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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 0 183 130 B B B (Major agrees Nested with high confidence)


Detailed result for env (major) Outlierness: 0.659948 (all), 0.541204 (group)
Subtype Posterior Probability
01_AE 0.00000000000000263691
A 4.78745e-18
B 0.999988
C 0.0000000001838
D 0.00000000064562
F 0.0000121779
G 0.0000000559978
H 0.00000000000000187705
J 0.00000000153715
K 0.00000000140626

Cross-Validation of Discriminant Models
Miss-Classification Rate: 26 / 1175 at 10 Dimensional MDS
         Predicted
Objective 01_AE   A   B   C   D   F   G   H   J   K
    01_AE    70   0   0   0   0   0   0   0   0   0
    A         0  79   0   0   0   0   2   0   1   0
    B         0   0 454   0   0   0   0   0   0   0
    C         0   0   0 457   0   7   0   0   0   0
    D         0   0   0   0  57   1   1   1   0   0
    F         0   0   1   0   0  11   4   0   0   0
    G         0   2   0   0   0   2  19   0   0   0
    H         0   0   0   0   0   0   2   1   0   0
    J         0   0   0   0   0   0   0   0   0   0
    K         0   0   0   0   0   1   0   0   0   1

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for env (nested) Outlierness: 0.557342 (all), 0.543761 (group)
Subtype Posterior Probability
03_AB 0.0000335172
07_BC 1.17703e-18
08_BC 8.69311e-22
12_BF 0.000000977875
14_BG 0.0111331
15_01B 0.000134155
B 0.988698

Cross-Validation of Discriminant Models
Miss-Classification Rate: 14 / 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     2     0     0     0      0   0
   12_BF      0     0     0     8     0      0   2
   14_BG      0     0     0     0     0      0   3
   15_01B     0     0     0     0     0      2   2
   B          1     0     0     1     1      0 451

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