Figure 1.
Row by column arrangement for pooling of DNA samples.
576 DNA samples (Sn) were arranged in six 96 well plates. These samples were pooled in 4 matrices of 12 rows by 12 columns as illustrated. For each pool, 12 DNA samples were either pooled across the grid (row) or down the grid (column). Each pool of 12 DNA samples was then target enriched, barcoded and processed for Illumina sequencing.
Table 1.
Sequencing yield and efficiency of enrichment.
Figure 2.
Definition of variant classes.
Variant calls are classified based on their relationship to the pooled individuals. The three possible classes are Pinnable, Multiple and Singleton. (A) Pinnable variants were those where the carrying individuals may be identified because there is exactly one row or exactly one column containing a variant and at least one intersecting row or column pool. (B) Multiple variants were those where the variant is observed in more than one row and more than one column and it is not possible to determine precisely which individuals possess the variant. (C) Singletons were calls that are only observed in either a row or a column but not both.
Table 2.
Summary of SNV class by matrix.
Figure 3.
Bar graph of variant classes by frequency of observation.
A breakdown of the classifications of variants that were observed in exactly 1, 2, 3 or 4 of the 4 matrices. Variants that were rare within a matrix (and thus labeled Pinnable or Singleton) were predominantly seen in only 1 of the 4 matrices. Similarly, variants that were common within a matrix (Multiples) were also common between the 4 matrices.
Table 3.
SNV verification rates by class.