This track shows the difference in alignment between the Mm3X Best and the Mapped Mm3X tracks. Every aligned base in the Mm3X scaffold is colored one of three colors. The base is colored black if the base on the Mm3X scaffold maps to the same position on hg17 in both tracks. If the base is aligned in the Mm3X Best track, but not aligned at all by the Mapped Mm3X track, then the base is colored gray. If the scaffold base maps to two different positions, then it is colored red.