Question: What is the chance that two of the same genome fragments will be partitioned into the same GEM?
Answer: It is a rare event when two haplotypes of the same locus “collide” in a droplet but it does happen and is well-characterized. The rate is about 1:7000*. The assay has been optimized with the following: a) the genome mass loaded (~1.25ng), b) size of the human genome and c) the average molecule length (50kb). With these criteria met, there will be enough copies of the genome in solution, whereas two fragments are NOT in the same droplet.
*The Genome assay has a capture efficiency rate of approximately 40%, which means that about 0.5ng is partitioned into GEMs (based on genome mass 1.25 in the human genome). This translates into approximately 150 haploid copies of the genome. Assuming that a total of 1 million GEMs were generated, approximately 150 copies of a human genome will have been partitioned into the 1 million total GEMs. The 150 genome copies partitioned into 1 million GEMs is equivalent to about 1/7000th of the genome captured inside each GEM.