Table 2.

Swap probability calculations for Human & E. coli library mixture experiment

	Read count
Total PF indexed readsa	842,853,260
Total Non-swapped reads	807,029,454
Total swapped reads	34,219,842
p(Total Swap) = (Total swapped reads) / (Total PF indexed reads) = 0.0406
Undetermined i7 or i5 swaps (Human to Human or E. coli to E. coli swaps)	17,136,498
Known i7 swaps (Human to E. coli or E. coli to Human swaps)	5,300,327
Known i5 swaps (Human to E. coli or E. coli to Human swaps)	12,697,618
Known double i7 and i5 swaps (Human to E. coli or E. coli to Human swaps)	689,363
Estimated total i7 swaps = i7 / (i5 + i7) * undetermined + i7 + double swaps	110,36,324
Estimated total i5 swaps = i5 / (i5 + i7) * undetermined + i5 + double swaps	25,476,845
p(i7 Swap) = (Estimated total i7) / (Non-swap + Undet. + Known i5 + Known i7 + Double) = 0.0131
p(i5 Swap) = (Estimated total i5) / (Non-swap + Undet. + Known i5 + Known i7 + Double) = 0.0302

^aAll passing filter reads with high quality index reads matching any index used in within pool