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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 0 592 537 K F Undecided


Subtype Prediction for Associated Protein Sequences

NCBI GI ACCESSION Gene Start Stop Length Major Subtype Nested Analysis Final Decision
71392198 AAZ31970 pol 0 197 184 B F Undecided


Detailed result for pol (major) Outlierness: 0.704403 (all), 26.1998 (group)
Subtype Posterior Probability
01_AE 4.99402e-23
A 2.61258e-22
B 1.46103e-16
C 2.70271e-19
D 1.91923e-27
F 0.426459
G 5.24555e-18
H 0.000000000329979
J 0.000000000014805
K 0.573541

Cross-Validation of Discriminant Models
Miss-Classification Rate: 6 / 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   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: 1.98545 (all), 2.63431 (group)
Subtype Posterior Probability
04_cpx 1.60275e-35
05_DF 0.00000108022
06_cpx 5.64764e-35
12_BF 0
F 0.999999
K 0.0000000139892

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