• FluTrackers.com Inc. does not provide medical advice. Information on this web site is collected from various internet resources, and the FluTrackers board of directors makes no warranty to the safety, efficacy, correctness or completeness of the information posted on this site by any author or poster. The information collated here is for instructional and/or discussion purposes only and is NOT intended to diagnose or treat any disease, illness, or other medical condition. Every individual reader or poster should seek advice from their personal physician/healthcare practitioner before considering or using any interventions that are discussed on this website. By continuing to access this website you agree to consult your personal physican before using any interventions posted on this website, and you agree to hold harmless FluTrackers.com Inc., the board of directors, the members, and all authors and posters for any effects from use of any medication, supplement, vitamin or other substance, device, intervention, etc. mentioned in posts on this website, or other internet venues referenced in posts on this website.
  • We are not asking for any donations. Do not donate to any entity who says they are raising funds for us.

seasonal H1N1, 2006/7

gsgs

gsgs

Registered User
I just found this old file on my PC

lots of genomes had been made available at the end of 2007
and I did a reassortment analysis


seasonal human H1N1 , USA , 2006/7 , 145 genomes

number of reassortment-separation-incidence of segment pairs

Code: 
     1    2    3    4    5    6    7    8 
-------------------------------------------
1:  ---  199  165   70  158  158  158  158
2:  199  ---   26 1583 1583  182  182  182
3:  165   26  ---  182  182  176    2    4
4:   70 1583  182  --- 1122  100  892  307
5:  158 1583  182 1122  ---  200  200  200
6:  158  182  176  100  200  ---   29   29
7:  158  182    2  892  200   29  ---   29
8:  158  182    4  307  200   29   29  ---



best reassortment candidates:

