Update Padded SAM example to match Introduction's example

Fix r001's flags (hat tip @arlin, further fixes #26), r003's flags,
and the header VN.  Add r001/2's sequence mismatch as introduced
in 80bc68f7619da60eaa4f43a16878c4675e930570 and c8c0a443c0ebfea4deb8484fb77f9cb428e65476.