Variation in the fraction aligning with mouse, lineage-specific repeats and inferred deletions in mouse for the human chromosomes. For each human autosome and the X-chromosome, the amount of sequence aligned with mouse was computed. The aligning DNA was separated into two categories; the fraction of sequenced bases in alignments not including gaps (i.e., matches and mismatches) is plotted in blue (aln _NGA), and the fraction of bases in gaps within alignments is plotted in orange (aln _IAG). The fraction of sequenced bases on each chromosome in lineage-specific repeats (RepLS) is plotted in red. The sequenced bases not in lineage-specific repeats (i.e., nonrepetitive DNA plus ancestral repeats) are considered the DNA derived from the last common ancestor to mouse and human; these are the bases potentially able to align with mouse. The fraction of the nonrepetitive DNA plus ancestral repeats in each chromosome that does not align with mouse is plotted in green (NA_anc ). This measure is likely dominated by deletions in mouse.