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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 0 105 58 B B B (Major agrees Nested with high confidence)


Detailed result for env (major) Outlierness: 0.838857 (all), 0.975755 (group)
Subtype Posterior Probability
01_AE 0.00000599258
A 0.00000358065
B 0.796146
C 0.188004
D 0.0000000000842673
F 0.0107967
G 0.00503787
H 0.00000113769
J 0.0000000176108
K 0.00000517462

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   0   2   0   0   0
    A         0  77   1   2   0   2
    B         1   0 412  39   1   1
    C         0   5 105 352   1   1
    D         0   0   7   3  50   0
    F         0   0   8   8   0   0
    G         0   2  10   7   0   4
    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: 1.00093 (all), 0.986799 (group)
Subtype Posterior Probability
03_AB 0.00000418101
05_DF 0.000137018
07_BC 0.00822654
08_BC 0.000300852
10_CD 0.00131245
12_BF 0.00953692
14_BG 0.0455653
15_01B 0.00210622
B 0.752753
C 0.175463
F 0.00459506

Cross-Validation of Discriminant Models
Miss-Classification Rate: 201 / 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  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