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  • recombinations

    December 2009, full avian sequences from genbank
    (identical sequences collapsed)

    25904=2360+2672+2945+4689+2593+4664+2723+3258
    HA:4689=118+119+367+316+2093+338+512+35+461+104+10 4+51+39+3+10+19
    NA:4664=1908+1318+305+63+90+314+170+363+133
    NS:3258=2626+632

    examination of one breakpoint only


    #candidates
    segment
    china p-value<10^-19
    china p-value>10^-19 but < ~10^-10
    non-china p-value<10^-19
    non-china p-value>10^-19 but < ~10^-10
    -----------------------
    1:13,11,9,8
    2:8,11,0,4
    3:9,13,4,9
    4:0,1,0,0 0,1,0,0
    5:0,7,1,2
    6:0,2,0,0
    7:0,1,0,18
    8:0,0,2,0 0,0,0,1



    ----------------------------------------------------------------------------------

    recombination candidates in avian PB2:

    gsbi1.13 , 152342 sequences
    Code:
    p=0.0000000000000000000   199 Ck/China/Guangxi14/00(H9N2)   4 Ck/Nigeria/641/06(H5N1) 
    p=0.0000000000000000000   483 mallard/ZhaLong/88/04(H4N6)   5 Ck/Nigeria/957-20/06(H5N1)
    p=0.0000000000000000000   183 Ck/Guangxi/6/00(H9N2)       104 teal/HK/W312/97(H6N1)
    p=0.0000000000000000000   569 Dk/Guangxi/51/05(H9N2)      105 parakeet/Chiba/1/97(H9N2)
    p=0.0000000000000000000   386 Ck/Henan/210/04(H5N1)       114 Ck/Hubei/wj/97(H5N1)
    p=0.0000000000000000000   244 Ck/Hebei/B1/01(H9N2)        124 Ck/Beijing/8/98(H9N2)
    p=0.0000000000000000000   752 Ck/Shandong/B4/07(H9N2)     143 Ck/Ningxia/4/99(H9N2)
    p=0.0000000000000000000   612 mallard/Yan chen/05(H4N6)   164 Dk/Zhejiang/11/00(H5N1)
    p=0.0000000000000000000   194 Ck/China/Guangxi1/00(H9N2)  167 Ck/Guangdong/10/00(H9N2)
    p=0.0000000000000000000   702 Ck/Shandong/B2/07(H9N2)     184 Ck/Shandong/B1/00(H9N2)
    p=0.0000000000000000000   213 Ck/Jilin/53/01(H9N2)        234 Ck/Yokohama/aq120/01(H9N2)
    p=0.0000000000000000000   395 Tree sparrow/Henan/4/04(H5N1)   393 Tree sparrow/Henan/2/04(H5N1)
    p=0.0000000000000000000   621 Dk/VNM/205/05(H5N1)         605 Ck/Ninh Binh/209/05(H5N1)
    p=0.0000000000000000001   751 Ck/Shandong/B3/07(H9N2)      99 Ck/Shandong/6/96(H9N2)
    p=0.0000000000000000001   390 WildDk/Guangdong/314/04(H5N1)  276 Ck/Jilin/hg/02(H5N1)
    p=0.0000000000000000010   427 mallard/Guangxi/wt/04(H5N1)  292 pheasant/Shantou/4567/02(H5N1)
    p=0.0000000000000001583   426 Ck/Henan/wu/04(H5N1)         392 Tree sparrow/Henan/1/04(H5N1)
    p=0.0000000000000246087   810 Ck/Henan/L1/08(H9N2)         809 Ck/Henan/L3/08(H9N2)
    p=0.0000000000000419214   318 Ck/Jilin/ha/03(H5N1)         275 Ck/Jilin/he/02(H5N1)
    p=0.0000000000005844575   607 Ck/Lang Son/200/05(H5N1)     617 Ck/VNM/200/05(H5N1)
    p=0.0000000000010026328   570 Ck/Guangxi/55/05(H9N2)       801 Ck/Henan/L2/08(H9N2)
    p=0.0000000000014111689   338 pheasant/Shantou/3535/03(H5N1)    337 partridge/Shantou/2886/03(H5N1)
    p=0.0000000000031325073   648 bird/Guangxi/H1/06(H9N2)   646 Qa/Guangxi/B1/06(H9N2)
    p=0.0000000000957121259   323 Ck/Jilin/hm/03(H5N1)       319 Ck/Jilin/xw/03(H5N1)
    
