great to hear you are using our data in your projects.
About issue 1 I have to check and will come back to you later.
Issue 2: First of all, in the big 55 (morphological types) by 55 matrices we did not want to report values for connection types that might be just statistical fluctuation. After all, the connectome derivation has substantially stochastic components. So, we used a rather conservative approach: We show data in the 55 by 55 matrices only if there is at least one connected pair within 100 um* in seven statistical instantiations of the microcircuit. And the value we show is the average over all instantiations.
On the other hand in the portal data we give data for one statistical instantiation and without such filtering.
In your issue 2, what happened is that that the connection types were filtered out because they are not present in all instantiations, but they are present in the instantiations selected for the portal.
Take for example L4_NGC:L4_ChC, which indeed has a 100% connection probability. However, compare the total number of synapses to the mean number of synapses per connection: They are the same! In other words, there is only 1 connection. One potential pair, and it happens to be connected. Since this does not really mean much and might even be misleading, we applied the filter rules described above to the figures.
For issue 3: That is odd, they should be in the json data. I checked the connection type you mentioned manually and these are its values:
convergence 1.25 +- 0.43
divergence 0.59 +- 0.69
synapses per connection 11.7 +- 3.2
total synapse count 117
connection probability 0.1
I'll look into why it was missing.
*100 um in 3d space if both types are in the same layer, otherwise only in the x-z plane. Also it might be 125um, I'll have to check, not sure right now.