              .attr("cy", (d) -> chrYScale[data.probes[d.probe].chr](data.probes[d.probe].pos_cM))
              .attr("r", peakRad)
              .attr("stroke", "none")
-             .attr("fill", "darkslateblue")
+             .attr("fill", (d) ->
+                 if (chrindex[d.chr] + chrindex[data.probes[d.probe].chr]) % 2 == 0
+                   return darkblue
+                 else
+                   return darkgreen)
              .attr("opacity", (d) -> Zscale(d.lod))
              .on "mouseover", (d) ->
                  d3.select(this).attr("r", bigRad)
                                 .attr("fill", pink)
-                                .attr("stroke", "darkslateblue")
+                                .attr("stroke", darkblue)
                                 .attr("stroke-width", 1)
                                 .attr("opacity", 1)
                  eqtltip.call(this,d)
              .on "mouseout", (d) ->
                  d3.select(this).attr("r", peakRad)
-                                .attr("fill", "darkslateblue")
+                                .attr("fill", (d) ->
+                                    if (chrindex[d.chr] + chrindex[data.probes[d.probe].chr]) % 2 == 0
+                                      return darkblue
+                                    else
+                                      return darkgreen)
                                 .attr("stroke", "none")
                                 .attr("opacity", (d) -> Zscale(d.lod))
                  d3.selectAll("#eqtltip").remove()

       .attr("cy", top[1])
       .attr("r", bigRad)
       .attr("fill", pink)
       .attr("stroke", "darkslateblue")
       .attr("stroke-width", 1)
       .attr("opacity", 1)

  # circles at eQTL peaks
  peaks = svg.append("g").attr("id", "peaks")

  # colors definitions
  lightGray = d3.rgb(230, 230, 230)
  darkGray = d3.rgb(200, 200, 200)
  darkblue = "darkslateblue"
  darkgreen = "darkslateblue" # <- was highlighting eqtl peaks in different colors, but I didn't like it
  pink = "hotpink" # "#E9CFEC"
  purple = "#8C4374"
  # bgcolor = "black"
