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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 2 620 561 K 06_cpx Undecided


Detailed result for pol (major) Outlierness: 0.686828 (all), 13.5918 (group)
Subtype Posterior Probability
01_AE 9.8859e-28
A 5.44982e-21
B 0.000101687
C 1.74653e-26
D 0.0000000000000463645
F 0.0000000751716
G 0.0000000000164727
H 0.0000000000881519
J 0.00000258832
K 0.999896

Cross-Validation of Discriminant Models
Miss-Classification Rate: 5 / 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         2  56   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   0   0  46   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: 21.1672 (all), 12.3659 (group)
Subtype Posterior Probability
04_cpx 0.00000000000000105107
06_cpx 1
K 5.10196e-30

Cross-Validation of Discriminant Models
Miss-Classification Rate: 8 / 10 at 9 Dimensional MDS
         Predicted
Objective 04_cpx 06_cpx K
   04_cpx      1      0 2
   06_cpx      2      1 2
   K           1      1 0

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