Fig. 5

Characterization of index swapping mechanism. a Diagram of a HiSeqX flow cell lane colored by number of index swaps detected at each surface tile, showing relatively uniform distribution of swapping across the entire lane and both surfaces. b Read counts for all 36 index combinations in a 6-plex pool of uniquely dual indexed libraries. The combinations in heavy bordered cells with blue text along the diagonal are the correct index combinations; read counts for all other combinations are due to index swapping. Note all indexes participate in swapping relatively equally. c Mean insert size (bp) and percent chimerism calculated by Picard for both swapped and non-swapped reads. Swapped reads have shorter inserts and higher rates of chimeric read pairs. d Normalized human coverage across GC content bins, indicating there are less high GC reads in the swapped population (blue) compared to non-swapped (red) and all other non-demultiplexed (green) populations