Part 2
Rob, your LivingDNA results were not from three tests bundled together for one price. They just weren't, despite LivingDNA's marketing claims. Neither LivingDNA nor 23andMe run for-purpose yDNA or mtDNA tests. Here's what happens.
They buy the Illumina Infinium Global Screening Array bead-chips in bulk. That's the only chipset they and 23andMe currently use for genealogy/population testing (FTDNA, Ancestry, and MyHeritage are still using the OmniExpress chip, but that may change in the future). Out of the box, the GSA chip looks at around 640,000 autosomal markers (including just over 17,000 on the X-chromosome), 1,456 yDNA SNPs, and 137 mtDNA SNPs. The microarrays can be configured (relatively easily, but it is a process that has to be done with all chips before testing begins) for up to an additional max of <50,000 company-specified target loci.
We don't know how 23andMe and LivingDNA customize their GSA chips. Somebody could gather a number of sets of raw data results and probably figure it out, but I would imagine that they make tweaks from time to time to the programmed chip configuration.
It's a minimum three-day lab process to get the results. On day one is an amplification and incubation procedure that has to sit overnight. On day two that incubated sample goes through enzymatic fragmentation, after which is a stopping point if the lab decides to batch and resume later or the next day. The fragmented DNA then undergoes an alcohol precipitation procedure (another possible stopping point). Then the sample material goes back into the suspension material. The next step is called hybridization; this is where the suspension is washed over the (now presumably customized) microarray chip and the fragmented DNA strings align to the beads on the chip...the remarkable technology where the microarray is able to trick the DNA into thinking it is attaching to its complementary nucleotides, adenine to thymine, and cytosine to guanine. The suspension is left on the chip overnight. On day three (or four or five), there's another enzymatic procedure and then a fluorescent stain is applied. The final step--other than any analyses performed--is to actually image the microarray chip and convert all the squishy biological stuff to digital data. The actual imaging step only takes about three minutes.
Pretty fascinating stuff. The chip itself can be reused a couple of times once ablated and sterilized. Bottom line is that this is the only test 23andMe and LivingDNA perform. They do not do separate yDNA or mtDNA testing; they do not do multiple passes on selected SNPs. Wouldn't be remotely feasible, economically, to do so. If the entire process goes smoothly and the overall results from imaging meet minimum overall quality control standards, away you go.
We all have no-calls in our raw autosomal data, and there will be no-calls, almost certainly, in the targeted yDNA and mtDNA SNPs. For example, your Z19 and Z14 Y-SNPs may not even have been tested, and S375 may have been a no-call, but since L257 showed up as positive, L257 you became. And looking at the lists of WikiTree 23andMe test takers the Y-haplogroups entered are all over the place; I have no idea how granular they may have recently become, but the haplogroups on WikiTree range from I1 to I-Y7232 and R1 to R-PF6570. I have to think that some people who also tested at FTDNA included their deepest-known SNP in their 23andMe entry even if that wasn't the 23andMe reported result.
Again, I don't know how 23andMe and LivingDNA customize their GSA chips for those additional <50K markers available, but I think it's a pretty good bet that 23andMe, at least, don't focus the majority of their targets at the Y-chromosome or mtDNA molecule. They're no doubt programming the chips for more medically-relevant, gene-specific loci. Can't comment about LivingDNA. But remember also that the marketing wars are all about ethnicity and admixture, and the GSA chip is multi-purpose; that isn't its main goal. If I had to guess, it would be that the companies are using a sizable portion of their customizable beads to match loci with whatever population genomics database(s) they're using.
But even if LivingDNA decided to expend all their chip customization on yDNA, they fall far short of known-stable SNPs today, and the counts are growing regularly as more and more Y-chromosome full-sequence tests are completed and evaluated. The estimate right now is that about 385,000 stable yDNA SNPs have been identified; the ISOGG Y-haplotree alone has 76,352 cataloged; YSEQ offers individual tests for 80,659.
Oh, an aside: Yfull isn't actually "full" by any stretch; they catalog as tests are sent to them to process. For example, this is as far down as Yfull goes for my Williams clan, compared to the additional 40 or so SNPs that have been cataloged by Alex Williamson at The Big Tree (which, of course, doesn't include novels or InDels, insertions/deletions).
FTDNA and YSEQ offer for-purpose yDNA (STR and SNP) and mtDNA testing. I really can't comment about Oxford Ancestors: Bryan Sykes announced their closure last March, and then in May said that they would remain open. But the pricing and services are...odd...as in US$265 for a 26 Y-STR test or a 400-SNP mtDNA test (HVR1 alone is 569 base pairs, and HVR2 is 575 base pairs, so I'm not sure what they're testing).
When FTDNA and YSEQ do a SNP panel for yDNA or mtDNA, they look at every SNP defined by the panel or region, not selective loci set by an autosomal microarray chip. My bet is that if you check your Y-SNP results from FTDNA, every loci tested will be shown, and each will show as having tested with a positive or negative result. There are, as a matter of course, no-calls in the full-sequence test results, but a no call in a SNP panel is exceedingly rare (I haven't actually seen one) in part because the companies run multiple passes on each loci, not one-and-done like results from the GSA chip. Likewise, Y-STRs are fluoresced multiple times so that the amplitudes--representing the allele repeats--can be examined in detail and a determination made as to the correct, or modal value.
With mtDNA, we all carry more than one mitochondrial haplotype within us--but seldom more than two, and those differences are rarely more than a single base pair, not counting InDel copies--sometimes within a single one of our cells. The only way mtDNA changes is via heteroplasmic mutation. You have over 600 trillion (yep; with a "t") mitochondria in your body at any given time, happily working to produce ATP and to reproduce themselves. All plants and animals love their mitochondria. Even at the glacial rate of general mtDNA mutation (call it about 0.48 bp/My, per base pair per million years), copy errors and oddities happen.
The GSA chip looks only at the specifically programmed loci. It will miss any InDels (the result will be a no-call for a deletion and insertions will simply be overlooked), and there can be no checking to verify whether the reported allele at a particular locus is the result of a heteroplasmy or represents the mtDNA genome that's present in the other 99.9999% of those 600 trillion mitochondria. For a heteroplasmy to "stick" and start becoming the dominant mtDNA genotype, or homoplasmy, requires many, many generations. I can't talk to YSEQ's mtDNA testing, but since FTDNA does multiple passes for each loci, they have a whole nomenclature developed to describe detected heteroplamic variations and have established a threshold of 20% for such variations: if the multiple passes indicate a concentration lower than 20% of the less-common allele, it will be considered anomalous, not a heteroplasmy worth measuring, and they'll move on.
Told ya it was a rabbit hole, and I did warn you to stay out of it and stop reading. But there is, with the current technology and techniques, very much both a qualitative and functional difference among tests. There are good reasons that specific tests exist for yDNA and mtDNA.
Hm. Maybe doubling the 12,000-character post limit? I think I can work within 24,000-25,000. 
