   for ci,i in data.chrnames
       if(i % 2 == 0)
         checkerboard2.append("rect")
-           .attr("x", data.chr[ci].start_Xpixel)
-           .attr("width", data.chr[ci].end_Xpixel - data.chr[ci].start_Xpixel)
+           .attr("x", data.chr[ci].start_lowerXpixel)
+           .attr("width", data.chr[ci].end_lowerXpixel - data.chr[ci].start_lowerXpixel)
            .attr("y", top[1])
            .attr("height", h[1])
            .attr("stroke", "none")
            .attr("fill", darkGray)
            .style("pointer-events", "none")
+
+  # use just the peaks with LOD > 10
+  tmp = []
+  for p in data.peaks
+    tmp.push(p) if p.lod > 10
+  data.peaks = tmp
 
   # maximum lod score
   maxlod = d3.max(data.peaks, (d) -> d.lod)

  # slight adjustments
  top[0] = data.chr["X"].end_Ypixel-peakRad
  right[1] = right[0] = data.chr["X"].end_Xpixel+peakRad
  w[1] = w[0] = right[0] - left[0]
  h[0] = bottom[0] - top[0]
  data.chr["1"].start_Xpixel = left[0]
  data.chr["1"].start_Ypixel = bottom[0]
  data.chr["X"].end_Xpixel = right[0]
  data.chr["X"].end_Ypixel = top[0]

  # create SVGs
  svg = d3.select("div#cistrans").append("svg")

  peakRad = 2
  bigRad = 5

  # gap between chromosomes in lower plot
  chrGap = 8

  # height of marker ticks in lower panel
  tickHeight = (bottom[1] - top[1])*0.02

