Table 1.

A comparison of intactness inference in the NCI PSD [20] with results from HIVIntact

	Inferred intactness in the PSD	1. Reported intactness by HIVIntact (excluding small ORFs)	2. Reported intactness by HIVIntact (including small ORFs)
Intact	624	623	581
Defective	3519	3520	3562
Uniquely intact	3	2	2

The table reports how many sequences were called intact and defective in total in the PSD, as compared against HIVIntact in two modes: (1) assessing only the three major ORFs (gag, pol, env) and (2) including intactness checks for the 6 smaller ORFs (vif, vpr, tat, rev, vpu, nef). The table also reports how many sequences were called intact uniquely by only one tool, indicating a disagreement in intactness inference