gsgs
Registered User
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+104+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
--------------------------------------------------------------------------
recombination candidates in avian PB1:
gsbi2.13, 52475 sequences
-----------------------------------------------------------------------------
recombination candidates in avian PA:
gsbi3.13 ,74582 sequences
------------------------------------------------------------------------------
recombination candidates in avian H5:
gsbi45.13, 900 sequences
-----------------------------------------------------------------------------
recombination candidates in avian H8:
gsbi48.13 4 sequences
------------------------------------------------------------------------------
recombination candidates in avian NP:
gsbi5.13 , 6250 sequences
--------------------------------------------------------------------------------
recombination candidates in avian N1:
gsbi61.13 , 119 sequences
-------------------------------------------------------------------------
recombination candidates in avian MP:
gsbi7.13 , 24052 sequences
--------------------------------------------------------------------------------
recombination candidates in avian NSa:
gsbi81.r0 , 34231 sequences
------------------------------------------------------------------------------
recombination candidates in avian NSb:
gsbi82.13 3 sequences
----------------------------------------------------------------------
(identical sequences collapsed)
25904=2360+2672+2945+4689+2593+4664+2723+3258
HA:4689=118+119+367+316+2093+338+512+35+461+104+104+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/6412-05recombination 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),2005,3,3,0recombination 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)