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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 3 105 55 B B B (Major agrees Nested with high confidence)


Detailed result for env (major) Outlierness: 0.211448 (all), 0.540907 (group)
Subtype Posterior Probability
01_AE 0.0000000506778
A 0.0000000644336
B 0.926134
C 0.0623565
D 0.000512919
F 0.0101677
G 0.000412365
H 0.000000203882
J 0.0000000939415
K 0.000416085

Cross-Validation of Discriminant Models
Miss-Classification Rate: 221 / 1175 at 10 Dimensional MDS
         Predicted
Objective 01_AE   A   B   C   D   F   G   J
    01_AE    69   0   1   0   0   0   0   0
    A         0  75   0   3   0   1   1   2
    B         0   0 409  42   3   0   0   0
    C         0   3 107 352   2   0   0   0
    D         0   0  13   3  44   0   0   0
    F         0   0   8   8   0   0   0   0
    G         0   2  10   6   0   0   5   0
    H         0   2   0   0   0   0   1   0
    J         0   0   0   0   0   0   0   0
    K         0   0   1   1   0   0   0   0

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for env (nested) Outlierness: 0.608361 (all), 0.654106 (group)
Subtype Posterior Probability
03_AB 0.000625415
05_DF 0.00000548861
07_BC 0.000108903
08_BC 0.00000644413
10_CD 0.000000000665171
12_BF 0.000368586
14_BG 0.00141461
15_01B 0.00624044
B 0.973089
C 0.0150845
F 0.00305682

Cross-Validation of Discriminant Models
Miss-Classification Rate: 200 / 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     3      2 408  41
   C          1     3      1  98 361
   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