TABLE 1.

Metrics of genome-wide sequences collected for virus populations isolated after infection with SIVmac239^a

Animal	Wk postinfection	No. of paired reads that mapped	Avg coverage	Viral load (copies/ml)	MHC genotype
CY0163	95	1,986,662	27,830	2,375,000	M3/M3
CY0164	51	1,772,494	25,487	3,190,000	M3/M3
CY0166	156	1,131,991	13,803	15,449,965	M3/M3
CY0332	61	277,492	2,789	183,000	M3/M3
CY0333	52	239,513	2,422	9,183,333	M3/M3
CY0334	59	294,169	2,887	261,333	M3/M3
CY0335	86	230,096	2,322	639,100	M3/M3
CY0336	70	348,279	3,063	1,834,800	M3/M3
CY0337	73	381,424	3,293	3,806,000	M3/M3
CY0328	57	291,338	2,894	1,043,555	M1/M3
CY0329	57	237,608	2,324	3,952,222	M1/M3
CY0331	82	2,005,862	26,124	963,600	M1/M3
CY0353	64	363,532	3,190	24,420	M3/M5
CY0354	72	441,630	3,815	2,508	M3/M5

^aThe total number of paired-end sequencing reads for each virus population is listed. The average coverage of total A, C, T, and G nucleotides at each position from 1,300 to 10,200 was quantified.