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. 2014 Mar;88(5):2891–2902. doi: 10.1128/JVI.03014-13

TABLE 3.

Locations of hot spots and cold spotsa

Interval RR difference to mean (× 10−3) P value Nt position start (from 5′ LTR) Nt position end (from 5′ LTR) Interval length (nt) Amino acid 5′ interval Amino acid 3′ interval
GH2 0.38 <0.001 912 984 72 E42 Q65
GH3 −0.09 984 1032 48 P66 T81
GH4 −0.10 1032 1113 81 I82 Q108
GH5 0.51 <0.001 1113 1266 153 N109 V159
GH6 −0.74 <0.001 1266 1287 21 E160 P166
GH7 0.49 <0.001 1287 1374 87 E167 Q195
GH8 0.55 <0.001 1374 1476 102 A196 R229
GH9 −0.31 1476 1524 48 E230 E245
GH10 −0.56 <0.001 1524 1560 36 Q246 P257
GH11 0.32 <0.05 1560 1719 159 V258 S310
GH12 0.95 <0.001 1719 1821 102 Q311 E344
GH13 1.11 <0.001 1821 1896 75 E345 Q369
GH14 −0.31 <0.05 1896 1947 51 V370 Q386
PH6 0.78 <0.05 2573 2615 42 V8 K22
PH7 −0.22 2615 2651 36 Q22 L34
PH8 −0.55 2651 2681 30 V34 E44
PH9 0.55 2681 2726 45 G44 P59
PH10 −0.17 2726 2771 45 V59 L74
PH11 0.11 2771 2825 54 V74 L92
PH12 −0.63 <0.001 2825 2870 45 G92 T107
PH13 0.45 2870 2909 39 V107 L120
PH14 −0.02 2909 2966 57 D120 T139
PH15 −0.54 <0.05 2966 3011 45 P139 K154
PH16 −0.46 3011 3065 54 G154 R172
PH17 0.32 3065 3116 51 K172 V189
PH18 −0.10 3116 3167 51 G189 R206
PH19 0.57 <0.01 3167 3218 51 Q206 K223
PH20 0.43 <0.05 3218 3290 72 E223 P247
PH21 −0.93 <0.001 3290 3326 36 E247 K259
PH22 −0.46 <0.001 3326 3383 57 L259 Q278
PH24 −0.49 <0.01 3425 3479 54 V292 L310
PH26 −0.13 3530 3599 69 A327 K350
PH27 0.11 3599 3650 51 T350 Q367
PH28 0.68 <0.01 3650 3680 30 L367 T377
PH29 0.41 <0.05 3680 3746 66 E377 E399
PH30 0.46 3746 3815 69 A399 L422
PH31 −0.72 <0.01 3815 3860 45 V422 A437
PH32 −0.35 3860 3905 45 E437 L452
PH33 −1.29 <0.001 3905 3930 25 G453 D460
a

Using the final GLM (Table 2, model 5), we predicted the recombination rate for each interval after adjusting for the effects of viral phenotype and donor variability (Fig. 5). From the estimate of standard error for each interval, we determined which regions are significantly different to the average recombination rate across gag and pol regions. Intervals without P values were not significant at the 0.05 level.