H12/GNS/2/3

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 28,434,895 and 28,834,895. The evidence supporting this signal is moderate (\Delta_{i} >= 50 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 58 genes overlap the focal region: AGAP028453, AGAP006214, AGAP006215 (GPRMTH1 - methuselah receptor 1), AGAP006216 (GPRMTH2 - methuselah receptor 2), AGAP006217, AGAP006218 (GPRMTH4 - methuselah receptor 4), AGAP006219 (receptor tyrosine kinase-like orphan receptor 1), AGAP0062201 (aldehyde oxidase), AGAP0062211 (aldehyde oxidase), AGAP006222 (glucosyl/glucuronosyl transferases), AGAP006223 (glucosyl/glucuronosyl transferases), AGAP0062241 (aldehyde oxidase), AGAP0062251 (aldehyde oxidase), AGAP0062261 (Aldehyde_oxidase), AGAP0062271 (alpha esterase), AGAP0062281 (COEAE2F - carboxylesterase), AGAP006229 (Vps20 - vacuolar protein sorting 20), AGAP006231 (serine/threonine-protein phosphatase dullard homolog), AGAP006232 (peroxin-14), AGAP006233, AGAP006234 (protein SHQ1), AGAP006235, AGAP006236, AGAP006237 (Negative elongation factor E), AGAP006238 (ubiquitin-conjugating enzyme E2 C), AGAP006239 (Protein TSSC1), AGAP006240 (splicing factor 3B subunit 2), AGAP006241 (Innexin inx2), AGAP006242, AGAP006243 (phosphatidylinositol-4,5-bisphosphate 4-phosphatase), AGAP029069, AGAP006244 (CTL-like protein 1), AGAP006245 (zinc finger matrin-type protein 2), AGAP006246 (Sorcin), AGAP006247 (Survival of motor neuron-related-splicing factor 30), AGAP006248 (Med10 - Mediator of RNA polymerase II transcription subunit 10), AGAP006249 (solute carrier family 12 (potassium/chloride transporters), member 8), AGAP006250 (eukaryotic elongation factor, selenocysteine-tRNA-specific), AGAP006251 (syntaxin 6), AGAP006252 (Cysteine-rich venom protein), AGAP006253 (Cysteine-rich venom protein), AGAP006254 (polypeptide N-acetylglucosaminyltransferase), AGAP006255, AGAP006256 (Cad74A), AGAP028399, AGAP028454, AGAP006257, AGAP0062581 (PPO2 - prophenoloxidase 2), AGAP006259, AGAP006260 (Z band alternatively spliced PDZ-motif protein 66), AGAP0062614 (CPR135 - cuticular protein RR-2 family 135), AGAP006262, AGAP006263 (ARR2 - arrestin Arr2-like), AGAP006264 (Peroxisomal targeting signal 2 receptor), AGAP006265, AGAP006266 (HIV Tat-specific factor 1), AGAP006267 (CTL6 - C-type lectin (CTL)), AGAP006268.

No genes are within 50 kbp of the focal region.

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/BFS.UGS/2/1 XPEHH Burkina Faso An. gambiae 2L:28,354,895-28,674,895 1,933 99.2% nan
XPEHH/BFS.BFM/2/1 XPEHH Burkina Faso An. gambiae 2L:28,454,895-28,654,895 900 99.8% nan
XPEHH/BFS.GWA/2/2 XPEHH Burkina Faso An. gambiae 2L:28,374,895-28,694,895 863 98.0% nan
H12/BFS/2/3 H12 Burkina Faso An. gambiae 2L:28,494,895-28,634,895 834 98.3% nan
IHS/BFS/2/4 IHS Burkina Faso An. gambiae 2L:28,614,895-28,814,895 554 100.0% 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   = 73
    # data points      = 393
    # variables        = 4
    chi-square         = 0.920
    reduced chi-square = 0.002
    Akaike info crit   = -2372.472
    Bayesian info crit = -2356.576
[[Variables]]
    center:      0 (fixed)
    amplitude:   0.20107573 +/- 0.010483 (5.21%) (init= 0.5)
    sigma:       0.69942531 +/- 0.045780 (6.55%) (init= 0.5)
    skew:        0.57855145 +/- 0.075282 (13.01%) (init= 0)
    baseline:    0.06853384 +/- 0.002843 (4.15%) (init= 0.03)
    ceiling:     1 (fixed)
    floor:       0 (fixed)
[[Correlations]] (unreported correlations are <  0.100)
    C(amplitude, sigma)          = -0.453
    C(sigma, baseline)           = -0.305
    C(sigma, skew)               = -0.304
    C(amplitude, baseline)       = -0.192

Null model:

[[Model]]
    Model(constant)
[[Fit Statistics]]
    # function evals   = 11
    # data points      = 392
    # variables        = 1
    chi-square         = 1.980
    reduced chi-square = 0.005
    Akaike info crit   = -2071.009
    Bayesian info crit = -2067.038
[[Variables]]
    c:   0.09214068 +/- 0.003593 (3.90%) (init= 0.03)

Comments