XPEHH/CMS.GWA/2/1

This page describes a signal of selection found in the Cameroon An. gambiae population when compared with the Guinea Bissau population using the XPEHH (Cite et al. 20XX) statistic.The focus of this signal is on chromosome arm 2L between positions 3,474,895 and 3,814,895. 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 29 genes overlap the focal region: AGAP004783 (predicted G-protein coupled receptor GPCR), AGAP004784 (fatty acyl-CoA reductase 2), AGAP004785 (alpha-tocopherol transfer protein-like), AGAP004786 (Pyruvate dehydrogenase E1 component subunit alpha), AGAP004787 (Fatty acyl-CoA reductase), AGAP004788 (Up-regulated during skeletal muscle growth 5 homolog), AGAP004789 (high mobility group 20A), AGAP004790 (Up-regulated during skeletal muscle growth 5 homolog), AGAP004791 (high mobility group 20A), AGAP004792 (StAR-related lipid transfer protein 7), AGAP004793 (ornithine–oxo-acid transaminase), AGAP004794 (pancreatic triacylglycerol lipase), AGAP004795 (RNA polymerase II elongation factor ELL), AGAP004797, AGAP004798 (Coatomer protein complex, subunit beta 2), AGAP004799, AGAP004800, AGAP004801 (Huntingtin interacting protein), AGAP0048021 (4-hydroxyphenylpyruvate dioxygenase), AGAP004803, AGAP004804, AGAP004805, AGAP004806 (GALE6 - galectin 6), AGAP004807 (GALE7 - galectin 7), AGAP004808 (protease m1 zinc metalloprotease), AGAP004809 (APN1 - alanyl aminopeptidase N 1), AGAP004810 (CTL3 - C-type lectin (CTL)), AGAP004811 (CTL1 - C-type lectin (CTL)), AGAP004812 (calcium-independent phospholipase A2).

The following 12 genes are within 50 kbp of the focal region: AGAP004775 (Xaa-Pro dipeptidase), AGAP004778, AGAP004780 (cyclin-dependent kinase 12/13), AGAP004781 (beta-1,4-galactosyltransferase I), AGAP004782 (tubulin-specific chaperone D), AGAP004813, AGAP004814, AGAP004815, AGAP0048161, AGAP004817 (lig - Protein lingerer), AGAP004818 (mRpS16 - 28S ribosomal protein S16, mitochondrial), AGAP004819 (receptor expression-enhancing protein 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
H12/CMS/2/2 H12 Cameroon An. gambiae 2L:3,054,895-3,614,895 725 99.7% nan
XPEHH/AOM.BFM/2/2 XPEHH Angola An. coluzzii 2L:3,574,895-3,834,895 364 99.9% nan
XPEHH/GAS.GWA/2/2 XPEHH Gabon An. gambiae 2L:3,354,895-3,714,895 274 99.9% 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_exponential_peak)
[[Fit Statistics]]
    # function evals   = 59
    # data points      = 549
    # variables        = 4
    chi-square         = 343.584
    reduced chi-square = 0.630
    Akaike info crit   = -249.298
    Bayesian info crit = -232.065
[[Variables]]
    center:      0 (fixed)
    amplitude:   5.05327004 +/- 0.129550 (2.56%) (init= 3)
    decay:       3          +/- 4.65e-05 (0.00%) (init= 0.5)
    skew:        0.34316648 +/- 0.035400 (10.32%) (init= 0)
    baseline:    1.85888039 +/- 0.126257 (6.79%) (init= 1)
    ceiling:     100 (fixed)
    floor:       0 (fixed)
[[Correlations]] (unreported correlations are <  0.100)
    C(decay, baseline)           =  0.898
    C(amplitude, baseline)       = -0.601
    C(amplitude, decay)          = -0.299
    C(skew, baseline)            =  0.203
    C(amplitude, skew)           = -0.156
    C(decay, skew)               =  0.156

Null model:

[[Model]]
    Model(constant)
[[Fit Statistics]]
    # function evals   = 12
    # data points      = 548
    # variables        = 1
    chi-square         = 1388.447
    reduced chi-square = 2.538
    Akaike info crit   = 511.457
    Bayesian info crit = 515.763
[[Variables]]
    c:   3.63451003 +/- 0.068058 (1.87%) (init= 1)

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