Code: 
segments  1  2 , 199 reassortment pairs
p=0.0000000000003836578 #:  10, 197 0179,0003 s:12 #1:2297,  56 #2:2288,   4     >A/Tennessee/UR06-0055/2007(H1N1)     >A/Kentucky/UR06-0123/2007(H1N1)
p=0.0000000384634791474 #:   8, 252 0010,0003 s:12 #1:2294,  59 #2:2300,  14     >A/California/UR06-0479/2007(H1N1)     >A/Vermont/UR06-0051/2007(H1N1)
p=0.0000000399828055793 #:   9, 188 0010,0003 s:12 #1:2281,  59 #2:2283,  14     >A/California/UR06-0393/2007(H1N1)     >A/Kentucky/UR06-0181/2007(H1N1)
segments  1  3 , 165 reassortment pairs
p=0.0000000000000560484 #:   5,  10 0001,0165 s:13 #1:2295,   3 #2:2202,  54     >A/Mississippi/UR06-0378/2007(H1N1)     >A/Tennessee/UR06-0055/2007(H1N1)
segments  1  4 , 70 reassortment pairs
p=0.0000000000000000000 #:   5,  10 0001,0070 s:14 #1:2295,   3 #2:1734,  68     >A/Mississippi/UR06-0378/2007(H1N1)     >A/Tennessee/UR06-0055/2007(H1N1)
segments  1  5 , 158 reassortment pairs
p=0.0000000000330567046 #:  10, 262 0158,0001 s:15 #1:2282,  58 #2:1520,   2     >A/Tennessee/UR06-0055/2007(H1N1)     >A/North Carolina/UR06-0365/2007(H1N1)
segments  1  6 , 158 reassortment pairs
p=0.0000000000330567046 #:  10, 262 0158,0001 s:15 #1:2282,  58 #2:1520,   2     >A/Tennessee/UR06-0055/2007(H1N1)     >A/North Carolina/UR06-0365/2007(H1N1)
segments  1  7 , 158 reassortment pairs
p=0.0000000000330567046 #:  10, 262 0158,0001 s:15 #1:2282,  58 #2:1520,   2     >A/Tennessee/UR06-0055/2007(H1N1)     >A/North Carolina/UR06-0365/2007(H1N1)
segments  1  8 , 158 reassortment pairs
p=0.0000000000330567046 #:  10, 262 0158,0001 s:15 #1:2282,  58 #2:1520,   2     >A/Tennessee/UR06-0055/2007(H1N1)     >A/North Carolina/UR06-0365/2007(H1N1)
segments  2  3 , 26 reassortment pairs
p=0.0000000243515911935 #:   9, 252 0018,0002 s:23 #1:2291,  14 #2:2193,  58     >A/California/UR06-0393/2007(H1N1)     >A/Vermont/UR06-0051/2007(H1N1)
p=0.0000000608365559858 #:   8, 192 0008,0002 s:23 #1:2303,  15 #2:2202,  58     >A/California/UR06-0479/2007(H1N1)     >A/Kentucky/UR06-0258/2007(H1N1)
segments  2  4 , 1583 reassortment pairs
p=0.0000000000001367481 #:   9, 270 0275,0006 s:24 #1:2291,  14 #2:1729,  67     >A/California/UR06-0393/2007(H1N1)     >A/Florida/UR06-0412/2007(H1N1)
p=0.0000000000007189307 #:   8,  34 0275,0006 s:24 #1:2303,  15 #2:1729,  66     >A/California/UR06-0479/2007(H1N1)     >A/Tennessee/UR06-0312/2007(H1N1)
p=0.0000000000140056714 #:   6,  99 0274,0006 s:24 #1:2306,  16 #2:1727,  63     >A/Tennessee/UR06-0045/2007(H1N1)     >A/Illinois/UR06-0136/2007(H1N1)
p=0.0000000000307163294 #:   5,  27 0268,0006 s:24 #1:2287,  22 #2:1745,  72     >A/Mississippi/UR06-0378/2007(H1N1)     >A/Tennessee/UR06-0414/2007(H1N1)
p=0.0000000000904221001 #:   4,  89 0250,0006 s:24 #1:2309,  19 #2:1739,  65     >A/Kentucky/UR06-0476/2007(H1N1)     >A/New York/UR06-0386/2007(H1N1)
p=0.0000000001129237831 #:   7,  97 0241,0006 s:24 #1:2294,  18 #2:1724,  63     >A/Texas/UR06-0217/2007(H1N1)     >A/Illinois/UR06-0115/2007(H1N1)
segments  2  5 , 1583 reassortment pairs
p=0.0000000000001367481 #:   9, 270 0275,0006 s:24 #1:2291,  14 #2:1729,  67     >A/California/UR06-0393/2007(H1N1)     >A/Florida/UR06-0412/2007(H1N1)
