This track shows the difference in alignment between the Mm2X Best and the Mm2X Mapped tracks.

Every base aligned by the Mm2X Best track is colored one of three colors. The base is colored black if the base on the Mm2X scaffold aligns to the same position on hg17 in both tracks. If the base is aligned in the Mm2X Best track, but not aligned at all by the Mm2X Mapped track, then the base is colored gray. If the scaffold base is aligned by each track to two different positions on hg17, then it is colored red.