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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 0 120 58 D D D (Major agrees Nested with high confidence)


Detailed result for env (major) Outlierness: 0.745694 (all), 1.65351 (group)
Subtype Posterior Probability
01_AE 5.22936e-22
A 6.46621e-23
B 0.00000000149282
C 0.0000000000112557
D 1
F 0.000000000000418034
G 0.00000000000000576643
H 1.33491e-19
J 4.41569e-17
K 0.00000000645933

Cross-Validation of Discriminant Models
Miss-Classification Rate: 215 / 1175 at 10 Dimensional MDS
         Predicted
Objective 01_AE   A   B   C   D   G
    01_AE    67   1   2   0   0   0
    A         0  77   1   2   0   2
    B         1   0 411  41   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: 2.28408 (all), 2.25326 (group)
Subtype Posterior Probability
05_DF 0.00000253777
10_CD 0.000000212928
16_A2D 0.00000000000710793
D 0.999997

Cross-Validation of Discriminant Models
Miss-Classification Rate: 5 / 68 at 10 Dimensional MDS
         Predicted
Objective 05_DF 10_CD 16_A2D  D
   05_DF      3     0      0  0
   10_CD      1     1      0  1
   16_A2D     0     0      1  1
   D          1     1      0 58

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