Opening a bam file for just chr22, I was surprised to see that there were no reads aligned until around position 16,050,000. In UCSC Genome Browser, looking at a window of chr22:16,049,420-16,050,420, I can see that there's "nothing," but then different tracks start. In chr1, I also think I remember seeing that alignments started only at 10,000.
Why is there nothing earlier in the chromosome? Do those positions not correspond to DNA? I've downloaded data on the length/end position of each chromosome; can I find a list of these "start" positions?