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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
pol 0 571 516 K F Undecided


Subtype Prediction for Associated Protein Sequences

NCBI GI ACCESSION Gene Start Stop Length Major Subtype Nested Analysis Final Decision
32483502 AAP84920 pol 0 190 177 F F F (Major agrees Nested with high confidence)


Detailed result for pol (major) Outlierness: 0.918427 (all), 33.2081 (group)
Subtype Posterior Probability
01_AE 3.8202e-35
A 1.17513e-25
B 0.0000361913
C 1.89794e-38
D 0.00000000143632
F 0.207798
G 0.00000246972
H 3.8944e-16
J 0.00000124196
K 0.792162

Cross-Validation of Discriminant Models
Miss-Classification Rate: 7 / 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         3  55   0   1   0   0   0   0   0
    B         0   0 168   0   0   0   0   0   0
    C         0   0   0 370   0   0   0   1   0
    D         0   0   1   0  45   0   0   0   0
    F         0   0   0   0   0  12   0   0   0
    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   0   0   0   2

Download Multiple Alignment Distance Matrix GGobi XML

Plot in the First 3 Principal Coordinates


Detailed result for pol (nested) Outlierness: 1.70319 (all), 4.79547 (group)
Subtype Posterior Probability
04_cpx 0
05_DF 4.87894e-25
06_cpx 7.90383e-19
12_BF 7.15999e-27
F 1
K 1.24892e-31

Cross-Validation of Discriminant Models
Miss-Classification Rate: 0 / 34 at 10 Dimensional MDS
         Predicted
Objective 04_cpx 05_DF 06_cpx 12_BF  F  K
   04_cpx      3     0      0     0  0  0
   05_DF       0     3      0     0  0  0
   06_cpx      0     0      5     0  0  0
   12_BF       0     0      0     9  0  0
   F           0     0      0     0 12  0
   K           0     0      0     0  0  2

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