Do you understand what an SNP profile is and why there would be multiple profiles? (It's a profile, an algorithm). I have tried to explain it several times on these threads, but will do so again if someone asks. If you know what it means, then it's no surprise that the two profiles are different - they have to be. I assume you're just stating the facts rather than asking a question.
Where are you getting the idea that SNP's are ALTERED? That's not what an SNP does or is. There is no alteration to the physical DNA as the SNP profile is just a computer program. It is something that INSPECTS the full profile derived from the ISL.
Each criminal lab has its own SNP profile algorithm - I have given the contrast between the GG company and the FBI several times - they are intended for two different purposes and are radically different in formation.
Step one: (done by forensic geneticists)
Find DNA on sheath and run it through a DNA sequencer, resulting in ONE long piece of data (enormously large) which when there is sufficient DNA. Most humans share 99% of their actual codon sequences with other humans. At many points in the genome, we all have the same allele (and some of those alleles are identical to those of other mammals - and some are even the same as in the banana genome - in short, those alleles control bio-functioning of life on Planet Earth).
So, scientists all over the world study the smaller set of alleles where there is polymorphism. An SNP is a single nucleotide polymorphism. That means 1) there are several alleles and 2) they vary from each other by as little as 1 nucleotide (nucleotides are the A,T,C,G pattern we see in the report of any living thing's DNA).
If you want to identify someone in GG, you use a far greater number of SNP's locations in the genome (no one touches the genes - they are just looking at digital reports of SNP's).
Nothing about this process alters the original sequencing of the DNA. It's just a viewer to try and find out the variations that characterize individuals. There's no point (at all) in spending enormous scientific time and resources on studying the areas of the genome where we are all alike.
To identify individuals, we have to study the parts of the long long nucleotide map
where there is variation, where we are individually different.
FBI uses a very small number of SNP's across a population of felons because they want to be able to process hundreds of thousands of submitted FULL DNA DIGITAL FILES quickly and efficiently and, yes, cheaply. They have chosen each SNP after large committees of geneticists, medical doctors and anthropologists have weighed in. Hits are always partial. They lead to suspects. The suspects have their complete DNA files stored within the system - but the full run of data would be enormously bulky to study and it will all come down to polymorphisms in the end - so why not start there? If we're trying to find where we put our keys, we look in certain places - we don't start with Google satellite.
Othram uses WAY more SNP's than the FBI because they are trying to build and illustrate the human family tree (as are Ancestry and 23andme). And that's what they do. Each of these services has a proprietary SNP algorithm. Everyone is looking at the same DNA - just through different lenses, so to speak.
Sorry if this is unnecessary to the discussion - but hopefully we can all see why the Defense might want to inspect the algorithms. I do not see what the legal value of this inspection might be, but, being the Defense, they want everything they can get. It's likely that they are not fully understanding the system, either - and that the jury will hear dualing explainers. But the explainer to trust is someone in academia, with absolutely no ax to grind and is just going to walk the jury through the process.
If I were that explainer, I'd start with something visual, like Parabon. Parabon is a leading innovator and expert in SNP analysis that leads to information about how people look. Obviously, as humans, we distinguish each other by faces and Parabon has kept up with the worldwide research about which locii in the genome are related to facial structure and what the various known alleles are (the total number of alleles for any of these locii is not known or complete - it's ongoing work and their reconstructions continually get better).
If you were to submit your own DNA to Parabon, they'd use their recipe of SNP's to show you what you look like, and it will be eerily close - but not exact, as there are developmental factors involved post-conception.
(I just read further in the thread and it's clear we should try and discuss this - this is a very important technical point and I can try and explain a different way - feel free to ask questions).