TABLE 1.

Summary of VIS sequence analysis

Sample and expt.	Time (mos.)	Amt of genomic DNA (μg)	Junctiond	No. of sequences				No. of sequence counts/per unique VIS				No. of unique VIS ≤450 bp
				Totala	Uncertainb	VISc	Unique VIS	Maxf	Median	AvG	SD
In vivo repopulating PBC (95E132)
Expt. 1	5	5.3	L	3,873	543	3,332	192	346	6	17.35	41.35	109
			R	2,649	524	2,124	174	179	5	12.28	19.63	99
	50	2.8	L	4,165	358	3,814	187	300	5	20.40	41.34	85
			R	3,802	461	3,341	147	367	7	22.73	47.65	76
	88	2.5	L	3,747	211	3,537	192	222	8	18.42	27.77	84
			R	3,157	104	3,203	196	322	8	16.34	31.97	77
	108	10.7	L	4,692	228	4,475	225	371	5	19.89	43.00	125
			R	6,756	365	6,241	258	674	5	24.19	63.27	106
Expt. 2	5	5.3	L	3,669	648	3,025	178	183	7	16.99	28.44	110
			R	2,828	1,192	1,636	170	179	5	9.62	17.29	89
	50	2.8	L	3,193	147	3,049	121	287	7	25.20	41.99	67
			R	3,003	497	2,506	224	214	3	11.19	27.13	112
	88	2.5	L	3,936	216	3,725	134	265	8	27.80	46.79	71
			R	2,558	293	2,265	178	258	4	12.72	27.94	90
	108	10.7	L	3,372	220	3,161	233	169	4	13.57	24.60	110
			R	5,947	1,112	4,835	306	523	3.5	15.80	41.52	124
Total			L	30,647	2,571	28,118	559					216
			R	30,700	4,548	26,151	615					205
Combined (L-R match)e				61,347	7,119	54,269	1,174 (212)					422 (24)
In vitro acutely infected CD34+ cells
Expt. 1		10	L	2,670	1,288	1,330	861	22	1	1.54	1.39	739
			R	1,541	995	493	370	7	1	1.33	0.84	299
Expt. 2		10	L	2,478	1,252	1,165	752	15	1	1.55	1.39	642
			R	5,434	4,175	1,196	1,039	8	1	1.15	0.55	871
Total			L	5,148	2,540	2,495	1,591					1,362
			R	6,975	5,170	1,689	1,405					1,167
Combined (L-R match)e				12,123	7,710	4,184	2,996 (3)					2,529 (2)

^aTotal number of sequences that passed filtering after pyrosequencing.

^bUncertain sequences include low-quality sequences and vector sequences.

^cAuthenticated VIS sequences (vector DNA joined to cellular DNA).

^dAnalyzed vector-cellular DNA junctions L, left; R, right.

^eNumber of VIS pairs from the left and the right junctions originating from the same vector integrant. The number of matches is shown in parentheses.

^fMax, maximum.