TABLE 3.

Integration of HIV-1 viruses^a

Parameter	WT		N57S		N74D
	No.	% lost	No.	% lost	No.	% lost
Initial filtered readsb	1,288,748		1,655,553		1,517,568
Reads matching on human genomec	1,014,432	21.3	1,237,632	25.2	1,222,659	19.4
Quality filtered readsd	771,358	24.0	912,662	26.3	931,713	23.8
HIV Nef matchese	323,998	58.0	71,815	92.1	395,932	57.5
Reads with unique mappingf	310,619	4.1	69,787	2.8	383,341	3.2
Genomic integrationsg	105,329	66.1	6,137	91.2	116,138	69.7

^aNumber or percent lost indicates the number of integrations conserved or lost after the mapping steps.

^bRaw reads from HIV-1 integration sites library.

^cFiltered reads of HIV-1 integration sites were mapped against the UCSC hg19 release of the human genome.

^dFiltered reads of HIV-1 integration sites were mapped against the UCSC hg19 release of the human genome and processed for their quality.

^eFiltered reads of HIV-1 integration sites were mapped against the UCSC hg19 release of the human genome, processed for their quality, and matched with HIV Nef sequence.

^fReads obtained after unique mapping.

^gThe number of reads and percentage of HIV-1 integration sites is indicated for every HIV-1 variant.