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

Virus: HIV-1 / Sequence Type: Protein

Sequence Description: (Link to NCBI GenPept)

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
pol 0 440 421 ? B B B (Unambiguous Nested)


Detailed result for pol (major) Outlierness: 0.414559 (all), 0.51083 (group)
Subtype Posterior Probability
01_AE 5.43037e-34
A 2.42629e-21
B 1
C 2.32114e-18
D 0.0000000000483612
F 0.00000000000519334
G 1.31459e-39
H 0.0000000000151122
J 5.93974e-40
K 0.00000000000568078

Cross-Validation of Discriminant Models
Miss-Classification Rate: 9 / 735 at 10 Dimensional MDS
         Predicted
Objective 01_AE   A   B   C   D   F   G   H   K
    01_AE    57   0   0   0   0   0   0   0   0
    A         0  55   0   3   0   0   0   1   0
    B         0   0 168   0   0   0   0   0   0
    C         0   0   0 371   0   0   0   0   0
    D         0   0   1   0  45   0   0   0   0
    F         0   0   0   0   0  11   0   0   1
    G         0   0   0   0   0   0  16   0   0
    H         0   0   0   0   0   0   0   3   0
    J         0   0   0   0   0   0   0   0   0
    K         0   0   0   0   0   2   0   0   0

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for pol (nested) Outlierness: 0.587662 (all), 0.559051 (group)
Subtype Posterior Probability
03_AB 0.00000020004
07_BC 0.0000000000000584264
08_BC 1.20098e-20
12_BF 0.000779689
14_BG 2.51163e-32
15_01B 6.95894e-38
B 0.99922

Cross-Validation of Discriminant Models
Miss-Classification Rate: 7 / 184 at 10 Dimensional MDS
         Predicted
Objective 07_BC 12_BF 15_01B   B
   03_AB      0     0      0   0
   07_BC      0     0      0   0
   08_BC      0     0      0   0
   12_BF      0     8      0   1
   14_BG      0     0      0   0
   15_01B     0     0      3   0
   B          1     1      0 166

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