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It's a dog's breakfast up there really. Lot's of muons, neutrinos, pions and bog standard hadrons.

Taken from (https://physics.aps.org/articles/v9/125)

Cosmic rays are relativistic particles (mostly protons and light nuclei) that are produced by supernovae and other powerful sources in and beyond our galaxy. When a cosmic-ray particle collides with a molecule in Earth’s atmosphere, it generates a cascade of secondary particles. An incident proton, for example, will typically expend 40% of its energy producing a secondary proton or neutron, together with a large number of other hadrons, mostly pions. Neutral pions decay immediately to two photons that generate an electromagnetic “cascade” comprising electron-positron pairs and gamma rays. Charged pions with high energies interact again in the atmosphere. The neutral pions they produce contribute further to the electromagnetic component of the shower, while other particles carry energy forward to subsequent interactions. Lower-energy charged pions decay before interacting again and produce muons, which largely survive to the ground.

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