Breakpoints of CRFs
Here we provide breakpoint data for CRFs. For basic descriptions and references, see CRF page.
The breakpoints have been derived from one or more of the following sources, as indicated:
- breakpoints given in publications,
- breakpoints provided in correspondence with the authors,
- analysis of the reference strain with recombination analysis tools (e.g., jpHMM or RIP),
- approximate breakpoints assigned based on published drawings that did not specify exact breakpoints.
CRF01_AE
Breakpoints are approximate, based on Gao et al. 1996 Fig. 6.
790 5096 A1 5097 5320 E 5321 5450 A1 5451 5650 E 5651 6310 A1 6311 6500 E/A1 6501 7999 E 8000 8378 E/A1 8379 9085 A1 9086 9600 E
CRF02_AG
Breakpoints from Carr et al. 1998 (exact breakpoints transferred from reference sequence UG037 to HXB2).
1 789 G 790 2155 A 2156 2625 A/G 2626 3274 G 3275 4174 A 4175 4874 G 4875 6224 A/G 6225 8311 A 8312 8588 A/G 8589 9089 A/G 9090 9719 G
CRF03_AB
Breakpoints obtained from jpHMM, in full agreement with map and data in Liitsola et al. 2000.
1 2687 A 2688 8649 B 8650 9719 A
CRF04_cpx
Most breakpoints are approximate, based on figure in Preskevis et al. 2001; a few breakpoints were taken from jpHMM, but only when those breakpoints agreed with the published figure.
790 1838 A1 1839 2245 G 2876 3717 K 4415 4937 G 4938 5376 A1 5694 6310 A1 6311 6836 G 7510 7793 K 7794 8299 A1 8300 8795 H
CRF05_DF
Approximate breakpoints from Laukkanen et al. 2000; a few breakpoints were taken from jpHMM, but only when those breakpoints fully agreed with the published results.
790 2291 D 2501 2845 D 2846 3396 F1 3397 3750 D 5191 5700 D 6035 8360 F1 8361 8707 D 8708 9417 F1
CRF06_cpx
Approximate breakpoints from Montavon 1999, with some breakpoints taken from jpHMM. NOTE: our previous figure was taken from Oelrichs 1998, but the 1999 paper re-analyzed the reference strain.
790 1700 A1 1701 3110 G 3111 3900 K 3901 4266 G 4267 5040 A1 5041 6031 J 6032 8796 G 8797 9417 J
CRF07_BC
Breakpoints from Su et al. 2000 Fig. 3 and text descriptions.
790 1269 C 1270 1410 B 1411 2080 C 2081 2620 B 2621 3010 C 3011 3310 B 3311 5699 C 5700 6310 B 6311 8796 C 8797 9058 B 9059 9417 C
CRF08_BC
Breakpoints from Piyasirisilp et al. 2000 Figure 3 and text.
790 1233 C 1234 1680 B 1681 2852 C 2853 3149 B 3150 8796 C 8797 9417 B
CRF09_cpx
Some breakpoints and regional trees for CRF09 are shown in McCutchan et al. 2004. Many regions are the genome have uncertain phylogenetic derivation, so we do not attempt to provide breakpoints or a map.
CRF10_CD
Breakpoints from Koulinska et al. 2001, Fig 1, adding 789 bp to the given coordinates, which begin at gag.
790 3155 D 3156 3216 D/C 3217 3615 C 3616 4316 U 4317 4814 D 4815 4845 D/C 4846 5317 C 5318 5773 D 5774 6340 C 6341 7100 D 7101 7202 C 7203 8883 D 8884 8957 D/C 8958 9442 C
CRF11_cpx
Breakpoints from Montavon et al. Fig. 3 and Fig. 4.
790 2090 A 2091 3089 J 3090 3489 U 3490 4039 J 4040 6045 A 6046 6389 J 6390 6789 G 6790 7489 A 7490 7989 U 7990 8653 J 8654 9085 A 9086 9417 E
CRF12_BF
Breakpoints from Carr et al. 2001 as described in text.
739 951 B 952 2981 F1 2473 2640 B 2641 3025 F1 3026 3688 B 3689 5945 F1 5944 6209 B 6210 8482 F1 8483 8660 B 8661 9417 F1
CRF13_cpx
Breakpoints from Zhang et al. 2005 Table 2.
623 2311 G 2312 2453 G/J 2454 3115 J 3116 3163 G/J 3164 4717 G 4718 5096 G/J 5097 6032 J 6033 6283 J/U 6284 6370 U 6371 8215 A1 8216 8396 A1/01_AE 8397 9501 01_AE
CRF14_BG
Breakpoints from Delgado et al. 2002.
750 6322 G 6323 6359 B/G 6360 8260 B 8261 8279 B/G 8280 9500 G
CRF15_01B
Breakpoints from jpHMM, in full agreement with structure shown in Tovanabutra et al. 2003.
790 6308 01_AE 6309 8316 B 8317 9417 01_AE
CRF16_A2D
Breakpoints from Visawapoka et al. 2006.
796 1050 D 1051 2989 A2 2990 3167 D 3168 5510 A2 5511 5850 D 5851 9417 A2
CRF17_BF
Breakpoints that match CRF12 are exact from Carr et al. 2001. Breakpoints in vpu/env that do not match CRF12 are approximated to simulate ARMA038 as shown in Fig. 2.