    p=0.0000000000000000000  2341 Ck/Victoria/9306-04-0930/1992(H7N3)    2 ostrich/South Africa/9508103/95(H9N2)
    p=0.0000000000000000000   942 mallard/Sweden/49/02(H5N9)   88 whistling swan/Shimone/499/1983(H5N3)
    p=0.0000000000000000000   120 Dk/Singapore/F119/3/97(H5N3)   121 Dk/Singapore-Q/F119/97(H5N3)
    p=0.0000000000000000000  1079 Tk/Ontario/7732/1966(H5N9) 1077 Tk/Ontario/7732/1966(H5N9)
    p=0.0000000000000000000  1604 laughing gull/DE/94/00(H12N4)   1570 ruddy turnstone/DE/1444/00(H12N5)
    p=0.0000000000000000000  1778 shorebird/DE/236/03(H11N9) 1588 red knot/DE/1269/00(H10N7)
    p=0.0000000000000000000  1760 mallard/MD/185/03(H5N2)    1717 mallard/Ohio/667/02(H4N6)
    p=0.0000000000000000000  1998 ruddy turnstone/NJ/195/06(H7)  1980 shorebird/DE/22/06(H7N3)
    p=0.0000000000000000000  2303 mallard/Minnesota/Sg-00579/08(H1N1)  2205 ruddy turnstone/NJ/Sg-00476/08(H12N5)
    p=0.0000000000000000003  2024 ruddy turnstone/NJ/569/06(H7N3)   2004 ruddy turnstone/NJ/196/06(H7N3)
    p=0.0000000000000000012  1948 pintail/Alaska/211/05(H3N8) 1949 mallard/Alaska/256/05(H3N8)
    p=0.0000000000000000489  1994 ruddy turnstone/DE/892/06(H7N7)   1993 ruddy turnstone/DE/752/06(H7N7)
    p=0.0000000000000005803  1544 mallard/Minnesota/195/99(H4N6)    1545 mallard/Minnesota/212/99(H4N8)
    p=0.0000000000000005987  2031 mallard/Montana/458328-5/06(H5N3)    2159 bufflehead/CA/HKWF205/07(H4N8)
    p=0.0000000000000927462    59 Ck/Nigeria/OG5/07(H5N1)      58 Ck/Nigeria/OG2/07(H5N1)
    p=0.0000000000008345606  1706 ruddy turnstone/NJ/1315/02(H2N9)  1701 ruddy turnstone/DE/669/02(H2N1)
    p=0.0000000000018156295  2032 mallard/Pennsylvania/454069-12/06(H5N4)   1996 mallard/PA/454069-9/06(H5N1)
    --------------------------------------------------------------------------

    recombination candidates in avian PB1:

    gsbi2.13, 52475 sequences
    Code:
    p=0.0000000000000000000   152 Ck/Guangxi/4/99(H9N2)        99 teal/HK/W312/97(H6N1)
    p=0.0000000000000000000   222 Ck/Hebei/718/01(H5N1)       166 Dk/Zhejiang/52/00(H5N1)
    p=0.0000000000000000000   582 Dk/Guangxi/51/05(H9N2)      185 Ck/Guangxi/6/00(H9N2)
    p=0.0000000000000000000   689 bird/Guangxi/A1/06(H9N2)    199 Ck/China/Guangxi14/00(H9N2)
    p=0.0000000000000000000   583 Ck/Guangxi/55/05(H9N2)      217 Ck/Guangdong/47/01(H9N2)
    p=0.0000000000000000000   230 Gs/Guangdong/xb/01(H5N1)    245 Gs/Shantou/4325/01(H5N1)
    p=0.0000000000000000000   523 Dk/Yangzhou/02/05(H8N4)     587 mallard/Huadong/S/05(H5N1)
    p=0.0000000000000000000   684 garganey/SanJiang/160/06(H5N2)  731 Ck/Hunan/3157/06(H5N1)
    p=0.0000000000000000019   584 bird/Guangxi/62/05(H9N2)    586 bird/Guangxi/83/05(H9N2)
    p=0.0000000000000000896   331 Ck/Jilin/xw/03(H5N1)        268 Dk/HK/821/02(H5N1)
    p=0.0000000000000041435   923 Dk/Hunan/8/08(H5N1)        1061 Tk/Italy/4608/03(H7N3)
    p=0.0000000000000068215   825 Ck/Zhejiang/HJ/07(H9N2)     882 Ck/Zibo/L2/08(H9N2)
    p=0.0000000000000073080   292 Ck/Jilin/xv/02(H5N1)        342 mallard/Huadong/Y/03(H5N1)
    p=0.0000000000005092262   286 Ck/Jilin/he/02(H5N1)        335 Dk/Hubei/wq/03(H5N1)
    p=0.0000000000345060857   283 Ck/Hubei/wf/02(H5N1)        298 Gs/Shantou/157/02(H5N1)
    p=0.0000000000718519475   426 Ck/Jilin/hk/04(H5N1)        164 Dk/Guangdong/40/00(H5N1)
    p=0.0000000000828522213    80 Ck/Taiwan/G2/87(H6N1)        59 Dk/Taiwan/0526/72(H6N1)
    p=0.0000000000849638644   401 Tree sparrow/Henan/4/04(H5N1)  400 Tree sparrow/Henan/2/04(H5N1)
    p=0.0000000005107699869   635 Dk/VNM/208/05(H5N1)         636 Dk/VNM/207/05(H5N1)
    
