H12 / Uganda An. gambiae / Chromosome 3 / #1

This page describes a signal of selection found in the Uganda An. gambiae population using the H12 (Garud et al. 20XX) statistic.The focus of this signal is on chromosome arm 3R between positions 28,560,001 and 28,620,000. 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 15 genes overlap the focal region: AGAP009185, AGAP0091871 (Indanol dehydrogenase), AGAP009188 (solute carrier family 39 (zinc transporter), member 9), AGAP009189, AGAP0091901 (GSTE8 - glutathione S-transferase epsilon class 8), AGAP0091911 (GSTE6 - glutathione S-transferase epsilon class 6), AGAP0091921 (GSTE5 - glutathione S-transferase epsilon class 5), AGAP0091931 (GSTE4 - glutathione S-transferase epsilon class 4), AGAP0091941 (GSTE2 - glutathione S-transferase epsilon class 2), AGAP0091951 (GSTE1 - glutathione S-transferase epsilon class 1), AGAP0091961 (GSTE7 - glutathione S-transferase epsilon class 7), AGAP0091971 (GSTE3 - glutathione S-transferase epsilon class 3), AGAP009198, AGAP009199 (palmitoyltransferase ZDHHC24), AGAP009200 (collagen type IV alpha).

The following 4 genes are within 50 kbp of the focal region: AGAP009201 (collagen type IV alpha), AGAP009202 (selenoprotein T), AGAP028058, AGAP009203 (SPRY domain-containing SOCS box protein 3).

Key to insecticide resistance candidate gene types: 1 metabolic; 2 target-site; 3 behavioural; 4 cuticular.

Overlapping signals

The following selection signals have a focus which overlaps with the focus of this signal.

Signal Focus Score (Left | Right)
H12 / Cameroon An. gambiae / Chromosome 3 / #1 3R:28,540,001-28,640,000 1109 (680 | 428)
H12 / Burkina Faso An. gambiae / Chromosome 3 / #1 3R:28,480,001-28,620,000 818 (500 | 318)
H12 / Guinea An. gambiae / Chromosome 3 / #1 3R:28,480,001-28,600,000 755 (461 | 294)
H12 / Burkina Faso An. coluzzii / Chromosome 3 / #1 3R:28,520,001-28,620,000 676 (393 | 283)

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

Left flank, peak model:

[[Model]]
    Model(exponential)
[[Fit Statistics]]
    # function evals   = 27
    # data points      = 151
    # variables        = 3
    chi-square         = 0.007
    reduced chi-square = 0.000
    Akaike info crit   = -1497.293
    Bayesian info crit = -1488.241
[[Variables]]
    amplitude:   0.26111748 +/- 0.005388 (2.06%) (init= 0.5)
    decay:       0.17530508 +/- 0.005890 (3.36%) (init= 0.5)
    c:           0.01840311 +/- 0.000603 (3.27%) (init= 0.03)
    cap:         1 (fixed)
[[Correlations]] (unreported correlations are <  0.100)
    C(amplitude, decay)          = -0.592
    C(decay, c)                  = -0.249

Right flank, peak model:

[[Model]]
    Model(exponential)
[[Fit Statistics]]
    # function evals   = 35
    # data points      = 128
    # variables        = 3
    chi-square         = 0.016
    reduced chi-square = 0.000
    Akaike info crit   = -1144.356
    Bayesian info crit = -1135.800
[[Variables]]
    amplitude:   0.34255741 +/- 0.011732 (3.43%) (init= 0.5)
    decay:       0.21937595 +/- 0.010149 (4.63%) (init= 0.5)
    c:           0.02258691 +/- 0.001098 (4.86%) (init= 0.03)
    cap:         1 (fixed)
[[Correlations]] (unreported correlations are <  0.100)
    C(amplitude, decay)          = -0.743
    C(decay, c)                  = -0.305

Left flank, null model:

[[Model]]
    Model(constant)
[[Fit Statistics]]
    # function evals   = 6
    # data points      = 150
    # variables        = 1
    chi-square         = 0.117
    reduced chi-square = 0.001
    Akaike info crit   = -1071.074
    Bayesian info crit = -1068.063
[[Variables]]
    c:   0.02518364 +/- 0.002290 (9.10%) (init= 0.03)

Right flank, null model:

[[Model]]
    Model(constant)
[[Fit Statistics]]
    # function evals   = 6
    # data points      = 127
    # variables        = 1
    chi-square         = 0.196
    reduced chi-square = 0.002
    Akaike info crit   = -820.499
    Bayesian info crit = -817.655
[[Variables]]
    c:   0.03397464 +/- 0.003495 (10.29%) (init= 0.03)

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