    C(amplitude, baseline)       = -0.252

Null model:

[[Model]]
    Model(constant)
[[Fit Statistics]]
    # function evals   = 11
    # data points      = 310
    # variables        = 1
    chi-square         = 316.672
    reduced chi-square = 1.025
    Akaike info crit   = 8.601
    Bayesian info crit = 12.338
[[Variables]]
    c:   2.45470937 +/- 0.057496 (2.34%) (init= 1)

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