    p=0.0000000000026272984  1705 mallard/Minnesota/188/99(H4N8)  1711/mallard/Minnesota/313/99(H6N4)
    p=0.0000000000066020590  2617 gray teal/AUS/1/1979(H6N1) 2613 Eurasian coot/W.AUS/2727/1979(H6N2)
    p=0.0000000000473634301  1910 ruddy turnstone/DE/726/02(H2N1)  1915 ruddy turnstone/NJ/1780/02(H2N9)
    p=0.0000000000691796735  2225 ruddy turnstone/DE/752/06(H7N7)  2253 ruddy turnstone/NJ/604/06(H7N4)
    -----------------------------------------------------------------------------

    recombination candidates in avian PA:

    gsbi3.13 ,74582 sequences
    Code:
    p=0.0000000000000000000   248/Ck/China/Guangxi14/00(H9N2)     117/Ck/Shandong/6/96(H9N2)
    p=0.0000000000000000000   249/Ck/China/Guangxi17/00(H9N2)     118/Ck/Shandong/7/96(H9N2)
    p=0.0000000000000000000   166/Ck/Shandong/B1/98(H9N2)         932/Ck/Shandong/B3/07(H9N2)
    p=0.0000000000000000000   191/Ck/Guangxi/4/99(H9N2)           851/bird/Guangxi/A1/06(H9N2)
    p=0.0000000000000000000   243/Ck/China/Guangxi1/00(H9N2)      202/Ck/Guangdong/10/00(H9N2)
    p=0.0000000000000000000   333/SCk/HK/YU100/02(H5N1)           332/Ck/HK/31.2/02(H5N1)
    p=0.0000000000000000000   522/slaty-backed gull/Shandong/38/04(H5N1)  397/Dk/China/E319-2/03(H5N1)
    p=0.0000000000000000000   520/wild Dk/Shanghai/59/04(H5N1)    488/Tree sparrow/Henan/4/04(H5N1)
    p=0.0000000000000000000   891/Dk/Hai Phong /208/06(H5N1)      758/Dk/Lang Son/201/05(H5N1)
    p=0.0000000000000000093   770/Ck/VNM/200/05(H5N1)             769/Dk/VNM/201/05(H5N1)
    p=0.0000000000000000792   338/Ck/Hebei/108/02(H5N1)           430/Dk/Guangxi/12/03(H5N1)
    p=0.0000000000000001392   229/Ck/Guangxi/6/00(H9N2)           215/Ck/Jiangsu/1/00(H9N2)
    p=0.0000000000000007784   413/Ck/Jilin/xw/03(H5N1)            431/Dk/Guangxi/27/03(H5N1)
    p=0.0000000000000017168   961/Muscovy Dk/VNM/NCVD-22/07(H5N1)  965/Dk/VNM/NCVD-30/07(H5N1)
    p=0.0000000000000424770   352/Ck/Jilin/hg/02(H5N1)            519/curlew/Shandong/61/04(H5N1)
    p=0.0000000000000532711   412/Ck/Jilin/ha/03(H5N1)            350/Ck/Jiangsu/cz1/02(H5N1)
    p=0.0000000000010935018   414/Dk/Hubei/wp/03(H5N1)            521/blackbird/Hunan/1/04(H5N1)
    p=0.0000000000219673853   410/Ck/Jilin/hj/03(H5N1)            464/Ck/West Java/UT1001/03(H5N1)
    p=0.0000000000470507067   759/Ck/Lang Son/200/05(H5N1)        772/Dk/VNM/203/05(H5N1)
    p=0.0000000001764377263   152/Ck/Hubei/wl/97(H5N1)            263/Dk/Guangxi/22/01(H5N1)
    p=0.0000000004976125345   341/Ck/Taiwan/PF2/02(H6N1)          405/Dk/Taiwan/WB239/03(H6N1)
    p=0.0000000006843781416   483/WildDk/Guangdong/314/04(H5N1)   481/Ck/Henan/210/04(H5N1)
    