p=0.0000000000007189307 #:   8,  34 0275,0006 s:24 #1:2303,  15 #2:1729,  66     >A/California/UR06-0479/2007(H1N1)     >A/Tennessee/UR06-0312/2007(H1N1)
p=0.0000000000140056714 #:   6,  99 0274,0006 s:24 #1:2306,  16 #2:1727,  63     >A/Tennessee/UR06-0045/2007(H1N1)     >A/Illinois/UR06-0136/2007(H1N1)
p=0.0000000000307163294 #:   5,  27 0268,0006 s:24 #1:2287,  22 #2:1745,  72     >A/Mississippi/UR06-0378/2007(H1N1)     >A/Tennessee/UR06-0414/2007(H1N1)
p=0.0000000000904221001 #:   4,  89 0250,0006 s:24 #1:2309,  19 #2:1739,  65     >A/Kentucky/UR06-0476/2007(H1N1)     >A/New York/UR06-0386/2007(H1N1)
p=0.0000000001129237831 #:   7,  97 0241,0006 s:24 #1:2294,  18 #2:1724,  63     >A/Texas/UR06-0217/2007(H1N1)     >A/Illinois/UR06-0115/2007(H1N1)
segments  2  6 , 182 reassortment pairs
p=0.0000000000003112246 #:  10, 252 0179,0001 s:26 #1:2300,   4 #2:1423,  40     >A/Tennessee/UR06-0055/2007(H1N1)     >A/Vermont/UR06-0051/2007(H1N1)
p=0.0000000391016228819 #:   6,  63 0001,0003 s:26 #1:2297,  18 #2:1423,  46     >A/Tennessee/UR06-0045/2007(H1N1)     >A/Texas/UR06-0398/2007(H1N1)
segments  2  7 , 182 reassortment pairs
p=0.0000000000003112246 #:  10, 252 0179,0001 s:26 #1:2300,   4 #2:1423,  40     >A/Tennessee/UR06-0055/2007(H1N1)     >A/Vermont/UR06-0051/2007(H1N1)
p=0.0000000391016228819 #:   6,  63 0001,0003 s:26 #1:2297,  18 #2:1423,  46     >A/Tennessee/UR06-0045/2007(H1N1)     >A/Texas/UR06-0398/2007(H1N1)
segments  2  8 , 182 reassortment pairs
p=0.0000000000003112246 #:  10, 252 0179,0001 s:26 #1:2300,   4 #2:1423,  40     >A/Tennessee/UR06-0055/2007(H1N1)     >A/Vermont/UR06-0051/2007(H1N1)
p=0.0000000391016228819 #:   6,  63 0001,0003 s:26 #1:2297,  18 #2:1423,  46     >A/Tennessee/UR06-0045/2007(H1N1)     >A/Texas/UR06-0398/2007(H1N1)
segments  3  4 , 182 reassortment pairs
p=0.0000000000003112246 #:  10, 252 0179,0001 s:26 #1:2300,   4 #2:1423,  40     >A/Tennessee/UR06-0055/2007(H1N1)     >A/Vermont/UR06-0051/2007(H1N1)
p=0.0000000391016228819 #:   6,  63 0001,0003 s:26 #1:2297,  18 #2:1423,  46     >A/Tennessee/UR06-0045/2007(H1N1)     >A/Texas/UR06-0398/2007(H1N1)
segments  3  5 , 182 reassortment pairs
p=0.0000000000003112246 #:  10, 252 0179,0001 s:26 #1:2300,   4 #2:1423,  40     >A/Tennessee/UR06-0055/2007(H1N1)     >A/Vermont/UR06-0051/2007(H1N1)
p=0.0000000391016228819 #:   6,  63 0001,0003 s:26 #1:2297,  18 #2:1423,  46     >A/Tennessee/UR06-0045/2007(H1N1)     >A/Texas/UR06-0398/2007(H1N1)
segments  3  6 , 176 reassortment pairs
p=0.0000000000004451919 #:  10, 264 0176,0001 s:36 #1:2190,   5 #2:1424,  43     >A/Tennessee/UR06-0055/2007(H1N1)     >A/Vermont/UR06-0472/2007(H1N1)
segments  3  7 , 2 reassortment pairs
p=0.0000000017720786750 #:   5,  10 0001,0002 s:37 #1:2202,  54 #2: 984,   0     >A/Mississippi/UR06-0378/2007(H1N1)     >A/Tennessee/UR06-0055/2007(H1N1)
segments  3  8 , 4 reassortment pairs
p=0.0000000197642683806 #:   5,  10 0001,0004 s:38 #1:2202,  54 #2: 846,   0     >A/Mississippi/UR06-0378/2007(H1N1)     >A/Tennessee/UR06-0055/2007(H1N1)
segments  4  5 , 1122 reassortment pairs
p=0.0000000000011036477 #:   5,  19 0227,0006 s:45 #1:1724,  74 #2:1522,   9     >A/Mississippi/UR06-0378/2007(H1N1)     >A/Oregon/UR06-0185/2007(H1N1)
