H12/GNS/2/1

This page describes a signal of selection found in the Guinea An. gambiae populationusing the H12 (Garud et al. 20XX) statistic.The focus of this signal is on chromosome arm 2L between positions 1,294,895 and 2,474,895. The evidence supporting this signal is strong (\Delta_{i} >= 100 on both flanks).

This signal overlaps the Vgsc 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 21 genes overlap the focal region: AGAP004691 (LIM domain-binding protein 1), AGAP028433, AGAP004692, AGAP004693 (nuclear receptor subfamily 6 group A), AGAP004694, AGAP028434, AGAP028435, AGAP004695 (ESCRT-I complex subunit MVB12), AGAP004696 (exd - Homeobox protein extradenticle), AGAP004698 (pre-mRNA-splicing factor 38B), AGAP004699 (RAF proto-oncogene serine/threonine-protein kinase), AGAP004700, AGAP004701, AGAP028436, AGAP004702, AGAP004703 (DNA-directed RNA polymerase III subunit RPC1), AGAP004704 (COMPASS component SPP1), AGAP028437, AGAP004706, AGAP0047072 (para - voltage-gated sodium channel), AGAP004708 (arginyl-tRNA synthetase).

The following 4 genes are within 50 kbp of the focal region: AGAP004709 (mRpL18 - 39S ribosomal protein L18, mitochondrial), AGAP0047101 (ubiquinol-cytochrome c reductase subunit 9), AGAP004711 (ATP-dependent RNA helicase DDX41), AGAP004712.

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/2/1 H12 Burkina Faso An. coluzzii 2L:2,474,895-2,894,895 1,800 99.9% Vgsc
H12/BFS/2/1 H12 Burkina Faso An. gambiae 2L:1,454,895-2,694,895 1,776 100.0% Vgsc
H12/UGS/2/2 H12 Uganda An. gambiae 2L:1,814,895-3,094,895 1,377 100.0% Vgsc
XPEHH/BFS.GWA/2/1 XPEHH Burkina Faso An. gambiae 2L:2,234,895-3,274,895 938 99.6% Vgsc
XPEHH/BFM.GWA/2/1 XPEHH Burkina Faso An. coluzzii 2L:2,334,895-2,974,895 917 99.8% Vgsc

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   = 28
    # data points      = 589
    # variables        = 4
    chi-square         = 2.898
    reduced chi-square = 0.005
    Akaike info crit   = -3122.256
    Bayesian info crit = -3104.742
[[Variables]]
    center:      0 (fixed)
    amplitude:   0.78006524 +/- 0.008101 (1.04%) (init= 0.5)
    sigma:       0.90937861 +/- 0.014587 (1.60%) (init= 0.5)
    skew:       -0.20957819 +/- 0.018381 (8.77%) (init= 0)
    baseline:    0.11469217 +/- 0.004008 (3.50%) (init= 0.03)
    ceiling:     1 (fixed)
    floor:       0 (fixed)
[[Correlations]] (unreported correlations are <  0.100)
    C(sigma, baseline)           = -0.427
    C(amplitude, baseline)       = -0.403
    C(sigma, skew)               = -0.351
    C(amplitude, sigma)          = -0.225

Null model:

[[Model]]
    Model(constant)
[[Fit Statistics]]
    # function evals   = 12
    # data points      = 588
    # variables        = 1
    chi-square         = 50.895
    reduced chi-square = 0.087
    Akaike info crit   = -1436.819
    Bayesian info crit = -1432.442
[[Variables]]
    c:   0.31936156 +/- 0.012142 (3.80%) (init= 0.03)

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