    p=0.0000000000000000000  1790/Ck/PA/19241/97(H7N2)  1775/Ck/NY/3202-7/96(H7N2)
    p=0.0000000000000000000  2293/mallard/Ohio/1801/05(H3N8)     1796/blue-winged teal/ALB/16/97(H2N9)
    p=0.0000000000000000000  1805/Qa/PA/20304/98(H7N2)           1802/Ck/NY/13237-6/98(H6N8)
    p=0.0000000000000000000  1804/pheasant/NJ/1355/98(H5N2)      1803/pheasant/NJ/9804568/98(H5N2)
    p=0.0000000000000011358  1880/mallard/MN/263/99(H4N9)    1865/mallard/MN/327/99(H4N8)
    p=0.0000000000036332302  1875/mallard/MN/188/99(H4N8)    1885/mallard/MN/175/99(H6N8)
    p=0.0000000000044134907     1/tern/South Africa/1959(H5N3)   2/tern/South Africa/1961(H5N3)
    p=0.0000000000400185925  2467/ruddy turnstone/NJ/183/06(H7N3)   2472/ruddy turnstone/NJ/166/06(H7N3)
    p=0.0000000000829111411  2039/ruddy turnstone/DE/81/01(H10N7)   1994/red knot/DE/1587/01(H10N7)
    p=0.0000000000956235430  2763/laughing gull/NJ/Sg-00559/08(H13N9)   554/Ck/Korea/S21/04(H9N2)
    p=0.0000000001232932852  2875/blue-winged teal/North Dakota/Sg-00716/08(H4N6)   1932/ring-billed gull/Georgia/2658/00(H11N6)
    p=0.0000000004881476428  1397/mallard/Wisconsin/428/1975(H5N1)   1497/pintail Dk/ALB/189/1982(H6N6)08/10
    p=0.0000000005959146829  2273/shorebird/DE/68/04(H13N9)         1627/Ck/FL/22780-2/1988(H5N2)
    ------------------------------------------------------------------------------

    recombination candidates in avian H5:

    gsbi45.13, 900 sequences
    Code:
    p=0.0000000000000000035  1939 spotbill Dk/Xuyi/18/05(H5N2)      1771 mallard/Xuyi/10/05(H5N2)
    -----------------------------------------------------------------------------

    recombination candidates in avian H8:

    gsbi48.13 4 sequences
    Code:
    p=0.0000000033927794097   Tk/Ontario/6118/1968(H8N4)  A/Dk/Yangzhou/02/2005(H8N4)
    ------------------------------------------------------------------------------

    recombination candidates in avian NP:

    gsbi5.13 , 6250 sequences
    Code:
    p=0.0000000000000000003   332 Ck/HK/37.4/02(H5N1)    330 Gf/HK/38/02(H5N1)
    p=0.0000000000000004662   550 Ck/Jilin/hl/04(H5N1)   866 Ck/Hebei/L1/06(H9N2)
    p=0.0000000000000034132   533 Dk/Guangxi/13/04(H5N1) 532 Ck/Guangxi/12/04(H5N1)
    p=0.0000000000000221780   190 Ck/Guangxi/4/99(H9N2)  244 Ck/China/Guangxi14/00(H9N2) 
    p=0.0000000000130114382  1091 Dk/Hunan/8/08(H5N1)    979 grey heron/HK/3088/07(H5N1) 
    p=0.0000000000317618917   495 Ck/Henan/210/04(H5N1)  889 Ck/Banten/UT6025/06(H5N1)
    p=0.0000000000799307435   422 Dk/Hubei/wp/03(H5N1)   543 blackbird/Hunan/1/04(H5N1)
    
    p=0.0000000000000000000  2227 ruddy turnstone/NJ/1058/05(H11N6)  1543 ruddy turnstone/NJ/65/1985(H7N3)05/29
    p=0.0000000000000064368  1609 Dk/LA/17G/1987(H3N8)  2218 Tk/MN/366767/05(H3N2)
    p=0.0000000003261873294  2225 Northern shoveler/NC/6412-052/05(H7N6)  2237 N.shoveler/North Carolina/6412-05
    --------------------------------------------------------------------------------

    recombination candidates in avian N1:

