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Retrieval from the Database of Pre-calcuated Genotyping/Subtyping Results

Virus: HIV-1 / Sequence Type: Nucleotide

Sequence Description: (Link to NCBI GenBank)

Multiple Substitution Correction Algorithm: Jukes-Cantor

All sites that include gaps were deleted.


Gene by Gene Subtype Prediction Summary

Gene Start Stop Length LANL Subtype Major Subtype Nested Analysis Final Decision
env 0 111 58 B B B (Major agrees Nested with high confidence)


Detailed result for env (major) Outlierness: 0.15272 (all), 0.433161 (group)
Subtype Posterior Probability
01_AE 0.00000249319
A 0.000000108098
B 0.735298
C 0.242626
D 0.00000000320897
F 0.0213494
G 0.000708674
H 0.0000000955245
J 0.0000000116869
K 0.0000151988

Cross-Validation of Discriminant Models
Miss-Classification Rate: 212 / 1175 at 10 Dimensional MDS
         Predicted
Objective 01_AE   A   B   C   D   G
    01_AE    68   1   1   0   0   0
    A         0  77   1   2   0   2
    B         1   0 413  39   0   1
    C         0   5 106 351   1   1
    D         0   0   8   3  49   0
    F         0   0   8   8   0   0
    G         0   2  10   6   0   5
    H         0   3   0   0   0   0
    J         0   0   0   0   0   0
    K         0   0   1   1   0   0

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for env (nested) Outlierness: 0.464552 (all), 0.501314 (group)
Subtype Posterior Probability
03_AB 0.0000316565
05_DF 0.00139728
07_BC 0.0258982
08_BC 0.00302008
10_CD 0.0000000151581
12_BF 0.0252106
14_BG 0.0120459
15_01B 0.00783402
B 0.630956
C 0.27074
F 0.0228666

Cross-Validation of Discriminant Models
Miss-Classification Rate: 202 / 970 at 10 Dimensional MDS
         Predicted
Objective 08_BC 10_CD 15_01B   B   C
   03_AB      0     0      0   0   0
   05_DF      0     0      0   0   3
   07_BC      0     0      0   1   9
   08_BC      0     0      0   0   2
   10_CD      0     1      0   2   0
   12_BF      0     0      0   2   8
   14_BG      0     0      0   2   1
   15_01B     0     0      0   4   0
   B          0     2      2 407  43
   C          1     3      1  99 360
   F          0     0      0   8   8

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Copyrighted by Bio-Data Mining Lab, Department of Bioinformatics and Life Sciences, Soongsil University, Seoul, Korea