p=0.0000000000016065580 #:   7,  25 0212,0006 s:45 #1:1729,  65 #2:1522,   6     >A/Texas/UR06-0217/2007(H1N1)     >A/Texas/UR06-0012/2006(H1N1)
p=0.0000000000038666933 #:   4,  20 0163,0006 s:45 #1:1738,  70 #2:1505,   8     >A/Kentucky/UR06-0476/2007(H1N1)     >A/Oregon/UR06-0219/2007(H1N1)
p=0.0000000000243632762 #:   8,  21 0174,0006 s:45 #1:1722,  68 #2:1526,   9     >A/California/UR06-0479/2007(H1N1)     >A/Oregon/UR06-0179/2007(H1N1)
p=0.0000000000253115842 #:   6,  22 0182,0006 s:45 #1:1721,  68 #2:1523,   9     >A/Tennessee/UR06-0045/2007(H1N1)     >A/Oregon/UR06-0186/2007(H1N1)
p=0.0000000000426520132 #:   9,  18 0164,0006 s:45 #1:1729,  70 #2:1518,  10     >A/California/UR06-0393/2007(H1N1)     >A/Oregon/UR06-0230/2007(H1N1)
segments  4  6 , 100 reassortment pairs
p=0.0000000000000003556 #:   6,  10 0001,0100 s:46 #1:1723,  64 #2:1423,   1     >A/Tennessee/UR06-0045/2007(H1N1)     >A/Tennessee/UR06-0055/2007(H1N1)
segments  4  7 , 892 reassortment pairs
p=0.0000000000000327583 #:   5,  10 0218,0006 s:47 #1:1734,  68 #2: 984,   0     >A/Mississippi/UR06-0378/2007(H1N1)     >A/Tennessee/UR06-0055/2007(H1N1)
p=0.0000000000766318431 #:   4,  66 0189,0006 s:47 #1:1741,  69 #2: 984,   3     >A/Kentucky/UR06-0476/2007(H1N1)     >A/Texas/UR06-0526/2007(H1N1)
p=0.0000000003327849286 #:   6, 187 0183,0006 s:47 #1:1725,  65 #2: 984,   3     >A/Tennessee/UR06-0045/2007(H1N1)     >A/Vermont/UR06-0035/2007(H1N1)
p=0.0000000014115081996 #:   9,  65 0161,0006 s:47 #1:1723,  66 #2: 984,   4     >A/California/UR06-0393/2007(H1N1)     >A/Ohio/UR06-0429/2007(H1N1)
p=0.0000000076843191616 #:   7,  68 0096,0006 s:47 #1:1729,  62 #2: 984,   4     >A/Texas/UR06-0217/2007(H1N1)     >A/Tennessee/UR06-0124/2007(H1N1)
p=0.0000000244440314443 #:   8,  76 0045,0006 s:47 #1:1729,  63 #2: 988,   5     >A/California/UR06-0479/2007(H1N1)     >A/Michigan/UR06-0015/2006(H1N1)
segments  4  8 , 307 reassortment pairs
p=0.0000000000011856358 #:   5,  10 0062,0006 s:48 #1:1734,  68 #2: 846,   0     >A/Mississippi/UR06-0378/2007(H1N1)     >A/Tennessee/UR06-0055/2007(H1N1)
p=0.0000000037586128647 #:   9, 270 0115,0005 s:48 #1:1729,  67 #2: 848,   3     >A/California/UR06-0393/2007(H1N1)     >A/Florida/UR06-0412/2007(H1N1)
p=0.0000000117247711490 #:   8,  86 0071,0006 s:48 #1:1722,  64 #2: 843,   3     >A/California/UR06-0479/2007(H1N1)     >A/California/UR06-0125/2007(H1N1)
p=0.0000000421739002170 #:   4, 209 0022,0005 s:48 #1:1741,  66 #2: 843,   4     >A/Kentucky/UR06-0476/2007(H1N1)     >A/Vermont/UR06-0574/2007(H1N1)
p=0.0000000594979423749 #:   6,  89 0032,0006 s:48 #1:1725,  64 #2: 851,   4     >A/Tennessee/UR06-0045/2007(H1N1)     >A/New York/UR06-0386/2007(H1N1)
p=0.0000000904342120279 #:   7, 111 0005,0006 s:48 #1:1729,  63 #2: 850,   4     >A/Texas/UR06-0217/2007(H1N1)     >A/New York/UR06-0253/2007(H1N1)
segments  5  6 , 200 reassortment pairs
p=0.0000000000057939896 #:  10, 264 0173,0001 s:56 #1:1520,   2 #2:1424,  43     >A/Tennessee/UR06-0055/2007(H1N1)     >A/Vermont/UR06-0472/2007(H1N1)
p=0.0000000125473221509 #:   7,  51 0017,0004 s:56 #1:1522,   6 #2:1429,  42     >A/Texas/UR06-0217/2007(H1N1)     >A/Tennessee/UR06-0080/2007(H1N1)
