23andMe v4 differences

23andMe's v4 chip introduced Dec 2013 greatly reduced the number of SNPs (by more than a third) compared to v3. It features just over 602,000 total SNPs instead of the previous version's 967,000 SNPs.

However this chip was completely custom designed by 23andMe, instead of basing it on the Illumina OmniExpress chip. So many new SNPs have been added, and even more old SNPs have been removed. The v4 chip is designed to allow better imputing, and coverage of SNPs more useful to 23andMe. It is also designed to allow 3 times as many samples to be processed at once.

v4 has more SNPs on the Y Chromosome and the Mitochondria, for better analysis of Haplogroups:

• v4 has 2,329 Y SNPs compared to only 1,766 for v3 (562 more) and only 1,880 for v1.
• v4 added 1,009 new Y SNPs and removed 446 old ones. But most of the old removed ones were often no-calls.
• v4 has 3,154 Mitochondrial SNPs compared to only 2,459 for v3 (695 more) and only 2,019 for v2.
• v4 added 946 new Mitochondrial SNPs and removed 251 old ones.

v4 has less SNPs on the X Chromosome:

• v4 only has 19,487 X SNPs compared to 26,007 for v3. But it is still more than v2's 13,876.

v4 has much less SNPs on the main autosomal chromosomes:

• v4 only has 577,382 atDNA SNPs compared to 930,381 for v3. It is about the same (but slightly better) than v2's 561,846.

See 23andMe's blog post and Your Genetic Genealogist's analysis.