Fig. 3. Normalized sequencing coverage along the ChrY in samples from a young rat and old rats.

a Normalized sequencing coverage from a young rat (grey line) and the normalized sequencing coverage from a brain sample with minor LOY (red line). b Same as in (a) but showing the normalized sequencing coverage from a spleen sample with medium LOY (red line). c Same as in (a) but showing the normalized sequencing coverage from a kidney sample with marked LOY (red line). d Same as in a) but showing the normalized sequencing coverage from a skin sample with marked LOY (red line). a–d Significant differences, Mann–Whitney U test between the coverage of the young and old samples. P values were Benjamin–Hochberg corrected. Exact P values are indicated. The grey line indicates the expected coverage in the absence of LOY. e–h Log2 ratios of the sequencing coverage in the young rat (Cov.young) divided by the sequencing coverage in old rats (Cov.old) using non-overlapping sliding windows of 100 kb over the first 3.3 Mb of the Y chromosome sequence. The grey line indicates a log2 ratio of zero, which represents an identical coverage between the young and old rats. Log2 ratios above zero may indicate duplicated regions in the re-sequenced genomes that are not reported in the reference genomic sequence. Log2 ratios below zero may indicate loss of the Y chromosome in the re-sequenced genomes. Five samples from kidney are shown in yellow; five samples from blood are shown in red; five samples from spleen are shown in blue; five samples from skin are shown in green. Significant differences, Mann–Whitney U test against a distribution with a fixed median of 0 (similar sequencing coverage between the young and old samples). P values were Benjamin–Hochberg corrected: *** indicates P < 0.001.