Based on your written English you are doing very well indeed. Our ears and brains are very attuned to tiny details in language, because we use it all the time. So, although I know it is not the answer you want, it is a combination of hundreds of little things that make a non native speaker sound non native. It should also be said that this is true of accents in general: what makes an Irishman sound different than an Englishman? What makes a Western Australian sound different than an Eastern Australian? It is hundreds of tiny things combined.
However, there are certainly some things that stand out as important. For example, the pronunciation of vowels. Tiny variations can make a big difference. I work with many people originally from India. One thing I hear a lot from them is the emphasis is different. For example, "The shipping maniFEST is wrong." (Caps indicate the emphasized syllable.) Tiny word choices also make a difference, even if they are correct, they might not be idiomatic. For example, you can usually tell an Eastern European from listening to their use of the crazy English definite article. Even the very best, most fluent have problems with this.
Unfortunately, using video chat amplifies the problem, because the slight visual jitter and clipped phonics itself gives a slightly "off" feeling to the conversation to start with even with native speakers, and so when slight pronunciation problems are added on top, it makes it even more noticeable.
Unfortunately, I think the only way to get really, really fluent, where your accent is indistinguishable, is to spend a lot of time talking with native speakers, ideally by living in the country where that is the native language. If that is not possible, perhaps you can get together regularly with a bunch of native speakers. Many of the accent problems come from slight differences in the structure of your native language, which bleed into your English. So unfortunately speaking with other learners from the same language group as you can mean you feed off each others problems.
However, FWIW, your written English is very clear, and that, after all, is the ultimate purpose of language.