It looks like heterozygous base pairs are harder for 23andMe (or its Illumina chip) to call than homozygous base pairs.
I tested with 23andMe twice. Of the autosomal SNPs that were no-calls on one of my tests but were genotyped on the other test, about half were heterozygous and about half were homozygous.
This is in contrast to the fact that about 68% of the autosomal SNPs overall were homozygous.
So my heterozygous SNPs were disproportionately represented among the no-calls.
When you test with 23andMe, there are always some no-calls: locations at which the genotyping chip wasn't able to get a good reading, so no result is reported.
I tested twice with 23andMe. The first time I tested, there were 2607 no-calls, and the second time there were 3260 no-calls.
But these generally weren't the same SNPs. Most of the time, a no-call on one test was resolved by the other test. Only 459 SNPs were no-calls both times.
Merging the results from the two tests actually gives 544 no-calls, since I have to add as new no-calls the 85 SNPs that were reported differently on the two tests.
There are 578,320 SNPs that 23andMe reports on. So merging the two tests brings the no-call rate from 0.45% and 0.56% individually all the way down to 0.094% for the combo data.
By the way, it's possible that some of the 459 repeated no-calls don't represent inadequacies in the test at all but instead indicate microdeletions—short fragments of DNA that most people have but that are missing in my genome. (For the autosomes, this would require my having inherited a microdeletion from both parents, which seems unlikely.)
