AI companies need to be certain that the semen straws that they sell contain only the sperm cells of the expected bull. Low-pass sequencing with imputation has the power to identify sperm from other bulls in a dose of semen with a detection limit of 5%.
The process involves sequencing the DNA from one straw of semen from each batch at 0.5x and then running the data through a bioinformatics pipeline that includes imputation and QC analysis. Customers receive a report stating if the sample is free from contamination, or is contaminated.
In addition customers receive the sequence data files (fastq) for the 0.5x coverage. Each time a semen dose from a bull is run through the process, the customer will receive fastq files, which can be accumulated so that after, for example, 20 straws have been sequenced, the customer will have 10x coverage on the bull.