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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 0 617 559 K 04_cpx Undecided


Subtype Prediction for Associated Protein Sequences

NCBI GI ACCESSION Gene Start Stop Length Major Subtype Nested Analysis Final Decision
134145820 ABO63167 pol 0 205 191 F 04_cpx Undecided


Detailed result for pol (major) Outlierness: 0.807965 (all), 10.8947 (group)
Subtype Posterior Probability
01_AE 1.10725e-17
A 8.2874e-24
B 0.0000000000000242753
C 2.18244e-24
D 3.17657e-23
F 0.188643
G 9.56484e-38
H 0.00000000089465
J 6.18718e-20
K 0.811357

Cross-Validation of Discriminant Models
Miss-Classification Rate: 4 / 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   0 371   0   0   0   0   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: 1.21 (all), 3.93795 (group)
Subtype Posterior Probability
04_cpx 1
05_DF 0
06_cpx 0
12_BF 0
F 0
K 0

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