739 951 B 952 2981 F1 2473 2640 B 2641 3025 F1 3026 3688 B 3689 5945 F1 5944 6300 B 6301 6450 F1 6451 6600 B 6601 8482 F1 8483 8660 B 8661 9417 F1
CRF18_cpx
Breakpoints from Thomson et al. 2005.
795 2080 A 2081 2470 G 2471 2630 U 2631 3040 F 3041 3439 U 3440 3730 A 3761 4130 H 4131 4470 U 4471 4850 G 4851 5710 A/G 5711 6070 K 6071 6300 H 6301 6900 G/J 6920 7750 H 7770 8270 A 8280 8570 H 8790 9442 A
CRF19_cpx
Breakpoints from Casado et al. 2005.
776 1207 A 1208 4239 D 4240 4670 A 4671 5010 G 5011 5290 A 5291 6415 G 6416 8190 A 8191 8510 G 8511 8720 A 8721 9412 D
CRF20_BG
Breakpoints from Sierra et al. 2007.
545 2551 G 2552 2740 B 2741 2974 G 2975 3181 B 3182 3292 G 3293 4148 B 4149 8696 G 8697 8750 B 8751 9488 G
CRF21_A2D
Breakpoints from from Dowling et al. 2002 and Visawapoka et al. 2006.
796 1178 D 1179 1364 A2 1365 3564 D 3565 5510 A2 5511 8639 D 8640 8833 A2 8834 9013 D 9014 9412 A2
CRF22_01A1
Breakpoints from authors.
796 5658 A1 5659 6728 01_AE 6729 8328 A1 8329 9719 01_AE
CRF23_BG
Breakpoints from Sierra et al. 2007.
571 2551 G 2552 2794 B 2795 2974 G 2975 4148 B 4149 5150 G 5151 5435 B 5436 8696 G 8697 8750 B 8751 9508 G
CRF24_BG
Breakpoints from Sierra et al. 2007.
571 2551 G 2552 2842 B 2843 2974 G 2975 3292 B 3293 3379 G 3380 4148 B 4149 8696 G 8697 8750 B 8751 9508 G
CRF25_cpx
N/ACRF26_AU
N/ACRF27_cpx
Breakpoints from author.
803 2151 G 2152 2698 H 2699 2779 U 2780 3986 J 3987 4898 H 4899 5606 J 5607 5986 K 5987 6387 J 6388 8355 01_AE 8356 8659 A 8660 9046 G 9047 9411 H
CRF28_BF
Breakpoints from De Sa Filho et al. 2006.
832 1322 B 1323 2571 F1 2572 9432 B
CRF29_BF
Breakpoints from De Sa Filho et al. 2006.
832 1322 B 1323 2571 F1 2572 3682 B 3683 5462 F1 5463 9432 B
CRF30_0206
N/ACRF31_BC
Breakpoints from Santos et al. 2006.
1 2964 C 2965 2984 B/C 2985 3190 B 3191 3203 B/C 3204 9719 C
CRF32_06A1
Overall structure based on Adojaan et al. 2005; A1 breakpoints determined by jpHMM.
1 789 06_cpx 790 2126 A1 2127 9719 06_cpx
CRF33_01B
Breakpoints from Tee et al. 2006.
634 2052 01_AE 2053 2063 B/01_AE unspecified 2064 2374 B 2375 2416 B/01_AE unspecified 2417 2537 01_AE 2538 2540 B/01_AE unspecified 2541 2840 B 2841 2875 B/01_AE unspecified 2876 9690 01_AE
CRF34_01B
Breakpoints from Tovanabutra et al. 2007.
796 2164 01_AE 2165 2679 B 2680 3142 B/01_AE unspecified 3143 8524 01_AE 8525 8749 B 8750 9190 01_AE
CRF35_A1D
Breakpoints from Sanders-Buell et al. 2007.
796 2166 A1 2166 2444 D 2444 2901 A1 2901 3098 D 3098 3184 A1 3184 3378 D 3378 3423 A1 3423 3538 D 3538 7575 A1 7575 7692 D 7692 9190 A1
CRF36_cpx
Breakpoints from Powell et al. 2007b.
796 1929 01_AE 1930 3356 02_AG 3357 4072 A 4073 4305 02_AG 4306 5288 G 5289 6051 02_AG 6080 6253 G 6254 6547 01_AE 6548 7538 A 7539 8368 02_AG 8369 9189 01_AE
CRF37_cpx
Breakpoints from Powell et al. 2007a.
796 1126 01_AE 1126 2142 A 2142 2913 G 2913 4663 A 4663 5120 U 5120 5772 G 5772 6068 U 6068 6431 G 6431 7743 A1 7743 8109 A 8109 8612 02_AG 8612 8873 A 8873 9189 G
CRF38_BF
N/ACRF39_BF
Breakpoints from Guimaraes et al. 2008.
654 2835 B 2836 3019 F1 3020 3648 B 3649 3865 F1 3866 5677 B 5678 9383 F1
CRF40_BF
Breakpoints from Guimaraes et al. 2008.
654 1339 B 1340 2457 F1 2458 2630 B 2631 3865 F1 3866 4583 B 4584 5036 F1 5037 6563 B 6564 8033 F1 8034 8977 B 8978 9359 F1 9360 9409 B
CRF41_CD
Breakpoints from author.
796 1202 D 1203 1463 C 1464 1672 C/D 1673 1857 C 1858 1935 D 1936 2162 C 2163 8326 D 8327 8505 C 8506 9016 D 9017 9510 C
