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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 0 177 50 B B B (Major agrees Nested with high confidence)


Detailed result for env (major) Outlierness: 0.570399 (all), 0.566906 (group)
Subtype Posterior Probability
01_AE 0.000314262
A 0.0000169204
B 0.99047
C 0.0000000000277241
D 0.00916609
F 0.0000000000328308
G 0.000000970806
H 0.0000000000195367
J 0.000000467938
K 0.0000309551

Cross-Validation of Discriminant Models
Miss-Classification Rate: 82 / 1175 at 10 Dimensional MDS
         Predicted
Objective 01_AE   A   B   C   D   F   G   H   K
    01_AE    42  10   9   0   0   0   9   0   0
    A        11  57   7   0   0   0   7   0   0
    B         0   2 445   0   1   0   1   1   4
    C         0   0   0 461   3   0   0   0   0
    D         0   1   2   0  57   0   0   0   0
    F         0   0   2   0   1  13   0   0   0
    G         1   4   3   0   0   0  15   0   0
    H         0   0   0   0   0   0   1   2   0
    J         0   0   0   0   0   0   0   0   0
    K         0   0   1   0   0   0   0   0   1

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for env (nested) Outlierness: 0.520939 (all), 0.528603 (group)
Subtype Posterior Probability
03_AB 0.0000246203
07_BC 7.53411e-27
08_BC 9.92965e-39
12_BF 0.00000000315941
14_BG 0.0510333
15_01B 0.000905113
B 0.948037

Cross-Validation of Discriminant Models
Miss-Classification Rate: 23 / 484 at 10 Dimensional MDS
         Predicted
Objective 03_AB 07_BC 08_BC 12_BF 14_BG 15_01B   B
   03_AB      0     0     0     0     0      0   0
   07_BC      0     9     1     0     0      0   0
   08_BC      0     1     1     0     0      0   0
   12_BF      0     0     0     7     0      0   3
   14_BG      0     0     0     0     0      0   3
   15_01B     0     0     0     0     0      0   4
   B          4     0     0     0     3      3 444

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