    gsbi61.13 , 119 sequences
    Code:
    p=0.0000000000299391874   234 Ck/Hebei/718/01(H5N1)    257 Gs/VNM/113/01(H5N1)
    p=0.0000000001380557442   509 tree sparrow/Henan/4/04(H5N1)   307 Ck/Jiangsu/cz1/02(H5N1)
    -------------------------------------------------------------------------

    recombination candidates in avian MP:

    gsbi7.13 , 24052 sequences
    Code:
    p=0.0000000001475598590    88 Dk/Nanchang/1681/1992(H3N8)      2354 Ck/Canada/314514-1/05(H7N3)
    
    p=0.0000000000206000055  2369 guinea fowl/NY/10196-7/05(H7N2)   417 Qa/Shantou/1978/03(H9N2)
    p=0.0000000000597710350  2380 chukar/NY/21211-7/05(H7N2)        552 chukkar/Shantou/2478/04(H6N1)
    p=0.0000000000934473874  1102 Dk/England/1962(H4N8)            2098 green-winged teal/TX/7/01(H8N4)
    p=0.0000000000958950374  2435 Guinea fowl/NY/101276-1/05(H7N2)  171 Dk/Shantou/2134/00(H9N2)
    p=0.0000000001001766711  2409 Dk/NY/98616-5/05(H7N2)            158 Ck/Guangxi/4/99(H9N2)
    p=0.0000000001534967198  2378 Ck/NY/21211-2/05(H7N2)            363 Qa/Shantou/1825/02(H6N1)
    p=0.0000000001534967198  2379 Dk/NY/21211-6/05(H7N2)            443 chukkar/Shantou/4360/03(H6N1)
    p=0.0000000001534967198  2399 guinea fowl/NY/37982-3/05(H7N2)   543 chukkar/Shantou/121/04(H6N1) 
    p=0.0000000001534967198  2400 Ck/NY/37982-4/05(H7N2)            545 Qa/Shantou/815/04(H6N1)
    p=0.0000000001588965233  2410 Guinea fowl/NY/98616-3/05(H7N2)   188 Ck/Jiangsu/1/00(H9N2)
    p=0.0000000001606390403  2131 mallard/Maryland/252/01(H5N2)     132 Ck/Taiwan/na3/98(H6N1)
    p=0.0000000001606390403  2234 mallard/Maryland/789/02(H5N2)     260 Ck/Taiwan/1212/01(H6N1)
    p=0.0000000002451259020  2368 Ck/NY/10196-6/05(H7N2)            204 partridge/Shantou/25/00(H6N2)
    p=0.0000000002451259020  2407 Ck/NY/22067-12/05(H7N2)           444 Qa/Shantou/4443/03(H6N1)
    p=0.0000000002451259020  2406 Ck/NY/22067-7/05(H7N2)            547 chukkar/Shantou/1550/04(H6N1)
    p=0.0000000002451259020  2408 Dk/NY/22067-11/05(H7N2)           555 pheasant/Shantou/2798/04(H6N1)
    p=0.0000000002509885597  2290 Ck/NJ/294508-12/04(H7N2)          267 Ck/Yunnan/nh/01(H9N2)
    p=0.0000000003277701257     4 whiskered tern/Egypt/04/04(H6N2)  218 Dk/Nanchang/4-165/00(H4N6)
    --------------------------------------------------------------------------------

    recombination candidates in avian NSa:

    gsbi81.r0 , 34231 sequences
    Code:
    p=0.0000000000000000000  1949 blue winged teal/LA/B228/1986(H1N1)    1 tern/South Africa/1959(H5N3)
    p=0.0000000000000000000  2182/mallard/Minnesota/204/99(H6N8)         3 tern/South Africa/1961(H5N3)
    p=0.0000000000000484587  1675/mallard/Sweden/S90599/05(H7N7)      1683 mallard/Sweden/S90780/05(H1N1)
    p=0.0000000000185016827  1665/mallard/Sweden/S90419/05(H3N8)      1660 mallard/Sweden/S90360/05(H6N8),2005,3,3,0
    ------------------------------------------------------------------------------

    recombination candidates in avian NSb:

    gsbi82.13 3 sequences
    Code:
    p=0.0000000022916521995  287/Ck/Mexico/28159-541/1995(H5N2)   279/Ck/Mexico/28159-541/95(H5N2)
    ----------------------------------------------------------------------
    I'm interested in expert panflu damage estimates
    my current links: http://bit.ly/hFI7H ILI-charts: http://bit.ly/CcRgT
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