The shape (but not the colors) you see in the diagram are based on what you would see through a microscope during the last phase of cell division (after the copied chromosomes are separated but before the chromosome unwinds to its normal shape). Most of the time, chromosomes are too thin to see with a microscope, but during cell division, the DNA strands coil up into a thicker compact form that is visible.
The notch represents the position of the centromere. The centromere is a non-genetic portion of the DNA strand that, with its attached proteins, serves as a connection point during the cell division process. Its attached proteins prevent it from coiling up, so it stays thin, giving the chromosome a pinched "waist".
The lengths of the chromosomes in the diagram are based on the actual lengths of the chromosome in its compact form. The "grand design" to the numbering system is some scientist who decided "I'll call the longest one #1".
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