XPEHH/AOM.GAS/3/1

This page describes a signal of selection found in the Angola An. coluzzii population when compared with the Gabon An. gambiae population using the XPEHH (Cite et al. 20XX) statistic.The focus of this signal is on chromosome arm 3R between positions 43,460,000 and 44,120,000. The evidence supporting this signal is strong (\Delta_{i} >= 100 on both flanks).

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 53 genes overlap the focal region: AGAP029125, AGAP009796, AGAP009797, AGAP009798 (protein kinase, cGMP-dependent), AGAP009799 (ABCC13 - ATP-binding cassette transporter (ABC transporter) family C member 13), AGAP009800, AGAP009801, AGAP0098023 (Gr12 - gustatory receptor 12), AGAP0098033 (Gr11 - gustatory receptor 11), AGAP0098043 (Gr10 - gustatory receptor 10), AGAP0098053 (Gr9 - gustatory receptor 9), AGAP009806 (MAX-like protein X), AGAP009807 (E2F transcription factor 4/5), AGAP009808 (ATP-dependent RNA helicase DDX47/RRP3), AGAP009809, AGAP009810 (peptidyl-prolyl isomerase E (cyclophilin E)), AGAP009811 (Cdk5rap3), AGAP009812, AGAP028647, AGAP009815, AGAP009816 (anterior pharynx defective 1), AGAP009817, AGAP009818 (methyltransferase-like protein 6), AGAP009819, AGAP009820, AGAP009821, AGAP009822 (DNA-binding protein rfxank), AGAP009823, AGAP009824 (NADH dehydrogenase (ubiquinone) Fe-S protein 5), AGAP009825, AGAP009826, AGAP009827 (CCR4-NOT transcription complex subunit 4), AGAP009828, AGAP009829 (beat protein), AGAP009830, AGAP009831, AGAP009832 (CASPS8 - short caspase 8), AGAP028572 (Gustatory receptor), AGAP009833 (voltage-dependent anion-selective channel protein 2), AGAP009834 (COP9 signalosome subunit 4), AGAP009835 (ABCC14 - ATP-binding cassette transporter (ABC transporter) family C member 14), AGAP009836, AGAP009837, AGAP009838 (Non-imprinted in Prader-Willi/Angelman syndrome region protein 2-like protein), AGAP009839 (Phosphatase 1 regulatory subunit 7), AGAP009840 (USO1 vesicle docking protein homolog), AGAP009841, AGAP009842 (ribonuclease T2), AGAP009843, AGAP009844 (CLIPB15 - CLIP-domain serine protease), AGAP009845, AGAP009846 (Ras-related protein Rab-9A), AGAP009847 (Outspread).

The following 2 genes are within 50 kbp of the focal region: AGAP009793, AGAP009848.

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
XPEHH/CMS.GAS/3/1 XPEHH Cameroon An. gambiae 3R:43,920,000-44,560,000 538 99.5% nan
XPEHH/AOM.BFM/3/1 XPEHH Angola An. coluzzii 3R:43,860,000-44,500,000 314 99.7% nan
XPEHH/UGS.CMS/3/2 XPEHH Uganda An. gambiae 3R:43,940,000-43,980,000 263 99.7% nan
XPEHH/UGS.BFS/3/2 XPEHH Uganda An. gambiae 3R:43,920,000-43,980,000 214 99.7% nan
IHS/UGS/3/3 IHS Uganda An. gambiae 3R:43,800,000-43,920,000 160 97.7% nan
IHS/AOM/3/1 IHS Angola An. coluzzii 3R:43,740,000-44,560,000 112 99.2% nan
XPEHH/UGS.GWA/3/3 XPEHH Uganda An. gambiae 3R:43,940,000-44,000,000 93 99.7% 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   = 38
    # data points      = 468
    # variables        = 4
    chi-square         = 106.483
    reduced chi-square = 0.229
    Akaike info crit   = -684.865
    Bayesian info crit = -668.271
[[Variables]]
    center:      0 (fixed)
    amplitude:   2.06748114 +/- 0.058881 (2.85%) (init= 3)
    sigma:       2.21345373 +/- 0.090026 (4.07%) (init= 0.5)
    skew:       -0.77777979 +/- 0.042288 (5.44%) (init= 0)
    baseline:    1.41154968 +/- 0.037161 (2.63%) (init= 1)
    ceiling:     100 (fixed)
    floor:       0 (fixed)
[[Correlations]] (unreported correlations are <  0.100)
    C(sigma, baseline)           = -0.562
    C(amplitude, baseline)       = -0.529
    C(sigma, skew)               =  0.265
    C(amplitude, skew)           =  0.130
    C(skew, baseline)            = -0.129

Null model:

[[Model]]
    Model(constant)
[[Fit Statistics]]
    # function evals   = 11
    # data points      = 467
    # variables        = 1
    chi-square         = 392.241
    reduced chi-square = 0.842
    Akaike info crit   = -79.469
    Bayesian info crit = -75.323
[[Variables]]
    c:   2.16498081 +/- 0.042454 (1.96%) (init= 1)

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