p=0.0000000567967277789 #:   4,  22 0004,0003 s:56 #1:1505,   8 #2:1423,  44     >A/Kentucky/UR06-0476/2007(H1N1)     >A/Oregon/UR06-0186/2007(H1N1)
p=0.0000000874895285963 #:   5,  63 0005,0002 s:56 #1:1522,  10 #2:1429,  47     >A/Mississippi/UR06-0378/2007(H1N1)     >A/Texas/UR06-0398/2007(H1N1)
segments  5  7 , 200 reassortment pairs
p=0.0000000000057939896 #:  10, 264 0173,0001 s:56 #1:1520,   2 #2:1424,  43     >A/Tennessee/UR06-0055/2007(H1N1)     >A/Vermont/UR06-0472/2007(H1N1)
p=0.0000000125473221509 #:   7,  51 0017,0004 s:56 #1:1522,   6 #2:1429,  42     >A/Texas/UR06-0217/2007(H1N1)     >A/Tennessee/UR06-0080/2007(H1N1)
p=0.0000000567967277789 #:   4,  22 0004,0003 s:56 #1:1505,   8 #2:1423,  44     >A/Kentucky/UR06-0476/2007(H1N1)     >A/Oregon/UR06-0186/2007(H1N1)
p=0.0000000874895285963 #:   5,  63 0005,0002 s:56 #1:1522,  10 #2:1429,  47     >A/Mississippi/UR06-0378/2007(H1N1)     >A/Texas/UR06-0398/2007(H1N1)
segments  5  8 , 200 reassortment pairs
p=0.0000000000057939896 #:  10, 264 0173,0001 s:56 #1:1520,   2 #2:1424,  43     >A/Tennessee/UR06-0055/2007(H1N1)     >A/Vermont/UR06-0472/2007(H1N1)
p=0.0000000125473221509 #:   7,  51 0017,0004 s:56 #1:1522,   6 #2:1429,  42     >A/Texas/UR06-0217/2007(H1N1)     >A/Tennessee/UR06-0080/2007(H1N1)
p=0.0000000567967277789 #:   4,  22 0004,0003 s:56 #1:1505,   8 #2:1423,  44     >A/Kentucky/UR06-0476/2007(H1N1)     >A/Oregon/UR06-0186/2007(H1N1)
p=0.0000000874895285963 #:   5,  63 0005,0002 s:56 #1:1522,  10 #2:1429,  47     >A/Mississippi/UR06-0378/2007(H1N1)     >A/Texas/UR06-0398/2007(H1N1)
segments  6  7 , 29 reassortment pairs
p=0.0000000234283584351 #:   5,  85 0013,0004 s:67 #1:1429,  47 #2: 984,   3     >A/Mississippi/UR06-0378/2007(H1N1)     >A/Colorado/UR06-0499/2007(H1N1)
p=0.0000000564221261431 #:   6,  79 0007,0004 s:67 #1:1423,  45 #2: 984,   3     >A/Tennessee/UR06-0045/2007(H1N1)     >A/Ohio/UR06-0177/2007(H1N1)
p=0.0000000825447476242 #:   4,  80 0007,0003 s:67 #1:1415,  44 #2: 984,   3     >A/Kentucky/UR06-0476/2007(H1N1)     >A/California/UR06-0302/2007(H1N1)
segments  6  8 , 29 reassortment pairs
p=0.0000000234283584351 #:   5,  85 0013,0004 s:67 #1:1429,  47 #2: 984,   3     >A/Mississippi/UR06-0378/2007(H1N1)     >A/Colorado/UR06-0499/2007(H1N1)
p=0.0000000564221261431 #:   6,  79 0007,0004 s:67 #1:1423,  45 #2: 984,   3     >A/Tennessee/UR06-0045/2007(H1N1)     >A/Ohio/UR06-0177/2007(H1N1)
p=0.0000000825447476242 #:   4,  80 0007,0003 s:67 #1:1415,  44 #2: 984,   3     >A/Kentucky/UR06-0476/2007(H1N1)     >A/California/UR06-0302/2007(H1N1)
segments  7  8 , 29 reassortment pairs
p=0.0000000234283584351 #:   5,  85 0013,0004 s:67 #1:1429,  47 #2: 984,   3     >A/Mississippi/UR06-0378/2007(H1N1)     >A/Colorado/UR06-0499/2007(H1N1)
p=0.0000000564221261431 #:   6,  79 0007,0004 s:67 #1:1423,  45 #2: 984,   3     >A/Tennessee/UR06-0045/2007(H1N1)     >A/Ohio/UR06-0177/2007(H1N1)
p=0.0000000825447476242 #:   4,  80 0007,0003 s:67 #1:1415,  44 #2: 984,   3     >A/Kentucky/UR06-0476/2007(H1N1)     >A/California/UR06-0302/2007(H1N1)
 
You must log in or register to reply here.
Back
Top