Very much better than even odds.

We report the detection of a high-energy neutrino by IceCube and the multiwavelength/multi-instrument observations of a flaring γ-ray blazar, TXS 0506+056, which was found to be positionally coincident with the neutrino direction (16). Chance coincidence of the IceCube-170922A event with the flare of TXS 0506+056 is statistically disfavored at the level of 3σ in models evaluated below, associating neutrino and γ-ray production.

Supposing it was astrophysical, the chance coincidence is low yes, but:

> The muon-neutrino astrophysical spectrum, together with simulated data, was used to calculate the probability that a neutrino at the observed track energy and zenith angle in IceCube is of astrophysical origin. This probability, the so-called signalness of the event (14), was reported to be 56.5% (17).

Meaning there is about even odds this was not from outer space, but from a cosmic ray hitting the atmosphere, and we know cosmic rays point back at nothing in particular.

But does that probability take into account the coincidence of the putative source being lined up, or not?

No, that is purely the chance that they correctly identified the event as being signal, it doesn't take into account known sources.

Given that the background is basically isotropic, I doubt adding in a source catalogue will move the probability much.

You're saying there are blazars everywhere, such that no matter the trajectory, it would match to something? That doesn't sound right.

No, I'm saying cosmic rays come from anywhere (as the get deflected by magnetic fields) and when hitting the atmosphere they can create high energy neutrinos that can look like they are from space despite actually being from the atmosphere.

Which is to say 1:370