   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)

  # dimensions of panels
  w = [800, 300]
  h = [w[0], 300]
  w = [w[0], w[0], w[1]]
  h = [h[0], h[1], h[0]]
  pad = {left:60, top:40, right:40, bottom: 40}

  left = [pad.left, pad.left,
          pad.left + w[0] + pad.right + pad.left]

  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

