XPEHH/UGS.BFS/X/1

This page describes a signal of selection found in the Uganda An. gambiae population when compared with the Burkina Faso An. gambiae population using the XPEHH (Cite et al. 20XX) statistic.The focus of this signal is on chromosome arm X between positions 14,960,000 and 15,320,000. The evidence supporting this signal is moderate (\Delta_{i} >= 50 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 11 genes overlap the focal region: AGAP000817, AGAP000816, AGAP013474, AGAP013173, AGAP013424, AGAP012997, AGAP0008181 (CYP9K1 - cytochrome P450), AGAP000819 (nuclear receptor subfamily 2 group E member (Tailless)), AGAP0008204 (CPR125 - cuticular protein RR-2 family 125), AGAP000821, AGAP000822.

The following 9 genes are within 50 kbp of the focal region: AGAP0008131 (Frataxin homolog, mitochondrial), AGAP000814, AGAP000815 (INTB - integrin beta subunit), 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).

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/BFS.UGS/X/1 XPEHH Burkina Faso An. gambiae X:14,960,000-15,140,000 961 99.9% nan
XPEHH/BFS.GWA/X/1 XPEHH Burkina Faso An. gambiae X:15,060,000-15,220,000 866 99.6% 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
IHS/GNS/X/1 IHS Guinea An. gambiae X:15,240,000-15,780,000 553 99.3% Cyp9k1
IHS/UGS/X/1 IHS Uganda An. gambiae X:14,640,000-15,360,000 517 96.7% Cyp9k1
XPEHH/BFM.AOM/X/1 XPEHH Burkina Faso An. coluzzii X:15,040,000-15,180,000 511 100.0% nan
IHS/BFM/X/1 IHS Burkina Faso An. coluzzii X:14,760,000-15,620,000 501 100.0% Cyp9k1
IHS/BFS/X/2 IHS Burkina Faso An. gambiae X:14,660,000-14,980,000 477 99.9% nan
H12/GNS/X/1 H12 Guinea An. gambiae X:14,960,000-15,160,000 419 97.8% nan
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/AOM.GWA/X/2 XPEHH Angola An. coluzzii X:14,500,000-15,180,000 228 98.5% 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   = 44
    # data points      = 565
    # variables        = 4
    chi-square         = 45.767
    reduced chi-square = 0.082
    Akaike info crit   = -1411.996
    Bayesian info crit = -1394.649
[[Variables]]
    center:      0 (fixed)
    amplitude:   1.16156867 +/- 0.101817 (8.77%) (init= 3)
    sigma:       1.31441569 +/- 0.077678 (5.91%) (init= 0.5)
    skew:       -0.45458350 +/- 0.047958 (10.55%) (init= 0)
    baseline:    1.06232733 +/- 0.015202 (1.43%) (init= 1)
    ceiling:     100 (fixed)
    floor:       0 (fixed)
[[Correlations]] (unreported correlations are <  0.100)
    C(amplitude, sigma)          = -0.729
    C(sigma, baseline)           = -0.438
    C(amplitude, skew)           =  0.191

Null model:

[[Model]]
    Model(constant)
[[Fit Statistics]]
    # function evals   = 9
    # data points      = 564
    # variables        = 1
    chi-square         = 66.060
    reduced chi-square = 0.117
    Akaike info crit   = -1207.493
    Bayesian info crit = -1203.158
[[Variables]]
    c:   1.17441547 +/- 0.014423 (1.23%) (init= 1)

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