New human Y chromosome sequences. Snapshot of the IGV browser (Thorvaldsdóttir et al. 2012) showing the end of scaffold DS486227, which contains 32 kb of sequence not included in the reference Y. The three tracks show the coverage (linear scale, range 0–100) of the alignment between DS486227 and male short reads (upper), male reads that align to the scaffold but not to the reference Y (middle; “differential male reads”), and female reads. Note that the full region aligns with male reads (upper track), which confirms its existence in males other than the HuRef donor; it does not align to female reads (bottom track), which confirms Y-linkage. From position 2315 kb until the end of the scaffold (2350 kb), DS486227 aligns to the “differential male reads” (middle track); this shows that it is new Y sequence. All 119 putative Y-linked scaffolds were similarly inspected and displayed a pattern of Y-linkage. A few of them (e.g., DS486227) reveal new sequences. The zero coverage regions in the upper tracks correspond to the sequence gaps in the DS486227 scaffold.
